Sodium in PDB 3mmo: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide, PDB code: 3mmo 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)	11.98 / 1.55
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	194.560, 194.560, 194.560, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 16.2

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

Iron	(Fe)	16 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide (pdb code 3mmo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide, PDB code: 3mmo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na537 b:22.9 occ:0.50 O A:HOH1089 1.6 24.7 0.5 O A:HOH1080 2.2 21.1 0.5 O A:HOH885 2.4 20.5 1.0 O A:HOH956 2.6 32.1 1.0 O A:HOH965 2.7 29.5 1.0 O A:HOH1054 3.3 23.0 0.5 HA A:SER84 3.4 12.8 1.0 HH11 A:ARG81 3.7 15.3 1.0 O A:HOH587 3.8 22.7 1.0 CA A:CA528 3.9 16.6 0.5 HD2 A:HIS85 4.1 23.2 1.0 H A:HIS85 4.1 13.8 1.0 O A:HOH955 4.1 37.7 1.0 O A:HOH967 4.2 35.8 1.0 O A:HOH1088 4.2 23.5 1.0 NH1 A:ARG81 4.3 15.9 1.0 HH12 A:ARG81 4.3 15.3 1.0 O1A A:HEC1007 4.3 10.5 0.5 O A:GLU83 4.3 14.0 1.0 CA A:SER84 4.4 12.3 1.0 OE1 A:GLU115 4.5 23.1 1.0 CD2 A:HIS85 4.5 23.8 1.0 O2A A:HEC1007 4.6 14.7 0.5 OG A:SER84 4.6 13.1 1.0 N A:HIS85 4.8 13.7 1.0 HB3 A:SER84 4.9 12.7 1.0 CGA A:HEC1007 4.9 13.7 0.5 CB A:SER84 4.9 13.5 1.0

Sodium binding site 2 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na538 b:36.2 occ:0.33 O A:HOH1018 2.4 43.5 1.0 O A:HOH881 2.4 34.9 1.0 O A:HOH898 4.0 26.1 1.0 OD2 A:ASP450 4.1 23.1 1.0 O A:HOH685 4.3 30.8 0.5 O2 A:TRS536 4.3 56.3 0.1 O3 A:TRS536 4.5 52.7 0.1 O1 A:TRS536 4.5 47.0 0.1 O A:HOH962 4.6 35.7 1.0 O A:HOH992 4.8 19.4 0.6 NZ A:LYS102 4.8 22.2 0.5 O A:HOH872 5.0 30.0 1.0 CG A:ASP450 5.0 21.6 1.0

Sodium binding site 3 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na539 b:19.9 occ:0.50 O A:SER399 2.4 21.4 1.0 OG A:SER397 2.7 18.0 1.0 HD2 A:PRO385 2.9 16.4 1.0 O A:HOH989 3.0 31.6 1.0 HB3 A:SER399 3.0 18.3 1.0 SD A:MET406 3.1 20.1 0.3 HB3 A:SER397 3.3 16.0 1.0 H A:SER399 3.3 17.0 1.0 HA A:MET384 3.3 18.1 1.0 C A:SER399 3.4 17.1 1.0 CE A:MET406 3.4 16.8 0.3 HG2 A:ARG401 3.5 15.4 1.0 CB A:SER397 3.5 16.8 1.0 O A:HIS383 3.6 15.7 1.0 CE A:MET406 3.7 15.6 0.7 CB A:SER399 3.8 19.0 1.0 CD A:PRO385 3.8 16.0 1.0 N A:SER399 3.8 17.4 1.0 CA A:SER399 3.9 17.4 1.0 O A:HOH954 3.9 42.6 1.0 HB2 A:SER397 4.0 16.0 1.0 HD3 A:PRO385 4.0 16.4 1.0 CA A:MET384 4.2 18.1 1.0 C A:HIS383 4.3 14.7 1.0 CG A:ARG401 4.3 14.9 1.0 HA A:GLN400 4.4 16.1 1.0 HB2 A:SER399 4.4 18.3 1.0 HD2 A:ARG401 4.5 17.8 1.0 H A:ARG401 4.5 14.0 1.0 SD A:MET406 4.5 13.8 0.7 HG3 A:ARG401 4.5 15.4 1.0 N A:GLN400 4.5 17.7 1.0 HE A:ARG401 4.5 20.2 1.0 N A:MET384 4.6 16.0 1.0 HG2 A:PRO385 4.6 18.6 1.0 OG A:SER399 4.6 21.4 1.0 N A:PRO385 4.6 15.9 1.0 C A:SER397 4.7 15.1 1.0 O A:SER397 4.7 17.0 1.0 CA A:SER397 4.8 15.3 1.0 C A:MET384 4.8 17.2 1.0 CD A:ARG401 4.8 18.1 1.0 CG A:PRO385 4.8 20.3 1.0 CG A:MET406 4.8 17.6 1.0 HA A:SER399 4.8 17.6 1.0 CA A:GLN400 4.9 15.3 1.0 N A:ARG401 4.9 13.1 1.0 NE A:ARG401 5.0 20.2 1.0 C A:HIS398 5.0 15.9 1.0

