Calcium in PDB 3lg1: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite), PDB code: 3lg1 was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, A.A.Filimonenkov, P.V.Dorovatovsky, 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)	19.90 / 1.95
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	192.620, 192.620, 192.620, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.3

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite) also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Sodium	(Na)	8 atoms

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite) (pdb code 3lg1). 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 Reduced By Sodium Borohydride (in Complex with Sulfite), PDB code: 3lg1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Reduced By Sodium Borohydride (in Complex with Sulfite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:19.9 occ:1.00 O A:LYS358 2.3 18.3 1.0 OE1 A:GLN360 2.3 22.1 1.0 O A:TYR303 2.3 19.5 1.0 OE2 A:GLU302 2.4 20.2 1.0 O A:HOH778 2.4 19.8 1.0 O A:HOH779 2.4 17.3 1.0 OE1 A:GLU302 2.6 18.1 1.0 CD A:GLU302 2.8 19.4 1.0 C A:LYS358 3.5 18.0 1.0 CD A:GLN360 3.6 24.3 1.0 C A:TYR303 3.6 19.1 1.0 N A:TYR303 4.0 17.1 1.0 CA A:LEU359 4.2 17.1 1.0 N A:GLN360 4.3 17.8 1.0 OD2 A:ASP346 4.3 18.8 1.0 OH A:TYR335 4.3 17.9 1.0 N A:LEU359 4.3 16.0 1.0 CG A:GLU302 4.4 17.0 1.0 CG A:GLN360 4.4 21.3 1.0 OD1 A:ASN304 4.4 23.4 1.0 CA A:TYR303 4.5 18.6 1.0 C A:LEU359 4.5 17.1 1.0 N A:ASN304 4.5 19.9 1.0 CA A:LYS358 4.5 17.6 1.0 NE2 A:GLN360 4.6 24.9 1.0 OD1 A:ASP346 4.6 18.6 1.0 CD1 A:TYR303 4.6 18.3 1.0 CB A:GLN360 4.6 18.5 1.0 CE1 A:PHE328 4.6 18.9 1.0 CB A:LYS358 4.6 18.3 1.0 CE1 A:TYR303 4.7 19.9 1.0 CA A:ASN304 4.8 20.3 1.0 N A:LYS358 4.8 17.7 1.0 CG A:ASP346 4.8 17.0 1.0 CG A:TYR303 4.9 18.3 1.0 O A:HOH916 4.9 35.9 1.0 CG A:LYS358 5.0 16.9 1.0

Calcium binding site 2 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Reduced By Sodium Borohydride (in Complex with Sulfite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca528 b:16.8 occ:0.50 O A:PRO116 2.3 15.1 1.0 O2A A:HEC1006 2.3 15.2 1.0 O A:HOH589 2.3 16.5 1.0 O A:HOH883 2.4 14.5 1.0 O A:HOH583 2.7 13.7 0.5 C A:PRO116 3.4 15.1 1.0 CGA A:HEC1006 3.5 15.8 1.0 O A:HOH603 3.6 13.5 0.5 OG A:SER84 3.9 13.6 1.0 NA A:NA535 3.9 13.1 0.5 CB A:SER84 3.9 14.2 1.0 O1A A:HEC1007 3.9 15.5 0.5 CG A:PRO116 3.9 15.3 1.0 N A:ARG117 4.2 14.1 1.0 CA A:ARG117 4.3 13.8 1.0 O A:HOH696 4.3 17.1 1.0 CAA A:HEC1006 4.3 14.5 1.0 CGA A:HEC1007 4.3 14.8 0.5 O1A A:HEC1006 4.3 14.9 1.0 CD A:PRO116 4.3 15.2 1.0 CA A:PRO116 4.4 15.1 1.0 N A:PRO116 4.4 15.3 1.0 O2A A:HEC1007 4.4 16.3 0.5 CB A:PRO116 4.5 14.6 1.0 CBA A:HEC1006 4.6 12.2 1.0 O A:HOH688 4.6 21.3 0.5 CA A:SER84 4.6 14.5 1.0 OE1 A:GLU115 4.7 19.5 1.0 CB A:GLU115 4.7 14.9 1.0 C A:GLU115 4.9 15.0 1.0 O A:HOH686 5.0 16.4 1.0

