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Magnesium in PDB 2ji7: X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate

Enzymatic activity of X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate

All present enzymatic activity of X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate:
4.1.1.8;

Protein crystallography data

The structure of X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate, PDB code: 2ji7 was solved by C.L.Berthold, C.G.Toyota, P.Moussatche, M.D.Wood, F.Leeper, N.G.J.Richards, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.82
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.181, 126.181, 151.938, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 17.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate (pdb code 2ji7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate, PDB code: 2ji7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2ji7

Go back to Magnesium Binding Sites List in 2ji7
Magnesium binding site 1 out of 2 in the X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1567

b:11.4
occ:1.00
O3B A:OXT1566 2.0 14.8 1.0
OD1 A:ASP452 2.1 22.9 1.0
O A:GLY481 2.1 21.1 1.0
OD1 A:ASN479 2.1 22.5 1.0
O1A A:OXT1566 2.1 14.9 1.0
O A:HOH2479 2.3 14.9 1.0
CG A:ASN479 3.1 21.5 1.0
PB A:OXT1566 3.2 15.6 1.0
CG A:ASP452 3.3 21.6 1.0
C A:GLY481 3.3 22.0 1.0
PA A:OXT1566 3.4 14.5 1.0
ND2 A:ASN479 3.4 22.4 1.0
O3A A:OXT1566 3.6 15.1 1.0
O2B A:OXT1566 3.8 15.0 1.0
OD2 A:ASP452 3.9 22.9 1.0
N A:ASP452 3.9 22.8 1.0
O76 A:OXT1566 4.0 15.3 1.0
N A:GLY481 4.1 22.0 1.0
N A:TYR483 4.2 23.2 1.0
O A:MET477 4.2 24.4 1.0
CA A:GLY481 4.3 21.9 1.0
N A:ILE482 4.3 22.0 1.0
N A:SER453 4.3 24.2 1.0
CB A:ASP452 4.4 22.8 1.0
CA A:ILE482 4.4 22.3 1.0
CB A:ASN479 4.5 21.3 1.0
O1B A:OXT1566 4.5 17.1 1.0
CA A:ASP452 4.6 23.2 1.0
O2A A:OXT1566 4.6 13.5 1.0
N A:ASN479 4.7 21.6 1.0
OH A:TYR377 4.7 22.1 1.0
C A:ILE482 4.7 22.1 1.0
C A:GLY451 4.8 22.6 1.0
CA A:GLY451 4.9 21.8 1.0
N A:GLY480 4.9 21.2 1.0
CA A:ASN479 4.9 21.4 1.0
C A:ASP452 5.0 23.5 1.0

Magnesium binding site 2 out of 2 in 2ji7

Go back to Magnesium Binding Sites List in 2ji7
Magnesium binding site 2 out of 2 in the X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Oxalyl-Coa Decarboxylase with Covalent Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1567

b:13.9
occ:1.00
O3B B:OXT1566 2.0 16.5 1.0
OD1 B:ASN479 2.1 23.7 1.0
O1A B:OXT1566 2.1 15.9 1.0
OD1 B:ASP452 2.2 22.6 1.0
O B:GLY481 2.2 22.7 1.0
O B:HOH2483 2.2 16.4 1.0
CG B:ASN479 3.0 21.9 1.0
PB B:OXT1566 3.2 17.9 1.0
ND2 B:ASN479 3.3 23.4 1.0
CG B:ASP452 3.3 23.4 1.0
PA B:OXT1566 3.3 17.0 1.0
C B:GLY481 3.4 23.4 1.0
O3A B:OXT1566 3.6 16.9 1.0
O2B B:OXT1566 3.7 17.4 1.0
OD2 B:ASP452 3.9 26.1 1.0
N B:ASP452 4.0 22.7 1.0
O76 B:OXT1566 4.0 16.2 1.0
N B:GLY481 4.1 23.0 1.0
O B:MET477 4.2 22.6 1.0
CA B:GLY481 4.3 23.3 1.0
N B:TYR483 4.3 24.0 1.0
N B:SER453 4.3 22.8 1.0
N B:ILE482 4.4 22.8 1.0
CB B:ASN479 4.4 23.1 1.0
O1B B:OXT1566 4.5 17.4 1.0
CA B:ILE482 4.5 23.3 1.0
CB B:ASP452 4.5 23.6 1.0
OH B:TYR377 4.6 25.3 1.0
O2A B:OXT1566 4.6 16.3 1.0
N B:ASN479 4.6 22.6 1.0
CA B:ASP452 4.6 23.1 1.0
C B:ILE482 4.8 23.0 1.0
C B:GLY451 4.8 22.2 1.0
CA B:GLY451 4.9 21.7 1.0
CA B:ASN479 4.9 22.5 1.0
N B:GLY480 4.9 21.7 1.0

Reference:

C.L.Berthold, C.G.Toyota, P.Moussatche, M.D.Wood, F.Leeper, N.G.J.Richards, Y.Lindqvist. Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis By Nonoxidative Thdp-Dependent Decarboxylases Structure V. 15 853 2007.
ISSN: ISSN 0969-2126
PubMed: 17637344
DOI: 10.1016/J.STR.2007.06.001
Page generated: Mon Dec 14 07:29:34 2020

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