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Potassium in PDB 3dv0: Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex

Enzymatic activity of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex

All present enzymatic activity of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex:
1.2.4.1; 2.3.1.12;

Protein crystallography data

The structure of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex, PDB code: 3dv0 was solved by X.Y.Pei, C.M.Titman, R.A.W.Frank, F.J.Leeper, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.17 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.312, 232.820, 92.004, 90.00, 91.83, 90.00
R / Rfree (%) 17.3 / 24.1

Other elements in 3dv0:

The structure of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex (pdb code 3dv0). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex, PDB code: 3dv0:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3dv0

Go back to Potassium Binding Sites List in 3dv0
Potassium binding site 1 out of 4 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1325

b:32.6
occ:1.00
 O B:ALA160 2.9 31.0 1.0
O B:ASP163 3.0 26.5 1.0
O B:HOH1344 3.1 17.3 1.0
O B:ASP165 3.1 13.1 1.0
OG1 B:THR113 3.2 19.6 1.0
O B:ILE112 3.2 24.0 1.0
C B:ILE112 3.7 15.3 1.0
C B:ASP163 3.8 25.7 1.0
CG2 B:VAL167 3.8 15.0 1.0
CB B:ASP163 3.8 23.0 1.0
C B:ALA160 3.9 26.9 1.0
N B:ILE112 3.9 17.4 1.0
CB B:VAL167 4.0 24.2 1.0
C B:PRO111 4.0 22.0 1.0
O B:ILE161 4.0 36.2 1.0
N B:VAL167 4.0 13.4 1.0
C B:ASP165 4.1 22.3 1.0
CA B:ASP163 4.2 22.5 1.0
N B:THR113 4.2 13.0 1.0
N B:ASP163 4.3 20.2 1.0
C B:ILE161 4.3 29.2 1.0
CA B:PRO111 4.3 13.9 1.0
CA B:ILE112 4.4 21.6 1.0
CA B:ILE161 4.4 25.1 1.0
CB B:THR113 4.4 18.7 1.0
O B:PRO111 4.4 25.9 1.0
CA B:THR113 4.4 16.1 1.0
N B:ILE161 4.5 26.4 1.0
N B:ASP165 4.6 21.4 1.0
OD1 B:ASP163 4.6 34.6 1.0
C B:PRO166 4.6 17.7 1.0
CA B:VAL167 4.6 19.9 1.0
CG B:ASP163 4.6 28.0 1.0
CA B:PRO166 4.6 22.5 1.0
N B:ASN164 4.7 26.1 1.0
CA B:ALA160 4.8 25.4 1.0
N B:PRO166 4.8 23.4 1.0
O B:MET110 5.0 20.1 1.0

Potassium binding site 2 out of 4 in 3dv0

Go back to Potassium Binding Sites List in 3dv0
Potassium binding site 2 out of 4 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1325

b:15.6
occ:1.00
 O D:ALA160 2.8 18.4 1.0
O D:ASP165 2.8 13.2 1.0
O D:ASP163 3.0 16.4 1.0
O D:HOH1328 3.0 7.5 1.0
O D:ILE112 3.2 17.8 1.0
OG1 D:THR113 3.3 6.2 1.0
C D:ILE112 3.5 16.1 1.0
N D:ILE112 3.8 13.7 1.0
C D:ASP163 3.8 21.6 1.0
CB D:ASP163 3.8 14.6 1.0
CG2 D:VAL167 3.9 17.1 1.0
C D:ASP165 3.9 16.2 1.0
C D:PRO111 4.0 8.6 1.0
N D:THR113 4.0 14.6 1.0
C D:ALA160 4.0 12.5 1.0
N D:VAL167 4.1 11.3 1.0
O D:ILE161 4.1 29.9 1.0
CB D:VAL167 4.1 16.3 1.0
CA D:ILE112 4.2 14.1 1.0
CA D:ASP163 4.2 13.4 1.0
CA D:THR113 4.3 18.3 1.0
CA D:PRO111 4.3 11.3 1.0
N D:ASP165 4.3 11.7 1.0
CB D:THR113 4.4 16.5 1.0
O D:PRO111 4.4 18.2 1.0
N D:ASP163 4.4 17.0 1.0
C D:ILE161 4.4 15.0 1.0
CA D:ILE161 4.5 9.8 1.0
C D:PRO166 4.5 9.2 1.0
OD1 D:ASP163 4.6 28.8 1.0
CA D:PRO166 4.6 15.7 1.0
CG D:ASP163 4.6 14.4 1.0
N D:PRO166 4.7 9.9 1.0
N D:ASN164 4.7 21.3 1.0
CA D:VAL167 4.7 12.9 1.0
N D:ILE161 4.7 17.4 1.0
O D:MET110 4.8 16.5 1.0
CA D:ASP165 4.8 15.2 1.0
C D:ASN164 4.9 20.2 1.0

