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Potassium in PDB 3exg: Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex:
1.2.4.1;

Protein crystallography data

The structure of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex, PDB code: 3exg was solved by M.Kato, R.M.Wynn, J.L.Chuang, S.-C.Tso, M.Machius, J.Li, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.01
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 119.278, 128.290, 228.410, 90.14, 90.05, 90.02
R / Rfree (%) 18.9 / 25.3

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex (pdb code 3exg). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 16 binding sites of Potassium where determined in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex, PDB code: 3exg:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 16 in 3exg

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Potassium binding site 1 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1003

b:65.4
occ:1.00
 O B:ASP163 2.6 52.8 1.0
O B:ALA160 2.9 53.4 1.0
O B:ILE161 2.9 50.9 1.0
C B:PRO111 3.5 47.6 1.0
O B:PRO111 3.6 47.3 1.0
C B:ASP163 3.6 52.7 1.0
O B:ILE112 3.7 48.7 1.0
C B:ILE161 3.7 51.2 1.0
CG2 B:VAL113 3.7 47.7 1.0
CA B:PRO111 3.8 48.1 1.0
CA B:ILE161 4.0 51.0 1.0
C B:ILE112 4.0 48.4 1.0
N B:ILE112 4.0 46.9 1.0
C B:ALA160 4.1 52.0 1.0
NH2 B:ARG75 4.1 47.8 1.0
O B:ASN165 4.1 53.4 1.0
CB B:PRO111 4.1 47.7 1.0
CA B:ILE112 4.4 47.3 1.0
N B:ASP163 4.4 52.3 1.0
CA B:ASP163 4.5 53.3 1.0
N B:ILE161 4.5 51.8 1.0
N B:VAL113 4.5 48.1 1.0
N B:ASN164 4.5 52.7 1.0
CA B:ASN164 4.7 52.9 1.0
CZ B:ARG75 4.7 47.1 1.0
CB B:ASP163 4.8 54.0 1.0
N B:ASN165 4.8 52.4 1.0
N B:ARG162 4.8 51.4 1.0
C B:ARG162 4.8 51.8 1.0
NE B:ARG75 4.9 48.6 1.0
C B:ASN164 4.9 53.0 1.0
CB B:VAL113 4.9 48.0 1.0

Potassium binding site 2 out of 16 in 3exg

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Potassium binding site 2 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1002

b:72.0
occ:1.00
 O D:ASP163 2.6 57.2 1.0
O D:ILE161 2.8 54.9 1.0
O D:ALA160 3.1 52.3 1.0
C D:ILE161 3.5 54.7 1.0
O D:PRO111 3.6 49.0 1.0
C D:PRO111 3.6 49.2 1.0
C D:ASP163 3.8 57.0 1.0
CG2 D:VAL113 3.8 46.3 1.0
CA D:ILE161 3.8 53.9 1.0
NH2 D:ARG75 3.9 37.6 1.0
CA D:PRO111 4.0 49.4 1.0
CB D:PRO111 4.0 48.7 1.0
N D:ILE112 4.1 48.8 1.0
C D:ALA160 4.1 52.5 1.0
N D:ASP163 4.4 57.3 1.0
CZ D:ARG75 4.4 40.0 1.0
C D:ILE112 4.5 49.3 1.0
CA D:ASP163 4.5 58.0 1.0
N D:ILE161 4.5 52.8 1.0
N D:ARG162 4.6 55.4 1.0
C D:ARG162 4.6 56.4 1.0
O D:ASN165 4.6 50.6 1.0
CA D:ILE112 4.6 48.7 1.0
NE D:ARG75 4.6 43.4 1.0
O D:ILE112 4.7 49.9 1.0
N D:ASN164 4.8 56.0 1.0
CB D:ASP163 4.8 58.6 1.0
N D:VAL113 4.8 48.9 1.0
CA D:ASN164 4.9 54.5 1.0
O D:ARG162 4.9 56.3 1.0

Potassium binding site 3 out of 16 in 3exg

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Potassium binding site 3 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K1008

