Calcium in PDB 3f29: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Sulfite

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Sulfite, PDB code: 3f29 was solved by A.A.Trofimov, 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)	19.97 / 2.00
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	193.568, 193.568, 193.568, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 17.4

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

Iron

(Fe)

16 atoms

The binding sites of Calcium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Sulfite (pdb code 3f29). 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 Complex with Sulfite, PDB code: 3f29:
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 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 in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:20.0 occ:1.00 O A:LYS358 2.3 18.7 1.0 OE1 A:GLN360 2.3 21.4 1.0 OE2 A:GLU302 2.3 20.0 1.0 O A:TYR303 2.3 19.0 1.0 O A:HOH758 2.4 22.3 1.0 O A:HOH759 2.5 18.7 1.0 OE1 A:GLU302 2.5 17.6 1.0 CD A:GLU302 2.8 18.1 1.0 CD A:GLN360 3.5 21.7 1.0 C A:LYS358 3.5 17.9 1.0 C A:TYR303 3.5 18.9 1.0 N A:TYR303 4.0 17.7 1.0 NE2 A:GLN360 4.1 24.0 1.0 CA A:LEU359 4.2 16.9 1.0 CG A:GLU302 4.3 16.5 1.0 N A:LEU359 4.3 17.1 1.0 OD1 A:ASN304 4.3 16.2 0.5 N A:GLN360 4.3 17.5 1.0 OH A:TYR335 4.4 19.1 1.0 OD1 A:ASP346 4.4 20.4 1.0 CA A:TYR303 4.4 18.7 1.0 N A:ASN304 4.5 19.1 1.0 OD2 A:ASP346 4.5 19.8 1.0 C A:LEU359 4.5 17.0 1.0 CE1 A:PHE328 4.6 20.1 1.0 CA A:LYS358 4.6 17.9 1.0 CB A:LYS358 4.7 17.6 1.0 CG A:GLN360 4.7 20.7 1.0 CA A:ASN304 4.7 19.7 1.0 CG A:ASP346 4.8 19.6 1.0 CB A:GLN360 4.8 18.9 1.0 N A:LYS358 4.9 18.1 1.0 OD1 A:ASN304 4.9 22.3 0.5 CD1 A:TYR303 4.9 19.6 1.0 C A:GLU302 4.9 17.1 1.0

Calcium binding site 2 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase 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 in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca528 b:19.6 occ:0.50 O A:PRO116 2.3 16.0 1.0 O A:HOH867 2.4 17.6 1.0 O A:HOH574 2.4 21.1 1.0 O2A A:HEC1006 2.4 17.8 1.0 O A:HOH946 2.7 31.6 1.0 O2A A:HEC1007 2.9 22.7 0.5 C A:PRO116 3.4 15.6 1.0 CGA A:HEC1006 3.6 16.0 1.0 CGA A:HEC1007 3.8 20.0 0.5 O1A A:HEC1007 3.8 19.9 0.5 O1A A:HEC1007 3.8 16.4 0.5 O A:HOH947 3.9 50.1 1.0 CG A:PRO116 4.0 15.9 1.0 OG A:SER84 4.0 17.2 1.0 CB A:SER84 4.0 17.1 1.0 O A:HOH676 4.1 23.2 1.0 CD A:PRO116 4.2 14.9 1.0 N A:PRO116 4.3 15.5 1.0 CA A:PRO116 4.3 15.1 1.0 N A:ARG117 4.3 14.9 1.0 CGA A:HEC1007 4.3 17.0 0.5 CA A:ARG117 4.4 14.8 1.0 CAA A:HEC1006 4.4 14.1 1.0 O1A A:HEC1006 4.4 17.2 1.0 CB A:PRO116 4.5 14.9 1.0 O2A A:HEC1007 4.5 17.3 0.5 O A:HOH668 4.5 36.7 1.0 CBA A:HEC1006 4.6 14.6 1.0 CA A:SER84 4.7 17.2 1.0 OE1 A:GLU115 4.7 23.4 1.0 CB A:GLU115 4.8 16.1 1.0 C A:GLU115 4.9 15.3 1.0

