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Calcium in PDB 3d1i: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite

Protein crystallography data

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite, PDB code: 3d1i was solved by K.M.Polyakov, K.M.Boyko, A.Slutsky, T.V.Tikhonova, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, 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) 11.99 / 1.80
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 193.412, 193.412, 193.412, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 16.5

Other elements in 3d1i:

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

Iron (Fe) 16 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (pdb code 3d1i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite, PDB code: 3d1i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3d1i

Go back to Calcium Binding Sites List in 3d1i
Calcium binding site 1 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite


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 Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca526

b:15.8
occ:1.00
OE1 A:GLN360 2.3 18.1 1.0
O A:LYS358 2.3 16.2 1.0
O A:TYR303 2.3 16.2 1.0
OE2 A:GLU302 2.4 17.8 1.0
O A:HOH1233 2.4 15.2 1.0
OE1 A:GLU302 2.4 16.0 1.0
O A:HOH1232 2.6 16.2 1.0
CD A:GLU302 2.8 19.4 1.0
H A:TYR303 3.3 17.4 1.0
HA A:LEU359 3.4 15.3 1.0
CD A:GLN360 3.4 16.5 1.0
HH A:TYR335 3.4 16.1 0.0
C A:LYS358 3.5 15.7 1.0
C A:TYR303 3.5 17.8 1.0
HE22 A:GLN360 3.7 17.3 0.0
HE1 A:PHE328 3.8 17.8 1.0
N A:TYR303 4.0 17.8 1.0
NE2 A:GLN360 4.0 17.5 1.0
H A:GLN360 4.0 15.2 1.0
HB3 A:LYS358 4.0 15.6 1.0
HA A:ASN304 4.1 17.7 1.0
CA A:LEU359 4.1 15.2 1.0
HD12 A:LEU359 4.1 15.6 0.0
HB2 A:GLN360 4.2 15.3 1.0
N A:LEU359 4.2 15.0 1.0
OH A:TYR335 4.3 16.0 1.0
N A:GLN360 4.3 15.2 1.0
CG A:GLU302 4.3 15.8 1.0
OD1 A:ASN304 4.4 22.9 1.0
CA A:TYR303 4.4 17.4 1.0
H A:LYS358 4.4 16.5 1.0
C A:LEU359 4.4 15.4 1.0
HG3 A:LYS358 4.4 15.2 1.0
OD1 A:ASP346 4.4 16.3 1.0
N A:ASN304 4.5 17.7 1.0
OD2 A:ASP346 4.5 18.1 1.0
CE1 A:PHE328 4.6 17.5 1.0
CA A:LYS358 4.6 15.4 1.0
HG3 A:GLU302 4.6 16.6 1.0
CB A:LYS358 4.7 16.1 1.0
CG A:GLN360 4.7 16.5 1.0
HA A:GLU302 4.7 15.6 1.0
HG2 A:GLU302 4.7 16.6 1.0
CA A:ASN304 4.8 17.5 1.0
CB A:GLN360 4.8 15.3 1.0
CG A:ASP346 4.8 14.8 1.0
N A:LYS358 4.8 16.8 1.0
HE21 A:GLN360 4.9 17.3 0.0
C A:GLU302 4.9 16.7 1.0
CG A:LYS358 5.0 15.4 1.0
HE1 A:TYR335 5.0 16.5 1.0
HD1 A:PHE328 5.0 17.6 1.0
HA A:TYR303 5.0 17.5 1.0

Calcium binding site 2 out of 4 in 3d1i

Go back to Calcium Binding Sites List in 3d1i
Calcium binding site 2 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite


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 Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca527

b:20.9
occ:0.50
O A:PRO116 2.3 15.2 1.0
O A:HOH1327 2.3 15.4 1.0
O A:HOH1048 2.5 21.2 1.0
O2A A:HEC1006 2.5 16.6 1.0
O A:HOH1386 2.6 25.9 1.0
O2A A:HEC1007 3.0 23.4 0.5
HB3 A:SER84 3.1 14.6 1.0
HG2 A:PRO116 3.3 15.8 1.0
C A:PRO116 3.4 14.9 1.0
HA A:ARG117 3.5 14.2 1.0
CGA A:HEC1006 3.7 14.9 1.0
HD2 A:PRO116 3.7 14.8 1.0
HB3 A:GLU115 3.8 14.7 1.0
CGA A:HEC1007 3.8 17.1 0.5
O1A A:HEC1007 3.8 13.8 0.5
O1A A:HEC1007 3.9 17.6 0.5
CB A:SER84 3.9 15.0 1.0
OG A:SER84 3.9 14.8 1.0
HG A:SER84 3.9 14.7 0.0
CG A:PRO116 4.0 16.3 1.0
HAA1 A:HEC1006 4.1 12.7 1.0
HAA2 A:HEC1006 4.1 12.7 1.0
O A:HOH1390 4.1 39.5 1.0
O A:HOH1149 4.2 18.4 1.0
HA A:SER84 4.2 14.8 1.0
CD A:PRO116 4.2 15.6 1.0
N A:PRO116 4.2 14.2 1.0
CA A:PRO116 4.3 14.3 1.0
N A:ARG117 4.3 13.9 1.0
HB2 A:PRO116 4.3 14.7 1.0
O A:HOH1141 4.3 36.3 1.0
CA A:ARG117 4.3 14.1 1.0
O1A A:HEC1006 4.4 15.0 1.0
CGA A:HEC1007 4.4 14.4 0.5
CB A:PRO116 4.5 14.7 1.0
CAA A:HEC1006 4.5 12.7 1.0
CA A:SER84 4.5 14.4 1.0
O2A A:HEC1007 4.6 16.4 0.5
HB2 A:SER84 4.6 14.6 1.0
CB A:GLU115 4.6 14.7 1.0
OE1 A:GLU115 4.7 23.9 1.0
HB2 A:GLU115 4.7 14.7 1.0
CBA A:HEC1006 4.7 14.2 1.0
C A:GLU115 4.8 13.5 1.0
HG3 A:PRO116 4.8 15.8 1.0
HB3 A:ARG117 4.9 14.3 1.0
C A:SER84 4.9 15.5 1.0

Calcium binding site 3 out of 4 in 3d1i

Go back to Calcium Binding Sites List in 3d1i
Calcium binding site 3 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite


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 Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca526

b:14.2
occ:1.00
O B:LYS358 2.3 14.6 1.0
OE1 B:GLN360 2.3 14.3 1.0
O B:TYR303 2.3 13.4 1.0
OE2 B:GLU302 2.4 14.2 1.0
O B:HOH1697 2.4 13.7 1.0
O B:HOH1696 2.5 16.3 1.0
OE1 B:GLU302 2.5 13.4 1.0
CD B:GLU302 2.8 13.8 1.0
H B:TYR303 3.3 13.8 1.0
HA B:LEU359 3.4 13.4 1.0
CD B:GLN360 3.4 17.9 1.0
C B:LYS358 3.5 14.1 1.0
C B:TYR303 3.5 15.1 1.0
HH B:TYR335 3.5 13.2 0.0
HE22 B:GLN360 3.6 16.4 0.0
HE2 B:PHE328 3.8 14.3 1.0
H B:GLN360 4.0 13.2 1.0
N B:TYR303 4.0 13.7 1.0
HB3 B:LYS358 4.0 13.7 1.0
NE2 B:GLN360 4.0 16.5 1.0
HA B:ASN304 4.0 16.1 1.0
CA B:LEU359 4.1 13.2 1.0
HB2 B:GLN360 4.2 14.0 1.0
OH B:TYR335 4.2 13.3 1.0
N B:LEU359 4.2 13.1 1.0
N B:GLN360 4.3 12.8 1.0
CG B:GLU302 4.3 12.9 1.0
OD1 B:ASN304 4.4 24.1 1.0
HD12 B:LEU359 4.4 13.8 0.0
H B:LYS358 4.4 14.1 1.0
CA B:TYR303 4.4 14.2 1.0
C B:LEU359 4.4 13.8 1.0
OD1 B:ASP346 4.4 14.4 1.0
HG3 B:LYS358 4.4 13.6 1.0
OD2 B:ASP346 4.5 16.2 1.0
N B:ASN304 4.5 15.2 1.0
CE2 B:PHE328 4.5 13.6 1.0
CA B:LYS358 4.5 13.6 1.0
HG3 B:GLU302 4.6 13.4 1.0
CB B:LYS358 4.6 14.2 1.0
CG B:GLN360 4.7 15.5 1.0
CA B:ASN304 4.7 16.1 1.0
HE21 B:GLN360 4.8 16.4 0.0
HG2 B:GLU302 4.8 13.4 1.0
HA B:GLU302 4.8 13.4 1.0
CG B:ASP346 4.8 14.1 1.0
CB B:GLN360 4.8 14.6 1.0
N B:LYS358 4.8 14.2 1.0
C B:GLU302 5.0 13.7 1.0
HD2 B:PHE328 5.0 14.3 1.0
HE1 B:TYR335 5.0 13.8 1.0
CG B:LYS358 5.0 13.1 1.0

Calcium binding site 4 out of 4 in 3d1i

Go back to Calcium Binding Sites List in 3d1i
Calcium binding site 4 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite


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 Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca527

b:18.2
occ:0.50
O B:HOH2002 1.4 19.9 0.5
O B:PRO116 2.3 13.9 1.0
O B:HOH1789 2.3 15.2 1.0
O B:HOH1512 2.3 20.8 1.0
O1A B:HEC1006 2.5 14.0 1.0
O B:HOH1845 2.6 26.2 1.0
O2A B:HEC1007 3.1 21.3 0.5
HB3 B:SER84 3.2 13.4 1.0
HG2 B:PRO116 3.3 12.9 1.0
C B:PRO116 3.4 13.7 1.0
HA B:ARG117 3.5 12.4 1.0
CGA B:HEC1006 3.7 13.0 1.0
HB3 B:GLU115 3.8 12.9 1.0
O1A B:HEC1007 3.8 12.8 0.5
HD2 B:PRO116 3.8 12.8 1.0
HG B:SER84 3.9 13.9 0.0
CB B:SER84 3.9 13.5 1.0
OG B:SER84 3.9 14.1 1.0
CGA B:HEC1007 3.9 18.8 0.5
O1A B:HEC1007 4.0 17.7 0.5
CG B:PRO116 4.1 13.1 1.0
HAA2 B:HEC1006 4.1 12.2 1.0
HAA1 B:HEC1006 4.1 12.2 1.0
O B:HOH1849 4.2 35.2 1.0
HA B:SER84 4.2 13.2 1.0
N B:PRO116 4.2 12.7 1.0
CD B:PRO116 4.2 12.9 1.0
O B:HOH1613 4.2 17.8 1.0
N B:ARG117 4.3 12.7 1.0
CA B:PRO116 4.3 12.7 1.0
CA B:ARG117 4.3 12.5 1.0
HB2 B:PRO116 4.3 12.7 1.0
O2A B:HEC1006 4.4 14.1 1.0
CGA B:HEC1007 4.4 13.9 0.5
CAA B:HEC1006 4.5 12.4 1.0
CB B:PRO116 4.5 12.7 1.0
O B:HOH1605 4.5 34.4 1.0
CA B:SER84 4.6 13.3 1.0
O2A B:HEC1007 4.6 14.0 0.5
CB B:GLU115 4.6 13.0 1.0
OE1 B:GLU115 4.6 20.5 1.0
HB2 B:GLU115 4.6 12.9 1.0
HB2 B:SER84 4.7 13.4 1.0
CBA B:HEC1006 4.7 13.1 1.0
C B:GLU115 4.8 12.4 1.0
HB3 B:ARG117 4.9 12.1 1.0
HG3 B:PRO116 4.9 12.9 1.0
C B:SER84 4.9 13.5 1.0

Reference:

K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, A.Slutsky, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, G.P.Bourenkov, V.S.Lamzin, V.O.Popov. High-Resolution Structural Analysis of A Novel Octaheme Cytochrome C Nitrite Reductase From the Haloalkaliphilic Bacterium Thioalkalivibrio Nitratireducens J.Mol.Biol. V. 389 846 2009.
ISSN: ISSN 0022-2836
PubMed: 19393666
DOI: 10.1016/J.JMB.2009.04.037
Page generated: Sat Dec 12 04:08:15 2020

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