Calcium in PDB 4l38: Nitrite Complex of Tvnir, Low Dose Data Set

All present enzymatic activity of Nitrite Complex of Tvnir, Low Dose Data Set:
1.7.2.2;

The structure of Nitrite Complex of Tvnir, Low Dose Data Set, PDB code: 4l38 was solved by A.A.Trofimov, K.M.Polyakov, V.A.Lazarenko, A.N.Popov, T.V.Tikhonova, A.V.Tikhonov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 1.80
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	193.970, 193.970, 193.970, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17

The structure of Nitrite Complex of Tvnir, Low Dose Data Set also contains other interesting chemical elements:

Iron

(Fe)

16 atoms

The binding sites of Calcium atom in the Nitrite Complex of Tvnir, Low Dose Data Set (pdb code 4l38). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Nitrite Complex of Tvnir, Low Dose Data Set, PDB code: 4l38:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Nitrite Complex of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Nitrite Complex of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:14.8 occ:1.00 O A:LYS358 2.3 11.1 1.0 OE1 A:GLN360 2.3 16.8 1.0 O A:TYR303 2.3 12.3 1.0 OE2 A:GLU302 2.4 13.2 1.0 OE1 A:GLU302 2.4 12.1 1.0 O A:HOH967 2.4 12.8 1.0 O A:HOH869 2.6 11.3 1.0 CD A:GLU302 2.7 13.1 1.0 CD A:GLN360 3.5 16.9 1.0 C A:TYR303 3.5 12.2 1.0 C A:LYS358 3.5 10.1 1.0 N A:TYR303 3.9 11.4 1.0 NE2 A:GLN360 4.1 18.0 1.0 CA A:LEU359 4.1 9.6 1.0 OH A:TYR335 4.2 12.1 1.0 CG A:GLU302 4.3 12.5 1.0 N A:LEU359 4.3 9.0 1.0 OD1 A:ASN304 4.3 9.4 0.5 N A:GLN360 4.3 10.2 1.0 CA A:TYR303 4.4 11.7 1.0 OD1 A:ASP346 4.4 11.7 1.0 N A:ASN304 4.4 12.1 1.0 C A:LEU359 4.4 10.2 1.0 CE1 A:PHE328 4.5 12.1 1.0 OD2 A:ASP346 4.5 12.6 1.0 CA A:LYS358 4.6 9.7 1.0 CB A:LYS358 4.7 9.3 1.0 CA A:ASN304 4.7 12.7 1.0 CG A:GLN360 4.7 15.5 1.0 CB A:GLN360 4.8 12.6 1.0 N A:LYS358 4.8 10.7 1.0 CG A:ASP346 4.8 11.2 1.0 C A:GLU302 4.9 12.0 1.0 OD1 A:ASN304 4.9 17.2 0.5 CG A:LYS358 5.0 9.4 1.0

Calcium binding site 2 out of 4 in the Nitrite Complex of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Nitrite Complex of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca611 b:12.3 occ:0.50 O A:HOH1037 2.2 21.4 1.0 O A:PRO116 2.3 10.0 1.0 O3 A:GOL613 2.4 12.8 1.0 O A:HOH912 2.4 10.9 1.0 O A:HOH930 2.6 15.3 1.0 O2A A:HEC603 2.6 9.4 1.0 C A:PRO116 3.4 9.3 1.0 C3 A:GOL613 3.5 13.1 1.0 O1A A:HEC604 3.7 13.6 1.0 CGA A:HEC603 3.8 9.7 1.0 O A:HOH1122 3.9 13.4 0.5 CB A:SER84 4.0 10.2 1.0 CD A:PRO116 4.1 8.0 1.0 OG A:SER84 4.1 10.7 1.0 O2 A:GOL613 4.1 11.2 0.5 O A:HOH1023 4.1 7.5 0.5 N A:PRO116 4.2 8.3 1.0 CA A:PRO116 4.2 8.7 1.0 CG A:PRO116 4.2 8.4 1.0 CB A:PRO116 4.3 8.5 1.0 N A:ARG117 4.3 8.8 1.0 C2 A:GOL613 4.4 14.3 1.0 CA A:ARG117 4.4 8.3 1.0 CAA A:HEC603 4.4 9.1 1.0 O1A A:HEC603 4.4 10.3 1.0 CGA A:HEC604 4.5 14.7 1.0 OE1 A:GLU115 4.6 11.2 1.0 CB A:GLU115 4.6 9.4 1.0 CA A:SER84 4.6 9.8 1.0 C A:GLU115 4.8 8.3 1.0 CBA A:HEC603 4.8 9.0 1.0

