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Calcium in PDB 3owm: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine

Protein crystallography data

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine, PDB code: 3owm was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, V.S.Lamzin, G.P.Bourenkov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 1.65
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 192.529, 192.529, 192.529, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 15.4

Other elements in 3owm:

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine also contains other interesting chemical elements:

Iron (Fe) 16 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine (pdb code 3owm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine, PDB code: 3owm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3owm

Go back to Calcium Binding Sites List in 3owm
Calcium binding site 1 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:14.6
occ:1.00
OE1 A:GLN360 2.3 16.8 1.0
O A:TYR303 2.3 14.0 1.0
O A:LYS358 2.3 14.5 1.0
O A:HOH882 2.3 14.7 1.0
OE2 A:GLU302 2.4 15.1 1.0
OE1 A:GLU302 2.5 14.7 1.0
O A:HOH881 2.5 16.3 1.0
CD A:GLU302 2.8 15.4 1.0
CD A:GLN360 3.4 18.1 1.0
C A:TYR303 3.5 14.8 1.0
C A:LYS358 3.5 14.3 1.0
N A:TYR303 3.9 15.0 1.0
NE2 A:GLN360 3.9 20.0 1.0
CA A:LEU359 4.1 13.3 1.0
N A:LEU359 4.3 13.6 1.0
N A:GLN360 4.3 13.2 1.0
OH A:TYR335 4.3 16.6 1.0
OD1 A:ASN304 4.3 19.1 1.0
CG A:GLU302 4.3 14.1 1.0
CA A:TYR303 4.4 14.8 1.0
OD1 A:ASP346 4.4 14.7 1.0
C A:LEU359 4.4 13.2 1.0
N A:ASN304 4.4 15.3 1.0
OD2 A:ASP346 4.5 18.1 1.0
CA A:LYS358 4.6 13.9 1.0
CE1 A:PHE328 4.6 15.7 1.0
CB A:LYS358 4.6 14.3 1.0
CG A:GLN360 4.6 16.9 1.0
CA A:ASN304 4.7 15.8 1.0
CB A:GLN360 4.8 15.3 1.0
CG A:ASP346 4.8 15.8 1.0
N A:LYS358 4.8 14.9 1.0
C A:GLU302 4.9 14.6 1.0
CG A:LYS358 4.9 14.5 1.0

Calcium binding site 2 out of 6 in 3owm

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Calcium binding site 2 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:25.4
occ:0.50
O A:HOH1077 2.2 19.0 1.0
O A:PRO116 2.4 14.4 1.0
O A:HOH652 2.5 28.4 1.0
O2A A:HEC1006 2.7 14.3 1.0
O A:HOH645 2.7 24.9 1.0
C A:PRO116 3.5 13.0 1.0
O1A A:HEC1007 3.5 13.2 0.5
CGA A:HEC1006 3.8 13.2 1.0
OG A:SER84 4.0 13.4 1.0
CG A:PRO116 4.0 14.4 1.0
CB A:SER84 4.0 13.2 1.0
CGA A:HEC1007 4.1 15.3 0.5
CD A:PRO116 4.1 13.1 1.0
O A:HOH668 4.1 31.3 1.0
O A:HOH779 4.2 20.6 1.0
N A:PRO116 4.3 12.6 1.0
CA A:PRO116 4.3 12.7 1.0
O2A A:HEC1007 4.3 12.0 0.5
N A:ARG117 4.4 12.4 1.0
O A:HOH771 4.4 30.1 1.0
CB A:PRO116 4.4 13.1 1.0
CA A:ARG117 4.4 11.6 1.0
O1A A:HEC1006 4.5 14.4 1.0
CAA A:HEC1006 4.5 11.7 1.0
CA A:SER84 4.6 12.6 1.0
OE1 A:GLU115 4.7 22.5 1.0
CB A:GLU115 4.7 13.1 1.0
CBA A:HEC1006 4.8 12.0 1.0
C A:GLU115 4.9 12.8 1.0

Calcium binding site 3 out of 6 in 3owm

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Calcium binding site 3 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca525

b:25.8
occ:0.20
O A:HOH1082 2.4 27.0 1.0
O A:HOH1068 2.4 30.1 1.0
O A:HOH1056 3.8 28.6 1.0
OD2 A:ASP450 4.1 22.5 1.0
O A:HOH1120 4.3 38.8 1.0
O3 A:TRS524 4.3 39.0 0.1
O2 A:TRS524 4.4 39.0 0.1
O1 A:TRS524 4.4 39.0 0.1
O A:HOH943 4.6 31.7 1.0
O A:HOH976 4.7 17.3 0.6
O A:HOH1125 4.7 21.8 0.5
NZ A:LYS102 4.8 18.3 0.3
CG A:ASP450 5.0 20.1 1.0

