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Potassium in PDB 3dva: 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: 3dva 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 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.673, 232.294, 91.936, 90.00, 91.20, 90.00
R / Rfree (%) 19 / 24.7

Other elements in 3dva:

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

Potassium binding site 1 out of 2 in 3dva

Go back to Potassium Binding Sites List in 3dva
Potassium binding site 1 out of 2 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:16.4
occ:1.00
O B:ALA160 2.6 21.2 1.0
O B:ASP163 2.6 22.2 1.0
O B:ASP165 2.7 20.7 1.0
O B:HOH1363 2.8 17.4 1.0
O B:ILE112 3.0 18.9 1.0
OG1 B:THR113 3.2 18.9 1.0
C B:ILE112 3.5 18.7 1.0
C B:ASP163 3.6 22.5 1.0
N B:ILE112 3.8 18.7 1.0
C B:ASP165 3.8 20.8 1.0
C B:ALA160 3.8 21.4 1.0
CG2 B:VAL167 3.9 21.0 1.0
CB B:ASP163 4.0 22.6 1.0
C B:PRO111 4.0 18.8 1.0
N B:VAL167 4.0 20.5 1.0
CB B:VAL167 4.1 20.9 1.0
N B:THR113 4.2 18.8 1.0
CA B:ASP163 4.2 22.7 1.0
O B:ILE161 4.2 22.2 1.0
CA B:ILE112 4.2 18.5 1.0
N B:ASP165 4.3 21.4 1.0
N B:ASP163 4.4 22.9 1.0
CB B:THR113 4.4 18.9 1.0
CA B:PRO111 4.4 18.8 1.0
CA B:THR113 4.4 18.8 1.0
O B:PRO111 4.5 18.8 1.0
C B:ILE161 4.5 22.3 1.0
CA B:ILE161 4.5 21.9 1.0
OD1 B:ASP163 4.5 22.5 1.0
C B:PRO166 4.5 20.4 1.0
CA B:PRO166 4.5 20.3 1.0
N B:ILE161 4.6 21.7 1.0
N B:PRO166 4.6 20.5 1.0
CA B:VAL167 4.7 20.6 1.0
N B:ASN164 4.7 22.4 1.0
CG B:ASP163 4.7 22.6 1.0
CA B:ASP165 4.7 21.0 1.0
CA B:ALA160 4.8 21.3 1.0
O B:MET110 4.9 18.3 1.0
C B:ASN164 4.9 21.7 1.0

Potassium binding site 2 out of 2 in 3dva

Go back to Potassium Binding Sites List in 3dva
Potassium binding site 2 out of 2 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:10.7
occ:1.00
O D:ALA160 2.6 17.4 1.0
O D:ASP163 2.7 18.3 1.0
O D:ASP165 2.7 17.2 1.0
O D:HOH1474 2.7 8.0 1.0
O D:ILE112 3.0 14.5 1.0
OG1 D:THR113 3.1 14.3 1.0
C D:ILE112 3.4 14.7 1.0
C D:ASP163 3.6 18.4 1.0
N D:ILE112 3.7 15.0 1.0
C D:ALA160 3.8 17.4 1.0
C D:ASP165 3.9 17.4 1.0
CG2 D:VAL167 3.9 16.3 1.0
C D:PRO111 3.9 15.1 1.0
CB D:ASP163 3.9 18.3 1.0
N D:THR113 4.0 14.7 1.0
N D:VAL167 4.1 16.4 1.0
O D:ILE161 4.1 18.1 1.0
CA D:ILE112 4.1 14.8 1.0
CB D:VAL167 4.1 16.3 1.0
CA D:ASP163 4.2 18.3 1.0
CA D:THR113 4.3 14.6 1.0
N D:ASP165 4.3 17.9 1.0
CB D:THR113 4.3 14.4 1.0
CA D:PRO111 4.3 15.2 1.0
OD1 D:ASP163 4.3 18.7 1.0
O D:PRO111 4.3 15.1 1.0
N D:ASP163 4.4 18.4 1.0
C D:ILE161 4.4 18.1 1.0
CG D:ASP163 4.5 18.4 1.0
CA D:ILE161 4.5 17.8 1.0
C D:PRO166 4.6 16.6 1.0
CA D:PRO166 4.6 16.9 1.0
N D:ILE161 4.6 17.5 1.0
N D:ASN164 4.7 18.2 1.0
N D:PRO166 4.7 17.2 1.0
CA D:VAL167 4.7 16.4 1.0
CA D:ALA160 4.8 17.2 1.0
CA D:ASP165 4.8 17.6 1.0
O D:MET110 4.9 15.1 1.0
C D:ASN164 5.0 18.1 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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