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Potassium in PDB 1w85: The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2

Enzymatic activity of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2

All present enzymatic activity of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2:
1.2.4.1; 2.3.1.12;

Protein crystallography data

The structure of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2, PDB code: 1w85 was solved by R.A.W.Frank, J.V.Pratap, X.Y.Pei, R.N.Perham, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.270, 232.330, 91.924, 90.00, 90.81, 90.00
R / Rfree (%) 17.6 / 21.5

Other elements in 1w85:

The structure of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2 also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2 (pdb code 1w85). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2, PDB code: 1w85:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1w85

Go back to Potassium Binding Sites List in 1w85
Potassium binding site 1 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1325

b:19.0
occ:1.00
 O B:ASP165 2.7 12.9 1.0
O B:ALA160 2.7 14.9 1.0
O B:ASP163 2.7 15.5 1.0
O B:HOH2069 2.9 17.0 1.0
O B:ILE112 3.0 13.1 1.0
OG1 B:THR113 3.4 13.6 1.0
C B:ILE112 3.5 13.0 1.0
N B:ILE112 3.7 12.7 1.0
C B:ASP163 3.7 16.0 1.0
CG2 B:VAL167 3.7 13.4 1.0
C B:ASP165 3.8 13.2 1.0
C B:PRO111 3.8 12.9 1.0
C B:ALA160 3.9 15.0 1.0
CB B:ASP163 4.0 16.6 1.0
N B:VAL167 4.0 12.7 1.0
N B:THR113 4.2 13.2 1.0
CA B:ILE112 4.2 12.7 1.0
CA B:PRO111 4.2 12.5 1.0
CB B:VAL167 4.2 13.2 1.0
CA B:ASP163 4.2 16.2 1.0
O B:ILE161 4.2 16.0 1.0
N B:ASP165 4.3 14.3 1.0
O B:PRO111 4.3 12.6 1.0
OD1 B:ASP163 4.4 17.0 1.0
N B:ASP163 4.4 16.6 1.0
CA B:PRO166 4.4 12.9 1.0
C B:PRO166 4.5 12.7 1.0
CA B:THR113 4.5 13.4 1.0
CB B:THR113 4.5 13.7 1.0
C B:ILE161 4.5 16.0 1.0
N B:PRO166 4.5 12.9 1.0
CA B:ILE161 4.6 15.8 1.0
CG B:ASP163 4.6 16.8 1.0
N B:ASN164 4.7 15.3 1.0
N B:ILE161 4.7 15.2 1.0
CA B:ASP165 4.7 13.6 1.0
CA B:VAL167 4.7 13.0 1.0
O B:MET110 4.8 12.5 1.0
CA B:ALA160 4.8 14.7 1.0
C B:ASN164 4.9 14.8 1.0

Potassium binding site 2 out of 4 in 1w85

Go back to Potassium Binding Sites List in 1w85
Potassium binding site 2 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1325

b:19.7
occ:1.00
 O D:ASP165 2.7 10.1 1.0
O D:ALA160 2.7 11.4 1.0
O D:ASP163 2.7 11.9 1.0
O D:HOH2087 2.9 12.0 1.0
O D:ILE112 2.9 10.8 1.0
OG1 D:THR113 3.3 11.0 1.0
C D:ILE112 3.5 10.3 1.0
N D:ILE112 3.6 10.0 1.0
C D:ASP163 3.7 12.8 1.0
CG2 D:VAL167 3.7 9.6 1.0
C D:ASP165 3.8 10.4 1.0
C D:PRO111 3.8 10.3 1.0
C D:ALA160 3.9 11.3 1.0
CB D:ASP163 4.0 13.2 1.0
N D:VAL167 4.1 10.2 1.0
N D:THR113 4.2 10.4 1.0
CA D:ILE112 4.2 10.0 1.0
O D:ILE161 4.2 11.4 1.0
CA D:ASP163 4.2 12.8 1.0
CB D:VAL167 4.2 10.2 1.0
CA D:PRO111 4.3 10.3 1.0
O D:PRO111 4.3 10.1 1.0
N D:ASP165 4.3 11.3 1.0
CA D:PRO166 4.4 10.0 1.0
N D:ASP163 4.5 12.5 1.0
CA D:THR113 4.5 11.0 1.0
CB D:THR113 4.5 10.8 1.0
C D:PRO166 4.5 10.0 1.0
C D:ILE161 4.5 11.4 1.0
OD1 D:ASP163 4.5 13.7 1.0
N D:PRO166 4.6 10.1 1.0
CA D:ILE161 4.6 11.4 1.0
N D:ASN164 4.7 12.4 1.0
N D:ILE161 4.7 11.0 1.0
CG D:ASP163 4.7 13.5 1.0
CA D:ASP165 4.7 10.8 1.0
CA D:VAL167 4.8 10.1 1.0
O D:MET110 4.8 10.7 1.0
CA D:ALA160 4.8 11.3 1.0
C D:ASN164 4.9 11.9 1.0
CA D:ASN164 5.0 12.4 1.0

