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Calcium in PDB 1vzi: Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction

Enzymatic activity of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction

All present enzymatic activity of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction:
1.15.1.2;

Protein crystallography data

The structure of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction, PDB code: 1vzi was solved by V.Adam, A.Royant, V.Niviere, F.P.Molina-Heredia, D.Bourgeois, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 1.15
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 123.608, 123.608, 73.016, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1vzi:

The structure of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction (pdb code 1vzi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction, PDB code: 1vzi:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1vzi

Go back to Calcium Binding Sites List in 1vzi
Calcium binding site 1 out of 2 in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1126

b:20.6
occ:0.50
 O A:HOH2109 2.3 36.6 0.5
OD2 A:ASP32 2.4 21.6 1.0
OD1 A:ASP32 2.5 20.1 1.0
OE1 A:GLU25 2.8 28.6 1.0
CG A:ASP32 2.9 17.8 1.0
O A:HOH2107 3.5 46.6 1.0
O A:HOH2103 3.7 20.7 1.0
CD A:GLU25 3.8 27.2 1.0
O A:HOH2106 4.2 30.4 1.0
OE2 A:GLU25 4.2 43.0 1.0
CB A:ASP32 4.4 15.7 1.0
CG A:GLU25 4.7 24.3 1.0
N A:ASP32 5.0 14.1 1.0

Calcium binding site 2 out of 2 in 1vzi

Go back to Calcium Binding Sites List in 1vzi
Calcium binding site 2 out of 2 in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1127

b:18.9
occ:0.75
 O B:HOH2060 2.6 38.9 1.0
OG1 A:THR89 2.8 11.8 1.0
OG1 B:THR89 2.8 12.9 1.0
O A:CYS87 2.8 10.6 1.0
O A:HOH2061 2.8 41.7 1.0
O B:CYS87 2.9 11.6 1.0
CB B:THR89 3.7 12.3 1.0
CB A:THR89 3.7 10.7 1.0
C A:CYS87 3.7 10.2 1.0
C B:CYS87 3.8 10.5 1.0
N B:THR89 3.9 11.2 1.0
N A:THR89 3.9 9.8 1.0
SG A:CYS87 3.9 15.7 1.0
OE2 A:GLU17 4.1 19.9 1.0
OE2 B:GLU17 4.1 19.9 1.0
SG B:CYS87 4.1 16.9 1.0
CB A:CYS87 4.3 11.7 1.0
CB B:CYS87 4.4 12.0 1.0
CA A:THR89 4.4 10.1 1.0
C A:TYR88 4.4 10.6 1.0
CA B:THR89 4.4 10.9 1.0
C B:TYR88 4.5 10.6 1.0
CA A:TYR88 4.5 10.0 1.0
N A:TYR88 4.5 10.1 1.0
CA B:TYR88 4.5 11.2 1.0
N B:TYR88 4.6 10.4 1.0
OE2 A:GLU80 4.6 13.7 1.0
OE2 B:GLU80 4.6 13.8 1.0
CA A:CYS87 4.6 10.8 1.0
CA B:CYS87 4.7 11.0 1.0
CG2 A:THR89 4.9 11.7 1.0
CG2 B:THR89 4.9 13.5 1.0

Reference:

V.Adam, A.Royant, V.Niviere, F.P.Molina-Heredia, D.Bourgeois. Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray-Induced Photo-Reduction. Structure V. 12 1729 2004.
ISSN: ISSN 0969-2126
PubMed: 15341736
DOI: 10.1016/J.STR.2004.07.013
Page generated: Tue Jul 8 03:02:08 2025

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