Calcium binding site 3 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase 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 in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca527 b:17.9 occ:1.00 OE2 B:GLU302 2.3 17.0 1.0 O B:LYS358 2.3 16.5 1.0 OE1 B:GLN360 2.3 20.1 1.0 O B:TYR303 2.3 16.7 1.0 O B:HOH869 2.4 21.8 1.0 O B:HOH870 2.5 17.1 1.0 OE1 B:GLU302 2.5 14.6 1.0 CD B:GLU302 2.8 16.1 1.0 CD B:GLN360 3.5 20.5 1.0 C B:LYS358 3.5 16.2 1.0 C B:TYR303 3.5 17.1 1.0 N B:TYR303 4.0 16.0 1.0 NE2 B:GLN360 4.1 21.3 1.0 CA B:LEU359 4.2 15.7 1.0 CG B:GLU302 4.3 15.5 1.0 OD1 B:ASN304 4.3 19.0 0.5 N B:LEU359 4.3 15.6 1.0 N B:GLN360 4.3 16.3 1.0 OH B:TYR335 4.4 16.1 1.0 OD1 B:ASP346 4.4 17.4 1.0 CA B:TYR303 4.5 17.0 1.0 N B:ASN304 4.5 17.7 1.0 C B:LEU359 4.5 16.0 1.0 CE2 B:PHE328 4.5 16.2 1.0 OD2 B:ASP346 4.6 17.1 1.0 CA B:LYS358 4.6 16.4 1.0 CB B:LYS358 4.7 16.4 1.0 CA B:ASN304 4.7 18.3 1.0 CG B:GLN360 4.7 18.9 1.0 CB B:GLN360 4.8 17.9 1.0 CG B:ASP346 4.8 16.4 1.0 OD1 B:ASN304 4.9 18.3 0.5 N B:LYS358 4.9 16.4 1.0 CD1 B:TYR303 4.9 18.5 1.0 C B:GLU302 5.0 15.6 1.0

Calcium binding site 4 out of 4 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase 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 in Complex with Sulfite within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca528 b:19.0 occ:0.50 O B:PRO116 2.3 15.7 1.0 O B:HOH688 2.3 20.2 1.0 O1A B:HEC1006 2.4 15.8 1.0 O B:HOH976 2.4 16.6 1.0 O B:HOH1063 2.8 29.3 1.0 O2A B:HEC1007 3.0 21.0 0.5 C B:PRO116 3.4 14.6 1.0 CGA B:HEC1006 3.6 14.4 1.0 O1A B:HEC1007 3.7 15.9 0.5 CGA B:HEC1007 3.9 18.7 0.5 O1A B:HEC1007 3.9 19.1 0.5 OG B:SER84 3.9 14.3 1.0 CG B:PRO116 3.9 14.7 1.0 CB B:SER84 4.0 15.2 1.0 O B:HOH1064 4.0 35.6 1.0 CD B:PRO116 4.3 13.9 1.0 N B:ARG117 4.3 14.4 1.0 O B:HOH787 4.3 23.7 1.0 N B:PRO116 4.3 14.1 1.0 CAA B:HEC1006 4.3 12.8 1.0 CA B:PRO116 4.3 14.3 1.0 CA B:ARG117 4.3 13.8 1.0 O2A B:HEC1006 4.3 15.7 1.0 CGA B:HEC1007 4.3 15.5 0.5 O B:HOH779 4.5 33.8 1.0 CB B:PRO116 4.5 13.6 1.0 CBA B:HEC1006 4.6 12.9 1.0 O2A B:HEC1007 4.6 15.8 0.5 CA B:SER84 4.7 15.0 1.0 OE1 B:GLU115 4.7 22.9 1.0 CB B:GLU115 4.8 15.3 1.0 C B:GLU115 4.9 14.2 1.0

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.