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Magnesium in PDB 4rgv: Crystal Structure of the Methanocaldococcus Jannaschii G1PDH

Enzymatic activity of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH

All present enzymatic activity of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH:
1.1.1.261;

Protein crystallography data

The structure of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH, PDB code: 4rgv was solved by V.Carbone, R.S.Ronimus, L.R.Schofield, A.J.Sutherland-Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.07 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.765, 59.552, 119.825, 90.00, 90.39, 90.00
R / Rfree (%) 19.3 / 23.1

Other elements in 4rgv:

The structure of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH (pdb code 4rgv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH, PDB code: 4rgv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4rgv

Go back to Magnesium Binding Sites List in 4rgv
Magnesium binding site 1 out of 2 in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:25.5
occ:1.00
O A:ASP148 2.4 45.4 1.0
OD1 A:ASN152 2.6 37.1 1.0
O A:ALA221 2.7 43.6 1.0
OG A:SER151 3.0 52.5 1.0
OD2 A:ASP105 3.4 53.8 1.0
C A:ASP148 3.5 45.3 1.0
C A:ALA221 3.7 44.7 1.0
OD1 A:ASP148 3.7 66.3 1.0
CG A:ASP148 3.8 58.8 1.0
OD2 A:ASP148 3.8 64.5 1.0
CG A:ASN152 3.9 37.1 1.0
CE1 A:HIS226 3.9 51.2 1.0
CB A:ALA221 3.9 43.3 1.0
CA A:ALA221 4.0 43.6 1.0
N A:ASN152 4.2 39.2 1.0
CB A:SER151 4.3 47.5 1.0
CA A:ASP148 4.3 47.6 1.0
ZN A:ZN402 4.3 59.7 0.5
OG A:SER208 4.4 47.0 1.0
CG A:ASP105 4.5 51.0 1.0
C A:SER151 4.5 41.4 1.0
N A:ILE149 4.5 42.3 1.0
CB A:ASP148 4.6 50.7 1.0
ND2 A:ASN152 4.6 39.7 1.0
NE2 A:HIS226 4.6 51.1 1.0
CA A:ILE149 4.7 42.5 1.0
O A:ILE149 4.8 43.9 1.0
CA A:ASN152 4.8 38.6 1.0
CA A:SER151 4.8 45.3 1.0
ND1 A:HIS226 4.8 51.2 1.0
CB A:ASN152 4.9 38.3 1.0
N A:SER222 4.9 48.3 1.0
C A:ILE149 5.0 44.1 1.0

Magnesium binding site 2 out of 2 in 4rgv

Go back to Magnesium Binding Sites List in 4rgv
Magnesium binding site 2 out of 2 in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:24.4
occ:1.00
OD1 B:ASN152 2.5 34.6 1.0
O B:ASP148 2.6 51.4 1.0
O B:ALA221 2.6 40.2 1.0
OG B:SER151 3.1 41.1 1.0
OD2 B:ASP105 3.6 54.7 1.0
C B:ALA221 3.6 40.7 1.0
C B:ASP148 3.7 44.8 1.0
OD1 B:ASP148 3.7 71.7 1.0
CB B:ALA221 3.7 40.6 1.0
CG B:ASN152 3.7 36.3 1.0
CA B:ALA221 3.8 40.4 1.0
CE1 B:HIS226 4.0 49.8 1.0
CG B:ASP148 4.1 59.8 1.0
N B:ASN152 4.1 37.6 1.0
CB B:SER151 4.3 41.1 1.0
OD2 B:ASP148 4.4 72.5 1.0
C B:SER151 4.4 38.6 1.0
CA B:ASP148 4.4 49.3 1.0
OG B:SER208 4.5 46.6 1.0
ND2 B:ASN152 4.5 37.2 1.0
CA B:ASN152 4.6 36.5 1.0
N B:ILE149 4.6 41.1 1.0
CG B:ASP105 4.7 45.8 1.0
O B:ILE149 4.7 37.8 1.0
ZN B:ZN402 4.7 58.4 0.5
NE2 B:HIS226 4.7 52.5 1.0
CB B:ASN152 4.7 36.2 1.0
CA B:ILE149 4.7 37.4 1.0
CA B:SER151 4.8 38.0 1.0
N B:SER222 4.8 40.2 1.0
CB B:ASP148 4.8 53.1 1.0
O B:SER151 4.9 38.2 1.0
C B:ILE149 5.0 39.5 1.0
N B:SER151 5.0 36.8 1.0
ND1 B:HIS226 5.0 46.8 1.0

Reference:

V.Carbone, L.R.Schofield, Y.Zhang, C.Sang, D.Dey, I.M.Hannus, W.F.Martin, A.J.Sutherland-Smith, R.S.Ronimus. Structure and Evolution of the Archaeal Lipid Synthesis Enzyme Sn-Glycerol-1-Phosphate Dehydrogenase. J.Biol.Chem. V. 290 21690 2015.
ISSN: ISSN 0021-9258
PubMed: 26175150
DOI: 10.1074/JBC.M115.647461
Page generated: Mon Dec 14 19:30:43 2020

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