Sodium binding site 4 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na540 b:23.5 occ:0.50 O B:HOH1167 1.6 23.0 0.5 O B:HOH1158 2.3 20.1 0.5 O B:HOH962 2.4 18.2 1.0 O B:HOH1050 2.6 27.6 1.0 O B:HOH1041 2.8 18.5 0.5 O B:HOH670 2.8 21.7 0.5 O B:HOH1133 3.3 21.2 0.5 HA B:SER84 3.4 11.7 1.0 O B:HOH714 3.7 19.9 1.0 HH11 B:ARG81 3.8 13.6 1.0 CA B:CA528 3.9 15.2 0.5 H B:HIS85 4.0 12.4 1.0 O B:HOH1166 4.0 22.3 1.0 HD2 B:HIS85 4.0 23.1 1.0 O B:HOH1052 4.2 31.7 1.0 O B:HOH1040 4.2 36.7 1.0 O B:GLU83 4.3 13.0 1.0 OE1 B:GLU115 4.4 20.6 1.0 O1A B:HEC1007 4.4 10.3 0.5 CA B:SER84 4.4 11.4 1.0 HH12 B:ARG81 4.4 13.6 1.0 NH1 B:ARG81 4.4 14.2 1.0 CD2 B:HIS85 4.5 24.0 1.0 OG B:SER84 4.6 12.6 1.0 O2A B:HEC1007 4.6 13.4 0.5 N B:HIS85 4.7 12.2 1.0 HB3 B:SER84 4.8 11.8 1.0 CB B:SER84 4.9 12.4 1.0 CGA B:HEC1007 5.0 13.2 0.5

Sodium binding site 5 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na541 b:23.0 occ:0.33 O B:HOH1095 2.5 25.0 1.0 O B:HOH958 2.7 27.7 1.0 O B:HOH975 4.0 22.1 1.0 OD2 B:ASP450 4.2 20.7 1.0 O B:HOH1047 4.7 31.3 1.0 O B:HOH667 4.8 22.4 0.5 O B:HOH1077 4.8 21.0 1.0 NZ B:LYS102 4.9 17.9 0.5

Sodium binding site 6 out of 6 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na542 b:28.5 occ:0.50 O B:HOH741 2.4 21.9 1.0 O B:HOH827 2.5 26.3 1.0 O B:HOH1017 2.9 33.7 1.0 HG3 B:GLN138 3.3 15.0 1.0 O B:HOH1131 3.4 36.6 1.0 HG2 B:GLN138 3.6 15.0 1.0 HA B:ALA162 3.8 18.2 1.0 O B:HOH828 3.8 32.2 1.0 CG B:GLN138 3.8 14.9 1.0 CB B:ALA162 3.8 18.3 1.0 HB2 B:GLN138 3.9 13.7 1.0 CA B:ALA162 4.3 17.7 1.0 CB B:GLN138 4.4 13.8 1.0 O B:ARG136 4.5 15.9 1.0 OG1 B:THR160 4.6 22.5 1.0 H B:ALA162 4.6 17.8 1.0 N B:ALA162 4.6 17.7 1.0 O B:GLY135 4.6 14.2 1.0 O B:HOH1011 4.7 30.8 1.0 O B:HOH963 4.8 26.2 0.5 HB3 B:GLN138 5.0 13.7 1.0

A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, T.N.Safonova, A.V.Tikhonov, A.N.Popov, V.O.Popov. Structures of Complexes of Octahaem Cytochrome C Nitrite Reductase From Thioalkalivibrio Nitratireducens with Sulfite and Cyanide. Acta Crystallogr.,Sect.D V. 66 1043 2010.
ISSN: ISSN 0907-4449
PubMed: 20944237
DOI: 10.1107/S0907444910031665