Calcium binding site 3 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Reduced By Sodium Borohydride (in Complex with Sulfite) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca527 b:18.9 occ:1.00 O B:LYS358 2.3 17.4 1.0 OE2 B:GLU302 2.3 17.4 1.0 O B:TYR303 2.3 18.9 1.0 OE1 B:GLN360 2.4 20.6 1.0 O B:HOH795 2.4 22.1 1.0 O B:HOH796 2.4 16.8 1.0 OE1 B:GLU302 2.5 16.6 1.0 CD B:GLU302 2.8 17.4 1.0 C B:LYS358 3.5 17.5 1.0 C B:TYR303 3.6 18.6 1.0 CD B:GLN360 3.6 24.6 1.0 N B:TYR303 4.0 17.4 1.0 CA B:LEU359 4.2 17.4 1.0 N B:GLN360 4.3 17.9 1.0 N B:LEU359 4.3 16.9 1.0 CG B:GLU302 4.3 15.4 1.0 OH B:TYR335 4.4 18.5 1.0 OD1 B:ASP346 4.4 17.9 1.0 CG B:GLN360 4.4 23.1 1.0 OD1 B:ASN304 4.4 25.3 1.0 CA B:TYR303 4.4 18.7 1.0 C B:LEU359 4.5 17.5 1.0 CE2 B:PHE328 4.5 15.7 1.0 N B:ASN304 4.5 19.4 1.0 CD1 B:TYR303 4.5 19.6 1.0 CB B:GLN360 4.5 19.6 1.0 CA B:LYS358 4.5 17.5 1.0 NE2 B:GLN360 4.5 26.3 1.0 OD2 B:ASP346 4.6 18.6 1.0 CE1 B:TYR303 4.6 21.9 1.0 CB B:LYS358 4.6 17.7 1.0 CA B:ASN304 4.7 19.8 1.0 CG B:ASP346 4.8 15.4 1.0 N B:LYS358 4.8 17.1 1.0 CG B:TYR303 4.9 19.0 1.0 O B:HOH932 5.0 33.0 1.0

Calcium binding site 4 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Reduced By Sodium Borohydride (in Complex with Sulfite) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca528 b:16.1 occ:0.50 O1A B:HEC1006 2.3 14.5 1.0 O B:HOH606 2.3 15.9 1.0 O B:PRO116 2.3 15.9 1.0 O B:HOH899 2.4 13.6 1.0 O B:HOH600 2.8 10.0 0.5 C B:PRO116 3.4 15.4 1.0 CGA B:HEC1006 3.5 14.8 1.0 O B:HOH620 3.5 17.2 0.5 NA B:NA535 3.8 17.2 0.5 CG B:PRO116 3.9 14.0 1.0 CB B:SER84 3.9 14.0 1.0 OG B:SER84 3.9 13.4 1.0 O1A B:HEC1007 4.1 15.2 0.5 O2A B:HEC1006 4.2 14.8 1.0 CAA B:HEC1006 4.2 14.7 1.0 CA B:ARG117 4.2 15.0 1.0 O B:HOH713 4.3 18.2 1.0 N B:ARG117 4.3 15.2 1.0 CD B:PRO116 4.3 13.8 1.0 CA B:PRO116 4.3 14.3 1.0 CGA B:HEC1007 4.4 13.8 0.5 N B:PRO116 4.4 13.6 1.0 O2A B:HEC1007 4.4 13.9 0.5 CB B:PRO116 4.4 13.2 1.0 CBA B:HEC1006 4.5 13.0 1.0 O B:HOH705 4.6 15.5 0.5 CA B:SER84 4.6 13.7 1.0 OE1 B:GLU115 4.7 20.0 1.0 CB B:GLU115 4.8 14.1 1.0 C B:GLU115 4.9 14.2 1.0 O B:HOH703 4.9 14.7 1.0

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