Calcium binding site 4 out of 6 in 3owm

Go back to Calcium Binding Sites List in 3owm
Calcium binding site 4 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:12.6
occ:1.00
OE1 B:GLN360 2.3 14.4 1.0
O B:LYS358 2.3 13.1 1.0
O B:TYR303 2.3 12.1 1.0
OE2 B:GLU302 2.4 14.0 1.0
O B:HOH919 2.4 12.5 1.0
OE1 B:GLU302 2.5 12.1 1.0
O B:HOH918 2.5 13.7 1.0
CD B:GLU302 2.8 14.5 1.0
CD B:GLN360 3.4 16.2 1.0
C B:LYS358 3.5 12.5 1.0
C B:TYR303 3.5 12.7 1.0
N B:TYR303 3.9 12.6 1.0
NE2 B:GLN360 4.0 18.6 1.0
CA B:LEU359 4.1 11.4 1.0
N B:LEU359 4.2 11.7 1.0
OH B:TYR335 4.3 13.2 1.0
N B:GLN360 4.3 11.8 1.0
CG B:GLU302 4.3 12.4 1.0
OD1 B:ASN304 4.3 19.3 1.0
CA B:TYR303 4.4 12.9 1.0
C B:LEU359 4.4 11.9 1.0
OD1 B:ASP346 4.4 13.8 1.0
N B:ASN304 4.4 12.9 1.0
OD2 B:ASP346 4.5 14.5 1.0
CE1 B:PHE328 4.6 13.2 1.0
CA B:LYS358 4.6 12.1 1.0
CG B:GLN360 4.6 15.3 1.0
CB B:LYS358 4.6 12.0 1.0
CA B:ASN304 4.7 13.9 1.0
CB B:GLN360 4.8 14.3 1.0
CG B:ASP346 4.8 12.5 1.0
N B:LYS358 4.9 12.5 1.0
C B:GLU302 4.9 12.4 1.0
CG B:LYS358 5.0 12.2 1.0

Calcium binding site 5 out of 6 in 3owm

Go back to Calcium Binding Sites List in 3owm
Calcium binding site 5 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:25.5
occ:0.50
O B:HOH1116 2.2 19.1 1.0
O B:PRO116 2.4 13.8 1.0
O B:HOH605 2.5 29.2 1.0
O1A B:HEC1006 2.6 13.0 1.0
O B:HOH598 2.8 26.3 1.0
O1A B:HEC1007 3.4 12.2 0.5
C B:PRO116 3.4 11.9 1.0
CGA B:HEC1006 3.7 12.6 1.0
CG B:PRO116 4.0 12.6 1.0
OG B:SER84 4.0 12.8 1.0
CB B:SER84 4.0 12.3 1.0
CGA B:HEC1007 4.1 14.7 0.5
O B:HOH705 4.1 31.5 1.0
O B:HOH816 4.1 18.3 1.0
CD B:PRO116 4.2 11.6 1.0
CA B:PRO116 4.3 10.8 1.0
N B:PRO116 4.3 10.2 1.0
O2A B:HEC1007 4.3 12.0 0.5
N B:ARG117 4.3 11.1 1.0
CB B:PRO116 4.4 11.5 1.0
O B:HOH808 4.4 30.2 1.0
CA B:ARG117 4.4 10.3 1.0
CAA B:HEC1006 4.4 10.9 1.0
O2A B:HEC1006 4.5 13.1 1.0
CA B:SER84 4.6 11.5 1.0
CBA B:HEC1006 4.7 10.5 1.0
CB B:GLU115 4.7 11.5 1.0
OE1 B:GLU115 4.8 22.6 1.0
C B:GLU115 4.9 10.4 1.0
O B:HOH806 5.0 12.2 1.0

Calcium binding site 6 out of 6 in 3owm

Go back to Calcium Binding Sites List in 3owm
Calcium binding site 6 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca525

b:24.2
occ:0.20
O B:HOH1121 2.4 24.5 1.0
O B:HOH1107 2.5 28.4 1.0
O B:HOH1095 3.9 23.7 1.0
OD2 B:ASP450 4.0 19.5 1.0
O B:HOH1159 4.4 24.5 0.5
O3 B:TRS524 4.5 31.9 0.1
O2 B:TRS524 4.5 31.9 0.1
O1 B:TRS524 4.5 31.9 0.1
O B:HOH1164 4.5 19.0 0.5
O B:HOH980 4.7 29.9 1.0
NZ B:LYS102 4.7 18.4 0.5
O B:HOH1021 4.7 13.7 0.6
CG B:ASP450 5.0 16.5 1.0

Reference:

A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, V.O.Popov. Binding of Sulfite By the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase To Be Published.
Page generated: Tue Jul 8 15:11:31 2025

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