b:75.6
occ:1.00
 O F:ALA160 2.7 50.7 1.0
O F:ILE161 2.7 54.2 1.0
O F:ASP163 2.9 55.5 1.0
C F:ILE161 3.5 53.0 1.0
CG2 F:VAL113 3.6 47.0 1.0
C F:PRO111 3.7 45.8 1.0
N F:ILE112 3.7 45.5 1.0
O F:ASN165 3.8 53.4 1.0
C F:ASP163 3.8 55.6 1.0
C F:ALA160 3.8 51.0 1.0
CA F:ILE161 3.9 52.3 1.0
O F:ILE112 4.0 45.8 1.0
CA F:PRO111 4.0 46.0 1.0
O F:PRO111 4.0 46.2 1.0
C F:ILE112 4.1 45.2 1.0
N F:ASP163 4.2 55.4 1.0
CB F:ASP163 4.3 57.4 1.0
CA F:ILE112 4.3 44.7 1.0
N F:ILE161 4.3 51.8 1.0
CA F:ASP163 4.3 56.3 1.0
CB F:PRO111 4.4 45.1 1.0
NH2 F:ARG75 4.4 48.4 1.0
N F:ARG162 4.5 53.3 1.0
N F:ASN165 4.6 53.6 1.0
N F:VAL113 4.6 45.5 1.0
N F:ASN164 4.7 55.5 1.0
C F:ARG162 4.7 54.3 1.0
CG2 F:VAL167 4.8 48.8 1.0
CA F:ASN164 4.8 55.6 1.0
C F:ASN165 4.9 52.4 1.0
CB F:VAL113 4.9 46.0 1.0

Potassium binding site 4 out of 16 in 3exg

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Potassium binding site 4 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K1013

b:79.1
occ:1.00
 O H:ALA160 2.7 49.9 1.0
O H:ASP163 2.8 54.1 1.0
O H:ILE161 3.2 52.4 1.0
C H:ASP163 3.6 53.4 1.0
C H:ILE161 3.7 51.3 1.0
C H:ALA160 3.8 50.0 1.0
CG2 H:VAL113 3.8 46.3 1.0
CA H:ILE161 3.8 50.0 1.0
N H:ASP163 3.9 51.9 1.0
C H:PRO111 3.9 49.8 1.0
N H:ILE112 4.0 48.9 1.0
O H:ASN165 4.0 50.0 1.0
O H:ILE112 4.0 49.1 1.0
C H:ILE112 4.1 48.3 1.0
CA H:ASP163 4.2 52.9 1.0
O H:PRO111 4.2 50.5 1.0
CA H:PRO111 4.2 49.9 1.0
N H:ILE161 4.2 50.0 1.0
CB H:ASP163 4.3 53.1 1.0
CB H:PRO111 4.4 49.2 1.0
CA H:ILE112 4.5 48.0 1.0
N H:ASN164 4.5 53.2 1.0
C H:ARG162 4.6 51.0 1.0
N H:VAL113 4.6 47.9 1.0
N H:ARG162 4.6 51.2 1.0
NH2 H:ARG75 4.6 48.2 1.0
N H:ASN165 4.8 50.6 1.0
CA H:ASN164 4.8 52.1 1.0
CB H:VAL113 5.0 46.5 1.0
CG2 H:VAL167 5.0 48.7 1.0

Potassium binding site 5 out of 16 in 3exg

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Potassium binding site 5 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K1014

b:78.9
occ:1.00
 O J:ASP163 2.4 53.6 1.0
O J:ILE161 2.7 49.6 1.0
O J:ALA160 3.0 49.6 1.0
C J:ILE161 3.3 50.3 1.0
C J:ASP163 3.6 54.0 1.0
CA J:ILE161 3.7 49.9 1.0
O J:PRO111 3.7 49.8 1.0
CG2 J:VAL113 3.7 48.7 1.0
C J:PRO111 3.9 50.1 1.0
C J:ALA160 3.9 50.1 1.0
NH2 J:ARG75 4.0 45.9 1.0
O J:ILE112 4.1 50.6 1.0
CA J:PRO111 4.2 50.2 1.0
N J:ASP163 4.2 53.7 1.0
N J:ARG162 4.3 51.2 1.0
N J:ILE161 4.3 49.7 1.0
CB J:PRO111 4.3 50.0 1.0
C J:ILE112 4.4 50.4 1.0
C J:ARG162 4.4 52.4 1.0
N J:ILE112 4.4 50.1 1.0
CA J:ASP163 4.5 54.5 1.0
CZ J:ARG75 4.5 48.2 1.0
N J:ASN164 4.6 53.8 1.0
NE J:ARG75 4.7 50.5 1.0
O J:ASN165 4.7 51.2 1.0
CA J:ASN164 4.7 53.3 1.0
O J:ARG162 4.8 52.3 1.0
CA J:ARG162 4.8 52.1 1.0
CA J:ILE112 4.8 50.3 1.0
CB J:ASP163 4.9 55.5 1.0
CB J:ILE161 4.9 50.0 1.0
CB J:VAL113 4.9 49.2 1.0
N J:VAL113 4.9 49.8 1.0
CG2 J:ILE161 5.0 48.9 1.0
N J:ASN165 5.0 52.0 1.0