Calcium binding site 3 out of 4 in the Nitrite Complex of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Nitrite Complex of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca610 b:12.4 occ:1.00 O B:LYS358 2.3 9.3 1.0 OE1 B:GLN360 2.3 15.1 1.0 O B:TYR303 2.4 9.1 1.0 OE2 B:GLU302 2.4 9.6 1.0 O B:HOH995 2.5 11.6 1.0 OE1 B:GLU302 2.5 9.1 1.0 O B:HOH896 2.6 10.9 1.0 CD B:GLU302 2.8 9.0 1.0 CD B:GLN360 3.5 14.3 1.0 C B:LYS358 3.5 8.6 1.0 C B:TYR303 3.5 9.2 1.0 N B:TYR303 4.0 8.7 1.0 NE2 B:GLN360 4.2 15.2 1.0 CA B:LEU359 4.2 8.1 1.0 OH B:TYR335 4.2 8.6 1.0 OD1 B:ASN304 4.2 9.4 0.5 N B:GLN360 4.3 9.0 1.0 N B:LEU359 4.3 8.3 1.0 CG B:GLU302 4.3 8.8 1.0 CA B:TYR303 4.4 8.8 1.0 OD1 B:ASP346 4.4 10.4 1.0 C B:LEU359 4.5 8.5 1.0 N B:ASN304 4.5 9.5 1.0 CE2 B:PHE328 4.5 10.0 1.0 OD2 B:ASP346 4.5 9.7 1.0 CA B:LYS358 4.6 8.6 1.0 CB B:LYS358 4.6 8.3 1.0 CA B:ASN304 4.7 10.3 1.0 CG B:GLN360 4.7 13.8 1.0 OD1 B:ASN304 4.8 13.6 0.5 CB B:GLN360 4.8 11.0 1.0 N B:LYS358 4.8 8.2 1.0 CG B:ASP346 4.8 9.3 1.0 C B:GLU302 5.0 8.3 1.0 CG B:LYS358 5.0 8.3 1.0

Calcium binding site 4 out of 4 in the Nitrite Complex of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Nitrite Complex of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca611 b:9.7 occ:0.50 O B:HOH1067 2.0 3.6 0.5 O B:PRO116 2.3 8.0 1.0 O1 B:GOL613 2.4 10.2 1.0 O B:HOH940 2.5 9.5 1.0 O B:HOH958 2.6 16.2 1.0 O1A B:HEC603 2.6 7.6 1.0 O1A B:HEC604 3.0 10.4 0.5 C B:PRO116 3.4 7.4 1.0 C1 B:GOL613 3.5 10.4 1.0 O1A B:HEC604 3.6 7.6 0.5 CGA B:HEC603 3.7 7.8 1.0 CGA B:HEC604 3.8 9.4 0.5 O B:HOH1153 3.9 11.6 0.5 O2A B:HEC604 3.9 9.5 0.5 OG B:SER84 4.0 8.4 1.0 CB B:SER84 4.0 8.4 1.0 O B:HOH1053 4.1 7.6 0.5 O2 B:GOL613 4.1 8.7 0.5 CD B:PRO116 4.1 7.2 1.0 N B:PRO116 4.2 7.0 1.0 CA B:PRO116 4.2 7.2 1.0 CG B:PRO116 4.3 7.3 1.0 N B:ARG117 4.3 7.2 1.0 CB B:PRO116 4.3 7.2 1.0 CA B:ARG117 4.3 7.0 1.0 CAA B:HEC603 4.3 6.7 1.0 C2 B:GOL613 4.4 11.2 1.0 O2A B:HEC603 4.4 8.5 1.0 CGA B:HEC604 4.6 7.5 0.5 OE1 B:GLU115 4.6 9.4 1.0 CA B:SER84 4.7 8.5 1.0 CB B:GLU115 4.7 7.8 1.0 CBA B:HEC603 4.7 7.0 1.0 C B:GLU115 4.8 6.8 1.0

A.A.Trofimov, K.M.Polyakov, V.A.Lazarenko, A.N.Popov, T.V.Tikhonova, A.V.Tikhonov, V.O.Popov. Investigation of the X-Ray-Induced Nitrite Reduction Catalysed By Cytochrome C Nitrite Reductase From the Bacterium Thioalkalivibrio Nitratireducens To Be Published.