Potassium binding site 3 out of 4 in 1w85

Go back to Potassium Binding Sites List in 1w85
Potassium binding site 3 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K1325

b:28.5
occ:1.00
 O F:ASP163 2.7 21.2 1.0
O F:ASP165 2.7 19.2 1.0
O F:ALA160 2.8 20.9 1.0
O F:HOH2060 2.9 19.9 1.0
O F:ILE112 3.0 19.9 1.0
OG1 F:THR113 3.3 19.4 1.0
C F:ILE112 3.5 19.9 1.0
N F:ILE112 3.6 20.5 1.0
C F:ASP163 3.6 21.4 1.0
C F:PRO111 3.8 21.0 1.0
C F:ASP165 3.8 19.4 1.0
CG2 F:VAL167 3.9 18.0 1.0
C F:ALA160 4.0 21.1 1.0
CB F:ASP163 4.0 21.9 1.0
N F:VAL167 4.1 18.6 1.0
CA F:PRO111 4.1 21.2 1.0
N F:THR113 4.2 19.5 1.0
O F:ILE161 4.2 21.6 1.0
CA F:ILE112 4.2 19.9 1.0
CA F:ASP163 4.2 21.7 1.0
CB F:VAL167 4.3 18.1 1.0
O F:PRO111 4.3 21.0 1.0
N F:ASP165 4.3 20.2 1.0
N F:ASP163 4.3 21.9 1.0
CA F:PRO166 4.4 19.0 1.0
C F:PRO166 4.5 18.7 1.0
C F:ILE161 4.5 21.5 1.0
CB F:THR113 4.5 19.5 1.0
CA F:THR113 4.5 19.3 1.0
CA F:ILE161 4.6 21.4 1.0
N F:PRO166 4.6 19.1 1.0
N F:ASN164 4.6 21.0 1.0
OD1 F:ASP163 4.6 21.9 1.0
N F:ILE161 4.7 21.2 1.0
CA F:ASP165 4.8 19.8 1.0
O F:MET110 4.8 21.5 1.0
CG F:ASP163 4.8 21.9 1.0
CA F:VAL167 4.8 18.1 1.0
C F:ASN164 4.8 20.5 1.0
CA F:ASN164 4.9 20.8 1.0
CA F:ALA160 4.9 21.2 1.0
CB F:PRO111 5.0 21.1 1.0

Potassium binding site 4 out of 4 in 1w85

Go back to Potassium Binding Sites List in 1w85
Potassium binding site 4 out of 4 in the The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K1325

b:21.2
occ:1.00
 O H:ALA160 2.7 14.3 1.0
O H:ASP165 2.7 15.1 1.0
O H:ASP163 2.8 16.3 1.0
O H:ILE112 3.0 15.5 1.0
O H:HOH2072 3.0 14.2 1.0
OG1 H:THR113 3.3 14.9 1.0
C H:ILE112 3.5 15.4 1.0
N H:ILE112 3.6 15.6 1.0
C H:ASP163 3.7 16.8 1.0
C H:PRO111 3.8 15.7 1.0
C H:ASP165 3.8 15.2 1.0
C H:ALA160 3.9 14.6 1.0
CG2 H:VAL167 3.9 13.8 1.0
N H:VAL167 4.0 14.0 1.0
CB H:ASP163 4.0 17.2 1.0
N H:THR113 4.1 15.1 1.0
CA H:PRO111 4.1 15.9 1.0
CA H:ILE112 4.2 15.5 1.0
O H:ILE161 4.2 15.0 1.0
CB H:VAL167 4.2 14.0 1.0
O H:PRO111 4.3 15.5 1.0
CA H:ASP163 4.3 16.6 1.0
N H:ASP165 4.4 15.9 1.0
CA H:THR113 4.4 15.2 1.0
CA H:PRO166 4.4 14.4 1.0
CB H:THR113 4.5 14.9 1.0
C H:PRO166 4.5 14.2 1.0
C H:ILE161 4.5 15.2 1.0
CA H:ILE161 4.5 14.8 1.0
N H:ASP163 4.5 16.3 1.0
OD1 H:ASP163 4.6 17.8 1.0
N H:PRO166 4.6 14.7 1.0
N H:ASN164 4.6 16.6 1.0
N H:ILE161 4.6 14.7 1.0
O H:MET110 4.7 15.8 1.0
CG H:ASP163 4.7 17.4 1.0
CA H:ASP165 4.8 15.7 1.0
CA H:VAL167 4.8 14.1 1.0
CA H:ALA160 4.8 14.4 1.0
C H:ASN164 4.9 16.3 1.0

Reference:

R.A.Frank, C.M.Titman, J.V.Pratap, B.F.Luisi, R.N.Perham. A Molecular Switch and Proton Wire Synchronize the Active Sites in Thiamine Enzymes. Science V. 306 872 2004.
ISSN: ESSN 1095-9203
PubMed: 15514159
DOI: 10.1126/SCIENCE.1101030
Page generated: Sun Dec 13 23:04:43 2020

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