Atomistry » Calcium » PDB 3ojn-3p0v » 3owm
Atomistry »
  Calcium »
    PDB 3ojn-3p0v »
      3owm »

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

Go back to Calcium Binding Sites List in 3owm
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

Go back to Calcium Binding Sites List in 3owm
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: Sat Dec 12 04:23:51 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy