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Calcium in PDB 3sce: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)

Protein crystallography data

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb), PDB code: 3sce was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 1.45
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 193.000, 193.000, 193.000, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 14

Other elements in 3sce:

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) 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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) (pdb code 3sce). 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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb), PDB code: 3sce:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3sce

Go back to Calcium Binding Sites List in 3sce
Calcium binding site 1 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)


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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:14.1
occ:1.00
O A:LYS358 2.3 13.5 1.0
OE1 A:GLN360 2.3 16.4 1.0
O A:TYR303 2.3 12.4 1.0
OE2 A:GLU302 2.4 13.6 1.0
O A:HOH808 2.4 15.0 1.0
O A:HOH807 2.5 15.3 1.0
OE1 A:GLU302 2.5 13.2 1.0
CD A:GLU302 2.8 12.0 1.0
C A:LYS358 3.5 11.4 1.0
CD A:GLN360 3.5 17.0 1.0
C A:TYR303 3.5 12.8 1.0
N A:TYR303 4.0 12.3 1.0
CA A:LEU359 4.2 12.8 1.0
N A:GLN360 4.2 13.3 1.0
OH A:TYR335 4.3 14.7 1.0
N A:LEU359 4.3 12.1 1.0
CG A:GLU302 4.3 12.2 1.0
CG A:GLN360 4.3 18.5 1.0
OD1 A:ASN304 4.3 19.0 1.0
OD2 A:ASP346 4.4 14.4 1.0
CA A:TYR303 4.4 12.9 1.0
C A:LEU359 4.4 12.9 1.0
NE2 A:GLN360 4.5 20.3 1.0
N A:ASN304 4.5 12.8 1.0
CB A:GLN360 4.5 17.0 1.0
CA A:LYS358 4.5 12.5 1.0
OD1 A:ASP346 4.6 16.8 1.0
CE1 A:PHE328 4.6 14.6 1.0
CD1 A:TYR303 4.6 16.1 1.0
CB A:LYS358 4.6 13.8 1.0
CE1 A:TYR303 4.6 17.6 1.0
CA A:ASN304 4.8 13.4 1.0
N A:LYS358 4.8 11.9 1.0
CG A:ASP346 4.8 15.2 1.0
O A:HOH910 4.9 22.2 1.0
CG A:LYS358 4.9 13.6 1.0
CG A:TYR303 5.0 12.0 1.0

Calcium binding site 2 out of 4 in 3sce

Go back to Calcium Binding Sites List in 3sce
Calcium binding site 2 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)


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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:14.5
occ:0.50
O A:HOH888 2.3 17.3 1.0
O2A A:HEC1006 2.4 11.9 1.0
O A:PRO116 2.5 11.5 1.0
O A:HOH582 2.5 19.2 1.0
O A:HOH571 2.8 17.1 0.7
O2A A:HEC1007 2.8 12.3 0.5
O1A A:HEC1007 3.3 13.7 0.5
C A:PRO116 3.5 10.1 1.0
CGA A:HEC1006 3.6 10.9 1.0
O A:HOH1033 3.7 13.1 0.3
CGA A:HEC1007 3.7 13.4 0.5
O1A A:HEC1007 3.8 11.6 0.5
OG A:SER84 3.9 11.5 1.0
O A:HOH1014 3.9 29.4 1.0
CB A:SER84 3.9 10.7 1.0
CG A:PRO116 4.0 12.0 1.0
CGA A:HEC1007 4.0 15.4 0.5
O A:HOH731 4.2 17.4 1.0
O2A A:HEC1007 4.3 13.6 0.5
O A:HOH723 4.3 17.8 0.5
O1A A:HEC1006 4.3 12.0 1.0
CD A:PRO116 4.4 11.0 1.0
CAA A:HEC1006 4.4 11.8 1.0
N A:ARG117 4.4 10.3 1.0
CA A:ARG117 4.4 9.5 1.0
CA A:PRO116 4.4 10.2 1.0
N A:PRO116 4.5 10.6 1.0
CB A:PRO116 4.6 11.0 1.0
CA A:SER84 4.6 10.8 1.0
CBA A:HEC1006 4.6 10.8 1.0
OE1 A:GLU115 4.8 19.6 1.0
O A:HOH722 4.9 13.2 1.0
CB A:GLU115 4.9 11.8 1.0

Calcium binding site 3 out of 4 in 3sce

Go back to Calcium Binding Sites List in 3sce
Calcium binding site 3 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)


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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:13.7
occ:1.00
OE1 B:GLN360 2.3 16.0 1.0
O B:LYS358 2.3 12.9 1.0
O B:TYR303 2.4 11.8 1.0
OE2 B:GLU302 2.4 13.3 1.0
O B:HOH869 2.4 15.2 1.0
O B:HOH868 2.5 15.6 1.0
OE1 B:GLU302 2.5 12.3 1.0
CD B:GLU302 2.8 12.8 1.0
C B:LYS358 3.5 11.4 1.0
CD B:GLN360 3.5 16.7 1.0
C B:TYR303 3.6 11.5 1.0
N B:TYR303 4.0 12.2 1.0
CA B:LEU359 4.2 11.6 1.0
N B:GLN360 4.3 12.1 1.0
OD1 B:ASN304 4.3 15.0 0.7
N B:LEU359 4.3 11.3 1.0
OH B:TYR335 4.3 14.3 1.0
CG B:GLU302 4.3 11.4 1.0
CG B:GLN360 4.3 17.4 1.0
OD1 B:ASP346 4.4 13.3 1.0
C B:LEU359 4.5 12.5 1.0
CA B:TYR303 4.5 12.2 1.0
NE2 B:GLN360 4.5 21.6 1.0
CB B:GLN360 4.5 16.7 1.0
N B:ASN304 4.5 12.9 1.0
OD2 B:ASP346 4.5 15.9 1.0
CA B:LYS358 4.5 11.7 1.0
CE2 B:PHE328 4.5 13.0 1.0
CD1 B:TYR303 4.6 15.2 1.0
CE1 B:TYR303 4.6 18.9 1.0
CB B:LYS358 4.6 13.2 1.0
CA B:ASN304 4.7 12.3 1.0
OD1 B:ASN304 4.8 13.6 0.3
CG B:ASP346 4.8 13.4 1.0
N B:LYS358 4.8 12.0 1.0
O B:HOH966 4.9 22.7 1.0
CG B:LYS358 5.0 12.5 1.0
CG B:TYR303 5.0 11.4 1.0

Calcium binding site 4 out of 4 in 3sce

Go back to Calcium Binding Sites List in 3sce
Calcium binding site 4 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)


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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:14.8
occ:0.50
O B:HOH944 2.3 17.9 1.0
O1A B:HEC1006 2.4 13.2 1.0
O B:PRO116 2.4 12.5 1.0
O B:HOH698 2.5 19.3 1.0
O B:HOH688 2.8 12.6 0.5
O2A B:HEC1007 2.8 14.6 0.5
O1A B:HEC1007 3.5 17.6 0.5
C B:PRO116 3.5 10.6 1.0
CGA B:HEC1006 3.6 11.7 1.0
CGA B:HEC1007 3.7 12.7 0.5
O B:HOH1090 3.7 19.2 0.5
O1A B:HEC1007 3.8 11.2 0.5
OG B:SER84 3.9 11.9 1.0
CB B:SER84 4.0 11.4 1.0
CG B:PRO116 4.0 12.1 1.0
O B:HOH1071 4.0 20.6 0.5
CGA B:HEC1007 4.1 14.0 0.5
O B:HOH792 4.2 18.8 1.0
O2A B:HEC1006 4.3 12.3 1.0
CD B:PRO116 4.3 11.8 1.0
O2A B:HEC1007 4.3 15.9 0.5
CAA B:HEC1006 4.4 10.3 1.0
O B:HOH784 4.4 17.9 0.5
N B:ARG117 4.4 10.0 1.0
CA B:ARG117 4.4 10.0 1.0
CA B:PRO116 4.4 10.2 1.0
N B:PRO116 4.4 10.4 1.0
CB B:PRO116 4.5 11.7 1.0
CBA B:HEC1006 4.6 11.2 1.0
CA B:SER84 4.6 10.7 1.0
OE1 B:GLU115 4.8 21.4 1.0
CB B:GLU115 4.9 12.2 1.0
O B:HOH783 4.9 12.7 1.0

Reference:

A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, A.V.Tikhonov, T.N.Safonova, K.M.Boyko, P.V.Dorovatovskii, V.O.Popov. Covalent Modifications of the Catalytic Tyrosine in Octahaem Cytochrome C Nitrite Reductase and Their Effect on the Enzyme Activity. Acta Crystallogr.,Sect.D V. 68 144 2012.
ISSN: ISSN 0907-4449
PubMed: 22281743
DOI: 10.1107/S0907444911052632
Page generated: Sat Dec 12 04:29:49 2020

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