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Calcium in PDB 2ji3: X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii

Enzymatic activity of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii

All present enzymatic activity of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii:
1.15.1.2;

Protein crystallography data

The structure of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii, PDB code: 2ji3 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) 47.13 / 1.95
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.450, 82.900, 202.660, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.9

Other elements in 2ji3:

The structure of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii (pdb code 2ji3). 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii, PDB code: 2ji3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2ji3

Go back to Calcium Binding Sites List in 2ji3
Calcium binding site 1 out of 4 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1129

b:31.9
occ:1.00
 O A:HOH2035 2.3 28.1 1.0
OD2 A:ASP33 2.5 36.6 1.0
O A:HOH2036 2.5 35.6 1.0
OD1 A:ASP33 2.5 30.3 1.0
CG A:ASP33 2.8 34.7 1.0
CA A:CA1130 3.9 26.5 1.0
CB A:ASP33 4.2 29.0 1.0
O A:HOH2038 4.4 31.9 1.0
O A:HOH2015 4.6 40.5 1.0

Calcium binding site 2 out of 4 in 2ji3

Go back to Calcium Binding Sites List in 2ji3
Calcium binding site 2 out of 4 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1130

b:26.5
occ:1.00
 O A:HOH2026 2.5 23.4 1.0
OD2 A:ASP33 2.8 36.6 1.0
CA A:CA1129 3.9 31.9 1.0
CG A:ASP33 4.0 34.7 1.0
OE1 A:GLU26 4.1 43.7 1.0
CG A:GLU26 4.2 38.5 1.0
O A:HOH2036 4.3 35.6 1.0
CD A:GLU26 4.4 43.0 1.0
CB A:ASP33 4.6 29.0 1.0
O A:HOH2039 4.8 18.4 1.0
OD1 A:ASP33 4.9 30.3 1.0
CB A:GLU26 4.9 31.6 1.0

Calcium binding site 3 out of 4 in 2ji3

Go back to Calcium Binding Sites List in 2ji3
Calcium binding site 3 out of 4 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1129

b:37.5
occ:1.00
 O B:HOH2024 2.2 48.8 1.0
O A:HOH2072 2.3 27.9 1.0
O B:HOH2075 2.3 31.3 1.0
O B:HOH2023 2.5 36.5 1.0
OE1 B:GLU18 2.9 40.5 1.0
OG1 B:THR90 3.6 22.7 1.0
OG1 A:THR90 3.9 23.5 1.0
SG B:CYS88 3.9 29.9 0.5
SG A:CYS88 4.0 31.5 0.5
CD B:GLU18 4.1 38.2 1.0
O B:HOH2025 4.4 40.0 1.0
O A:CYS88 4.4 24.9 0.5
O A:CYS88 4.4 24.3 0.5
CB B:THR90 4.6 21.8 1.0
OE2 B:GLU18 4.6 38.8 1.0
O B:CYS88 4.6 27.4 0.5
O B:CYS88 4.6 26.4 0.5
CB A:THR90 4.7 24.8 1.0
OE2 A:GLU81 4.7 33.2 1.0
OE2 A:GLU18 4.8 33.6 1.0
CB B:CYS88 4.9 31.8 0.5
OE1 A:GLU18 4.9 36.4 1.0
CB B:CYS88 4.9 28.0 0.5
CD A:GLU18 4.9 33.4 1.0
CB A:CYS88 5.0 27.6 0.5
OE2 B:GLU81 5.0 34.5 1.0
CB A:CYS88 5.0 29.0 0.5

Calcium binding site 4 out of 4 in 2ji3

Go back to Calcium Binding Sites List in 2ji3
Calcium binding site 4 out of 4 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1129

b:50.4
occ:1.00
 OE1 C:GLU18 2.6 37.8 1.0
OG1 D:THR90 3.7 34.7 1.0
CD C:GLU18 3.8 37.7 1.0
OG1 C:THR90 3.9 33.2 1.0
SG D:CYS88 4.1 51.6 1.0
OE2 D:GLU18 4.2 43.1 1.0
SG C:CYS88 4.3 42.0 0.5
OE2 C:GLU18 4.4 36.1 1.0
O C:CYS88 4.5 39.9 0.5
OE1 C:GLU81 4.5 42.8 1.0
OE2 D:GLU81 4.5 49.1 1.0
O C:CYS88 4.5 40.0 0.5
CD D:GLU18 4.7 38.3 1.0
CB D:THR90 4.7 35.4 1.0
CB C:THR90 4.7 33.3 1.0
O D:CYS88 4.7 35.6 1.0
OE1 D:GLU18 4.8 39.8 1.0
CG C:GLU18 5.0 31.8 1.0

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 06:43:09 2025

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