Potassium binding site 6 out of 16 in 3exg

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Potassium binding site 6 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K1011

b:69.9
occ:1.00
 O L:ASP163 2.6 54.3 1.0
O L:ILE161 2.8 50.5 1.0
O L:ALA160 3.1 51.8 1.0
C L:ILE161 3.4 50.7 1.0
O L:PRO111 3.7 49.5 1.0
CG2 L:VAL113 3.7 47.2 1.0
CA L:ILE161 3.7 50.7 1.0
C L:ASP163 3.8 54.0 1.0
C L:PRO111 3.8 49.6 1.0
C L:ALA160 4.0 51.2 1.0
O L:ILE112 4.1 48.0 1.0
N L:ASP163 4.1 53.2 1.0
O L:ASN165 4.2 50.2 1.0
CA L:PRO111 4.2 50.1 1.0
NH2 L:ARG75 4.2 41.8 1.0
N L:ILE161 4.3 51.1 1.0
C L:ILE112 4.3 48.4 1.0
N L:ILE112 4.3 49.1 1.0
CB L:PRO111 4.4 49.9 1.0
N L:ARG162 4.4 50.9 1.0
CA L:ASP163 4.5 53.9 1.0
C L:ARG162 4.5 52.1 1.0
CA L:ILE112 4.7 48.9 1.0
CZ L:ARG75 4.8 44.0 1.0
CB L:ASP163 4.8 53.9 1.0
N L:ASN164 4.8 54.2 1.0
N L:VAL113 4.9 47.9 1.0
CA L:ARG162 4.9 51.2 1.0
CB L:VAL113 4.9 46.9 1.0
NE L:ARG75 4.9 46.5 1.0
O L:ARG162 4.9 52.5 1.0
CA L:ASN164 5.0 53.5 1.0
N L:ASN165 5.0 51.4 1.0

Potassium binding site 7 out of 16 in 3exg

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Potassium binding site 7 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:K1009

b:79.9
occ:1.00
 O N:ASP163 2.5 56.6 1.0
O N:ALA160 2.7 52.5 1.0
O N:ILE161 3.2 53.9 1.0
O N:ILE112 3.5 48.4 1.0
CG2 N:VAL113 3.6 47.0 1.0
C N:ASP163 3.6 56.5 1.0
C N:PRO111 3.7 51.2 1.0
O N:PRO111 3.8 51.6 1.0
C N:ILE112 3.8 48.6 1.0
C N:ALA160 3.8 52.5 1.0
C N:ILE161 3.8 53.8 1.0
O N:ASN165 3.8 54.0 1.0
N N:ILE112 3.8 50.3 1.0
CA N:ILE161 4.0 53.6 1.0
CA N:PRO111 4.1 51.1 1.0
CA N:ILE112 4.3 49.2 1.0
N N:VAL113 4.3 47.8 1.0
CA N:ASP163 4.4 56.9 1.0
N N:ASP163 4.4 55.4 1.0
N N:ILE161 4.4 53.1 1.0
NH2 N:ARG75 4.5 47.2 1.0
CB N:ASP163 4.5 57.5 1.0
CB N:PRO111 4.6 50.8 1.0
N N:ASN164 4.6 56.3 1.0
CA N:ASN164 4.7 56.4 1.0
N N:ASN165 4.7 55.1 1.0
C N:ASN165 4.8 53.7 1.0
C N:ASN164 4.8 55.9 1.0
CB N:VAL113 4.8 47.2 1.0
N N:ARG162 4.8 53.9 1.0
CA N:VAL113 4.8 47.4 1.0
C N:ARG162 4.9 54.4 1.0
CG2 N:VAL167 5.0 48.5 1.0
CA N:ALA160 5.0 52.2 1.0

Potassium binding site 8 out of 16 in 3exg

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Potassium binding site 8 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:K1012

b:84.0
occ:1.00
 O P:ASP163 2.6 54.5 1.0
O P:ALA160 2.8 51.3 1.0
O P:ILE161 2.9 51.7 1.0
C P:ILE161 3.4 52.1 1.0
CA P:ILE161 3.6 51.5 1.0
CG2 P:VAL113 3.8 44.2 1.0
C P:ASP163 3.8 54.1 1.0
O P:PRO111 3.8 50.1 1.0
C P:ALA160 3.9 52.1 1.0
C P:PRO111 3.9 49.1 1.0
NH2 P:ARG75 4.0 41.5 1.0
CB P:PRO111 4.1 48.9 1.0
N P:ASP163 4.1 54.1 1.0
CA P:PRO111 4.2 49.3 1.0
N P:ILE161 4.2 51.9 1.0
C P:ARG162 4.3 54.1 1.0
O P:ASN165 4.3 51.3 1.0
N P:ARG162 4.3 52.6 1.0
N P:ILE112 4.4 48.1 1.0
NE P:ARG75 4.4 40.8 1.0
CZ P:ARG75 4.5 38.5 1.0
CA P:ASP163 4.5 54.3 1.0
O P:ARG162 4.6 54.7 1.0
C P:ILE112 4.7 46.7 1.0
O P:ILE112 4.7 47.4 1.0
CA P:ARG162 4.8 53.3 1.0
N P:ASN164 4.8 53.9 1.0
CA P:ILE112 4.9 47.0 1.0
CB P:ILE161 4.9 51.2 1.0
CB P:ASP163 4.9 55.0 1.0
CA P:ASN164 4.9 53.7 1.0
N P:VAL113 5.0 45.9 1.0

