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Magnesium in PDB 2iea: E. Coli Pyruvate Dehydrogenase

Enzymatic activity of E. Coli Pyruvate Dehydrogenase

All present enzymatic activity of E. Coli Pyruvate Dehydrogenase:
1.2.4.1;

Protein crystallography data

The structure of E. Coli Pyruvate Dehydrogenase, PDB code: 2iea was solved by W.Furey, P.Arjunan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.690, 141.600, 82.460, 90.00, 102.40, 90.00
R / Rfree (%) 17.7 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Pyruvate Dehydrogenase (pdb code 2iea). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E. Coli Pyruvate Dehydrogenase, PDB code: 2iea:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2iea

Go back to Magnesium Binding Sites List in 2iea
Magnesium binding site 1 out of 2 in the E. Coli Pyruvate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Pyruvate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg888

b:15.5
occ:1.00
OD1 A:ASN260 2.1 8.9 1.0
OD2 A:ASP230 2.2 17.5 1.0
O A:HOH910 2.2 10.7 1.0
O A:GLN262 2.3 16.9 1.0
O12 A:TDP887 2.5 13.2 1.0
O23 A:TDP887 2.5 15.5 1.0
CG A:ASN260 3.0 17.3 1.0
CG A:ASP230 3.2 21.9 1.0
ND2 A:ASN260 3.3 14.0 1.0
C A:GLN262 3.4 19.1 1.0
P2 A:TDP887 3.5 18.9 1.0
O11 A:TDP887 3.5 12.4 1.0
P1 A:TDP887 3.5 13.4 1.0
OD1 A:ASP230 3.6 12.7 1.0
N A:ASP230 3.8 10.4 1.0
O21 A:TDP887 3.9 18.0 1.0
N A:GLN262 3.9 17.4 1.0
O A:ASN258 3.9 11.5 1.0
N A:GLY231 4.1 13.0 1.0
CA A:GLN262 4.2 20.8 1.0
N A:ASN260 4.3 15.9 1.0
CB A:ASN260 4.4 13.1 1.0
CB A:ASP230 4.4 13.6 1.0
O5G A:TDP887 4.4 15.2 1.0
N A:ARG263 4.4 17.1 1.0
CA A:ASP230 4.5 10.7 1.0
N A:LEU261 4.6 12.6 1.0
CA A:ARG263 4.6 17.7 1.0
C A:GLY229 4.7 10.6 1.0
CA A:ASN260 4.7 15.3 1.0
O13 A:TDP887 4.7 12.0 1.0
C A:ASN260 4.7 14.2 1.0
CA A:GLY229 4.7 9.9 1.0
O22 A:TDP887 4.8 19.8 1.0
C A:ASP230 4.8 13.9 1.0
C A:LEU261 4.9 17.9 1.0
CB A:GLN262 4.9 24.1 1.0

Magnesium binding site 2 out of 2 in 2iea

Go back to Magnesium Binding Sites List in 2iea
Magnesium binding site 2 out of 2 in the E. Coli Pyruvate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Pyruvate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg888

b:15.8
occ:1.00
OD1 B:ASP230 2.1 11.6 1.0
OD1 B:ASN260 2.1 12.1 1.0
O B:GLN262 2.2 14.0 1.0
O B:HOH903 2.3 11.1 1.0
O12 B:TDP887 2.4 14.2 1.0
O23 B:TDP887 2.5 11.3 1.0
CG B:ASN260 3.0 12.3 1.0
CG B:ASP230 3.1 11.8 1.0
ND2 B:ASN260 3.3 14.9 1.0
C B:GLN262 3.3 17.8 1.0
P2 B:TDP887 3.5 13.4 1.0
P1 B:TDP887 3.5 13.3 1.0
O11 B:TDP887 3.5 13.4 1.0
OD2 B:ASP230 3.6 11.9 1.0
N B:GLN262 3.8 15.3 1.0
N B:ASP230 3.8 11.1 1.0
O21 B:TDP887 3.9 16.6 1.0
O B:ASN258 4.0 9.7 1.0
N B:GLY231 4.1 12.8 1.0
CA B:GLN262 4.1 17.6 1.0
N B:ARG263 4.3 13.4 1.0
N B:ASN260 4.4 11.6 1.0
CB B:ASP230 4.4 8.8 1.0
CB B:ASN260 4.4 9.9 1.0
O5G B:TDP887 4.4 14.8 1.0
CA B:ARG263 4.5 16.2 1.0
CA B:ASP230 4.5 10.8 1.0
N B:LEU261 4.5 10.3 1.0
O13 B:TDP887 4.7 12.6 1.0
NZ B:LYS392 4.7 32.4 1.0
CA B:ASN260 4.7 11.6 1.0
C B:GLY229 4.8 14.0 1.0
C B:ASN260 4.8 17.0 1.0
C B:ASP230 4.8 8.4 1.0
O22 B:TDP887 4.8 14.8 1.0
C B:LEU261 4.8 16.2 1.0
CA B:GLY229 4.8 11.2 1.0
CB B:GLN262 4.9 26.9 1.0
CE B:LYS392 4.9 37.2 1.0
CG2 B:VAL268 5.0 18.1 1.0
CA B:GLY231 5.0 10.8 1.0

Reference:

P.Arjunan, N.Nemeria, A.Brunskill, K.Chandrasekhar, M.Sax, Y.Yan, F.Jordan, J.R.Guest, W.Furey. Structure of the Pyruvate Dehydrogenase Multienzyme Complex E1 Component From Escherichia Coli at 1.85 A Resolution. Biochemistry V. 41 5213 2002.
ISSN: ISSN 0006-2960
PubMed: 11955070
DOI: 10.1021/BI0118557
Page generated: Mon Dec 14 07:27:14 2020

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