Potassium binding site 3 out of 4 in 3dv0

Go back to Potassium Binding Sites List in 3dv0
Potassium binding site 3 out of 4 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K1325

b:46.9
occ:1.00
 O F:ALA160 3.0 41.2 1.0
O F:ASP163 3.0 47.7 1.0
O F:ASP165 3.1 36.8 1.0
OG1 F:THR113 3.2 37.1 1.0
O F:ILE112 3.2 43.7 1.0
O F:HOH1408 3.3 56.5 1.0
C F:ILE112 3.5 38.3 1.0
N F:ILE112 3.6 36.9 1.0
C F:PRO111 3.8 33.8 1.0
C F:ASP163 3.8 48.2 1.0
CB F:ASP163 3.9 50.3 1.0
CG2 F:VAL167 3.9 38.6 1.0
C F:ALA160 4.0 37.1 1.0
C F:ASP165 4.0 38.0 1.0
CA F:ILE112 4.1 34.0 1.0
CA F:PRO111 4.1 31.5 1.0
N F:THR113 4.1 42.8 1.0
O F:ILE161 4.1 44.6 1.0
CB F:VAL167 4.3 38.2 1.0
CA F:ASP163 4.3 50.0 1.0
O F:PRO111 4.3 34.9 1.0
N F:VAL167 4.3 37.2 1.0
C F:ILE161 4.3 37.1 1.0
CA F:ILE161 4.4 36.6 1.0
N F:ASP163 4.4 47.0 1.0
CB F:THR113 4.4 38.5 1.0
CA F:THR113 4.4 41.5 1.0
N F:ASP165 4.5 42.4 1.0
OD1 F:ASP163 4.5 37.5 1.0
C F:PRO166 4.6 36.5 1.0
N F:ILE161 4.6 37.7 1.0
CA F:PRO166 4.6 36.7 1.0
CG F:ASP163 4.7 50.3 1.0
N F:PRO166 4.7 35.5 1.0
N F:ASN164 4.8 46.1 1.0
CB F:PRO111 4.8 25.8 1.0
O F:MET110 4.9 46.3 1.0
C F:ASN164 4.9 43.0 1.0
CA F:VAL167 4.9 36.7 1.0
CA F:ASP165 4.9 40.0 1.0

Potassium binding site 4 out of 4 in 3dv0

Go back to Potassium Binding Sites List in 3dv0
Potassium binding site 4 out of 4 in the Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multi-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K1325

b:26.4
occ:1.00
 O H:ALA160 2.9 25.6 1.0
O H:ASP163 2.9 26.6 1.0
O H:ASP165 2.9 16.5 1.0
O H:HOH1330 3.0 13.3 1.0
O H:ILE112 3.1 26.0 1.0
OG1 H:THR113 3.3 22.9 1.0
C H:ILE112 3.5 19.2 1.0
N H:ILE112 3.6 21.1 1.0
C H:ASP163 3.8 30.0 1.0
C H:PRO111 3.8 21.5 1.0
CB H:ASP163 3.9 26.0 1.0
C H:ASP165 3.9 16.9 1.0
C H:ALA160 4.0 22.1 1.0
CG2 H:VAL167 4.0 31.9 1.0
N H:THR113 4.1 18.1 1.0
CA H:PRO111 4.1 22.4 1.0
N H:VAL167 4.1 18.3 1.0
CA H:ILE112 4.1 14.7 1.0
CB H:VAL167 4.2 19.4 1.0
CA H:ASP163 4.3 30.3 1.0
O H:ILE161 4.3 28.2 1.0
O H:PRO111 4.4 23.4 1.0
N H:ASP163 4.4 27.9 1.0
CA H:THR113 4.4 12.6 1.0
N H:ASP165 4.4 24.4 1.0
CB H:THR113 4.4 17.2 1.0
CA H:PRO166 4.5 19.1 1.0
C H:ILE161 4.5 23.6 1.0
CA H:ILE161 4.5 20.1 1.0
C H:PRO166 4.5 20.8 1.0
N H:PRO166 4.6 17.4 1.0
N H:ILE161 4.7 21.6 1.0
CG H:ASP163 4.7 19.9 1.0
O H:MET110 4.7 20.1 1.0
OD1 H:ASP163 4.8 22.0 1.0
N H:ASN164 4.8 28.6 1.0
CA H:VAL167 4.8 19.2 1.0
CA H:ASP165 4.9 28.1 1.0
C H:ASN164 4.9 27.2 1.0
CA H:ALA160 5.0 16.8 1.0
CB H:PRO111 5.0 28.3 1.0

Reference:

X.Y.Pei, C.M.Titman, R.A.Frank, F.J.Leeper, B.F.Luisi. Snapshots of Catalysis in the E1 Subunit of the Pyruvate Dehydrogenase Multienzyme Complex Structure V. 16 1860 2008.
ISSN: ISSN 0969-2126
PubMed: 19081062
DOI: 10.1016/J.STR.2008.10.009
Page generated: Mon Aug 12 08:02:55 2024

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