Potassium binding site 9 out of 16 in 3exg

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Potassium binding site 9 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:K1001

b:70.8
occ:1.00
 O R:ALA160 2.7 51.1 1.0
O R:ASP163 2.7 51.6 1.0
O R:ILE161 3.2 51.8 1.0
C R:PRO111 3.5 47.6 1.0
C R:ASP163 3.6 52.2 1.0
CG2 R:VAL113 3.6 47.1 1.0
O R:PRO111 3.6 47.9 1.0
O R:ILE112 3.7 48.2 1.0
N R:ILE112 3.7 47.6 1.0
C R:ALA160 3.8 50.6 1.0
CA R:PRO111 3.8 47.8 1.0
C R:ILE161 3.8 51.8 1.0
C R:ILE112 3.9 47.7 1.0
O R:ASN165 3.9 52.5 1.0
CA R:ILE161 4.0 50.8 1.0
CB R:PRO111 4.2 47.4 1.0
CA R:ILE112 4.2 47.1 1.0
N R:ASP163 4.3 52.9 1.0
CA R:ASP163 4.3 53.3 1.0
NH2 R:ARG75 4.4 47.5 1.0
N R:ILE161 4.4 51.2 1.0
N R:VAL113 4.4 47.5 1.0
N R:ASN164 4.4 51.9 1.0
N R:ASN165 4.6 51.0 1.0
CA R:ASN164 4.6 51.6 1.0
CB R:ASP163 4.6 54.5 1.0
CB R:VAL113 4.7 47.3 1.0
C R:ASN164 4.8 51.4 1.0
C R:ARG162 4.9 52.3 1.0
C R:ASN165 4.9 51.2 1.0
N R:ARG162 4.9 51.8 1.0

Potassium binding site 10 out of 16 in 3exg

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Potassium binding site 10 out of 16 in the Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of the Pyruvate Dehydrogenase (E1P) Component of Human Pyruvate Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:K1006

b:76.7
occ:1.00
 O T:ASP163 2.7 56.2 1.0
O T:ILE161 2.8 52.5 1.0
O T:ALA160 3.0 50.4 1.0
O T:PRO111 3.4 47.2 1.0
C T:PRO111 3.5 47.0 1.0
C T:ILE161 3.6 52.3 1.0
CG2 T:VAL113 3.8 45.3 1.0
CB T:PRO111 3.8 47.3 1.0
CA T:PRO111 3.8 47.6 1.0
C T:ASP163 3.9 55.8 1.0
CA T:ILE161 3.9 51.6 1.0
N T:ILE112 4.0 46.6 1.0
NH2 T:ARG75 4.1 39.3 1.0
C T:ALA160 4.1 51.1 1.0
C T:ILE112 4.3 46.3 1.0
O T:ILE112 4.4 46.4 1.0
O T:ASN165 4.5 51.5 1.0
CA T:ILE112 4.5 46.2 1.0
N T:ILE161 4.5 51.1 1.0
N T:ASP163 4.6 55.2 1.0
N T:ARG162 4.6 53.0 1.0
CZ T:ARG75 4.6 41.5 1.0
NE T:ARG75 4.7 44.9 1.0
CA T:ASP163 4.7 56.2 1.0
C T:ARG162 4.7 53.7 1.0
CA T:ASN164 4.7 54.4 1.0
N T:ASN164 4.8 55.3 1.0
N T:VAL113 4.8 46.5 1.0
N T:ASN165 5.0 52.7 1.0
CB T:ASP163 5.0 56.4 1.0
C T:ASN164 5.0 54.2 1.0

Reference:

M.Kato, R.M.Wynn, J.L.Chuang, S.C.Tso, M.Machius, J.Li, D.T.Chuang. Structural Basis For Inactivation of the Human Pyruvate Dehydrogenase Complex By Phosphorylation: Role of Disordered Phosphorylation Loops. Structure V. 16 1849 2008.
ISSN: ISSN 0969-2126
PubMed: 19081061
DOI: 10.1016/J.STR.2008.10.010
Page generated: Mon Aug 12 08:11:43 2024

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