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Calcium in PDB 2ji1: X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii

Enzymatic activity of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii

All present enzymatic activity of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii:
1.15.1.2;

Protein crystallography data

The structure of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii, PDB code: 2ji1 was solved by G.Katona, P.Carpentier, V.Niviere, P.Amara, V.Adam, J.Ohana, N.Tsanov, D.Bourgeois, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.393, 82.985, 204.349, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.4

Other elements in 2ji1:

The structure of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii (pdb code 2ji1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii, PDB code: 2ji1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2ji1

Go back to Calcium Binding Sites List in 2ji1
Calcium binding site 1 out of 4 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1128

b:20.5
occ:1.00
 O B:HOH2193 2.2 20.3 1.0
OE2 A:GLU18 2.2 20.5 0.5
O A:HOH2043 2.3 27.6 1.0
O A:HOH2042 2.4 28.6 1.0
O B:HOH2196 2.4 40.0 1.0
CD A:GLU18 3.0 21.0 0.5
OE1 A:GLU18 3.0 22.4 0.5
SG A:CYS88 4.0 24.9 0.5
OG1 B:THR90 4.0 15.6 1.0
OG1 A:THR90 4.0 15.1 1.0
SG B:CYS88 4.2 26.4 0.5
O B:CYS88 4.4 16.0 0.5
O A:CYS88 4.5 13.9 0.5
CG A:GLU18 4.5 19.3 0.5
OE1 A:GLU18 4.5 11.0 0.5
O A:CYS88 4.5 15.3 0.5
O B:HOH2067 4.5 30.0 1.0
OE1 B:GLU18 4.6 24.3 0.5
OE1 B:GLU18 4.6 20.7 0.5
OE2 B:GLU18 4.6 21.1 0.5
O A:HOH2147 4.7 21.8 1.0
OE2 B:GLU18 4.7 15.0 0.5
O B:HOH2197 4.7 29.4 1.0
CD B:GLU18 4.7 20.8 0.5
CD B:GLU18 4.7 15.8 0.5
O B:CYS88 4.7 12.5 0.5
CB B:THR90 4.7 12.8 1.0
CB A:THR90 4.8 13.7 1.0
OE2 B:GLU81 4.8 18.7 1.0
OE2 A:GLU81 4.8 18.6 1.0
CD A:GLU18 4.8 11.3 0.5
OE2 A:GLU18 4.9 6.5 0.5
CB A:CYS88 4.9 18.8 0.5
CB A:CYS88 4.9 15.2 0.5
CB B:CYS88 4.9 19.9 0.5
CD2 B:LEU20 5.0 15.4 1.0

Calcium binding site 2 out of 4 in 2ji1

Go back to Calcium Binding Sites List in 2ji1
Calcium binding site 2 out of 4 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1129

b:14.6
occ:1.00
 O A:HOH2074 2.4 12.6 1.0
OD2 A:ASP33 2.4 14.6 1.0
OD1 A:ASP33 2.4 14.0 1.0
O A:HOH2076 2.5 23.8 1.0
CG A:ASP33 2.7 15.0 1.0
O A:HOH2075 4.0 16.4 1.0
O A:HOH2077 4.1 19.1 1.0
CB A:ASP33 4.2 14.1 1.0
O B:HOH2042 5.0 32.8 1.0

Calcium binding site 3 out of 4 in 2ji1

Go back to Calcium Binding Sites List in 2ji1
Calcium binding site 3 out of 4 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1128

b:14.2
occ:1.00
 O C:HOH2069 2.3 12.3 1.0
OE2 C:GLU26 2.5 13.8 1.0
O C:HOH2068 2.5 15.8 1.0
OD2 C:ASP33 2.5 14.9 1.0
OE1 C:GLU26 2.6 14.1 1.0
OD1 C:ASP33 2.6 15.2 1.0
CG C:ASP33 2.8 16.1 1.0
CD C:GLU26 2.9 13.1 1.0
O C:HOH2067 4.1 21.3 1.0
O C:HOH2064 4.1 15.2 1.0
CB C:ASP33 4.3 15.0 1.0
O C:HOH2065 4.4 23.7 1.0
CG C:GLU26 4.4 14.5 1.0
O C:HOH2052 4.4 22.3 1.0
O C:HOH2070 4.9 27.6 1.0

Calcium binding site 4 out of 4 in 2ji1

Go back to Calcium Binding Sites List in 2ji1
Calcium binding site 4 out of 4 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1129

b:24.2
occ:1.00
 O C:HOH2136 2.3 26.1 1.0
OE1 C:GLU18 2.3 16.2 0.5
O D:HOH2142 2.4 26.4 1.0
O C:HOH2039 2.4 30.2 1.0
OE2 C:GLU18 2.8 20.2 0.5
CD C:GLU18 2.9 17.2 0.5
OG1 D:THR90 3.9 21.8 1.0
SG C:CYS88 3.9 31.7 0.5
OG1 C:THR90 4.0 19.4 1.0
SG D:CYS88 4.2 28.3 0.5
OE2 D:GLU18 4.3 26.8 1.0
OE1 C:GLU18 4.3 20.0 0.5
CG C:GLU18 4.4 16.0 0.5
O C:HOH2139 4.5 37.0 1.0
OE2 C:GLU18 4.5 14.6 0.5
O C:CYS88 4.5 21.1 0.5
O D:HOH2056 4.5 36.4 1.0
CD C:GLU18 4.5 17.9 0.5
O D:CYS88 4.6 21.4 0.5
O C:CYS88 4.6 21.1 0.5
O D:CYS88 4.6 21.7 0.5
O D:HOH2141 4.6 26.0 1.0
CB D:THR90 4.8 20.7 1.0
CB C:THR90 4.8 17.8 1.0
OE1 C:GLU81 4.8 23.7 1.0
CD D:GLU18 4.8 21.7 1.0
OE2 D:GLU81 4.9 22.2 1.0
CD2 D:LEU20 5.0 17.4 1.0
CB C:CYS88 5.0 23.9 0.5

Reference:

G.Katona, P.Carpentier, V.Niviere, P.Amara, V.Adam, J.Ohana, N.Tsanov, D.Bourgeois. Raman-Assisted Crystallography Reveals End-on Peroxide Intermediates in A Nonheme Iron Enzyme. Science V. 316 449 2007.
ISSN: ESSN 1095-9203
PubMed: 17446401
DOI: 10.1126/SCIENCE.1138885
Page generated: Tue Jul 8 06:43:00 2025

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