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Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 4rgv

Go back to Zinc Binding Sites List in 4rgv
Zinc 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 Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:59.7
occ:0.50
NE2 A:HIS226 2.0 51.1 1.0
OD1 A:ASP148 2.1 66.3 1.0
NE2 A:HIS247 2.6 59.9 1.0
CE1 A:HIS226 2.8 51.2 1.0
CD2 A:HIS226 3.1 51.2 1.0
CG A:ASP148 3.3 58.8 1.0
CD2 A:HIS247 3.5 60.7 1.0
CE1 A:HIS247 3.6 62.9 1.0
OD2 A:ASP148 3.8 64.5 1.0
ND1 A:HIS226 4.0 51.2 1.0
CG A:HIS226 4.2 51.3 1.0
MG A:MG401 4.3 25.5 1.0
SG A:CYS251 4.4 52.6 1.0
OD1 A:ASP105 4.4 61.3 1.0
CB A:ASP148 4.5 50.7 1.0
OD2 A:ASP105 4.6 53.8 1.0
CG A:HIS247 4.7 58.3 1.0
ND1 A:HIS247 4.7 63.4 1.0
CG A:ASP105 4.7 51.0 1.0
CA A:ASP148 5.0 47.6 1.0
O A:ALA221 5.0 43.6 1.0

Zinc binding site 2 out of 2 in 4rgv

Go back to Zinc Binding Sites List in 4rgv
Zinc 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 Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:58.4
occ:0.50
NE2 B:HIS226 2.1 52.5 1.0
OD1 B:ASP148 2.4 71.7 1.0
NE2 B:HIS247 2.4 66.4 1.0
CE1 B:HIS226 3.1 49.8 1.0
CD2 B:HIS226 3.2 48.0 1.0
CE1 B:HIS247 3.4 65.5 1.0
CD2 B:HIS247 3.4 62.5 1.0
CG B:ASP148 3.6 59.8 1.0
OD2 B:ASP148 4.2 72.5 1.0
ND1 B:HIS226 4.2 46.8 1.0
CG B:HIS226 4.3 48.1 1.0
SG B:CYS251 4.4 49.4 1.0
ND1 B:HIS247 4.5 66.1 1.0
OD2 B:ASP105 4.5 54.7 1.0
CG B:HIS247 4.6 60.9 1.0
OD1 B:ASP105 4.6 47.4 1.0
CB B:ASP148 4.7 53.1 1.0
MG B:MG401 4.7 24.4 1.0
CG B:ASP105 4.8 45.8 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: Wed Dec 16 05:45:47 2020

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