Calcium in PDB 4wjy: Esherichia Coli Nitrite Reductase Nrfa H264N

All present enzymatic activity of Esherichia Coli Nitrite Reductase Nrfa H264N:
1.7.2.2;

The structure of Esherichia Coli Nitrite Reductase Nrfa H264N, PDB code: 4wjy was solved by T.A.Clarke, M.J.Edwards, C.W.J.Lockwood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.75 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.240, 89.490, 274.720, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 21.3

The structure of Esherichia Coli Nitrite Reductase Nrfa H264N also contains other interesting chemical elements:

Iron

(Fe)

10 atoms

The binding sites of Calcium atom in the Esherichia Coli Nitrite Reductase Nrfa H264N (pdb code 4wjy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Esherichia Coli Nitrite Reductase Nrfa H264N, PDB code: 4wjy:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Esherichia Coli Nitrite Reductase Nrfa H264N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Esherichia Coli Nitrite Reductase Nrfa H264N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:16.7 occ:1.00 O A:LYS261 2.3 12.4 1.0 O A:HOH644 2.4 16.9 1.0 OE2 A:GLU215 2.4 12.8 1.0 OE1 A:GLN263 2.5 16.8 1.0 OE1 A:GLU215 2.5 10.7 1.0 O A:TYR216 2.5 12.2 1.0 O A:HOH653 2.6 16.1 1.0 CD A:GLU215 2.8 12.2 1.0 C A:LYS261 3.5 12.7 1.0 CD A:GLN263 3.6 14.4 1.0 C A:TYR216 3.7 14.1 1.0 OH A:TYR242 3.9 13.1 1.0 N A:TYR216 4.1 11.7 1.0 CA A:ALA262 4.1 13.8 1.0 NE2 A:GLN263 4.1 17.3 1.0 N A:GLN263 4.2 13.7 1.0 CG A:GLU215 4.3 10.8 1.0 N A:ALA262 4.3 12.0 1.0 OD2 A:ASP249 4.3 13.0 1.0 C A:ALA262 4.3 13.8 1.0 OD1 A:ASP249 4.5 21.1 1.0 CA A:LYS261 4.6 11.5 1.0 CB A:LYS261 4.6 10.4 1.0 CB A:TYR217 4.6 15.3 1.0 CA A:TYR216 4.6 12.4 1.0 N A:TYR217 4.6 14.0 1.0 CA A:TYR217 4.6 15.8 1.0 CG A:ASP249 4.8 16.0 1.0 N A:LYS261 4.8 11.4 1.0 CZ3 A:TRP379 4.8 15.4 1.0 CG A:GLN263 4.9 15.6 1.0 O A:HOH877 4.9 37.8 1.0 CZ A:TYR242 4.9 13.5 1.0 CB A:GLN263 4.9 14.5 1.0

Calcium binding site 2 out of 4 in the Esherichia Coli Nitrite Reductase Nrfa H264N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Esherichia Coli Nitrite Reductase Nrfa H264N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:21.2 occ:1.00 O1A A:HEM504 2.4 21.3 1.0 O A:HOH688 2.4 19.3 1.0 O A:HOH697 2.4 24.2 1.0 O A:HOH662 2.4 19.2 1.0 O A:HOH798 2.4 34.1 1.0 O1A A:HEM503 2.5 12.7 1.0 O A:PRO91 2.5 15.8 1.0 CGA A:HEM504 3.5 17.6 1.0 C A:PRO91 3.6 14.3 1.0 CGA A:HEM503 3.6 13.0 1.0 O2A A:HEM504 4.0 23.1 1.0 O2A A:HEM503 4.1 12.0 1.0 O A:HOH767 4.1 23.9 1.0 CA A:ARG92 4.3 12.0 1.0 N A:ARG92 4.4 11.7 1.0 CG A:PRO91 4.4 14.2 1.0 O A:HOH901 4.5 40.2 1.0 O A:HOH701 4.6 23.8 1.0 N A:PRO91 4.6 14.1 1.0 CA A:PRO91 4.6 14.2 1.0 CAA A:HEM503 4.7 5.7 1.0 CB A:PRO91 4.7 12.4 1.0 CBA A:HEM504 4.7 11.7 1.0 CD A:PRO91 4.8 14.2 1.0 CBA A:HEM503 4.8 6.0 1.0 O A:HOH882 4.9 27.7 1.0 CB A:LYS90 5.0 14.7 1.0 CB A:ARG92 5.0 11.1 1.0 C A:LYS90 5.0 14.0 1.0

Calcium binding site 3 out of 4 in the Esherichia Coli Nitrite Reductase Nrfa H264N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Esherichia Coli Nitrite Reductase Nrfa H264N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:19.9 occ:1.00 O B:TYR216 2.4 18.9 1.0 O B:LYS261 2.4 18.7 1.0 O B:HOH646 2.4 13.4 1.0 OE2 B:GLU215 2.4 13.7 1.0 OE1 B:GLN263 2.5 24.7 1.0 O B:HOH638 2.5 15.3 1.0 OE1 B:GLU215 2.6 12.9 1.0 CD B:GLU215 2.8 15.9 1.0 C B:TYR216 3.6 18.4 1.0 C B:LYS261 3.6 17.1 1.0 CD B:GLN263 3.6 25.1 1.0 OH B:TYR242 4.0 14.8 1.0 N B:TYR216 4.1 17.0 1.0 CA B:ALA262 4.1 17.2 1.0 N B:GLN263 4.2 18.2 1.0 NE2 B:GLN263 4.2 23.0 1.0 OD2 B:ASP249 4.3 21.2 1.0 CG B:GLU215 4.3 16.4 1.0 N B:ALA262 4.3 16.6 1.0 C B:ALA262 4.4 18.8 1.0 N B:TYR217 4.5 18.1 1.0 CA B:TYR217 4.5 19.5 1.0 CA B:TYR216 4.5 17.5 1.0 CB B:TYR217 4.6 18.9 1.0 OD1 B:ASP249 4.6 18.9 1.0 CA B:LYS261 4.6 16.6 1.0 CB B:LYS261 4.7 17.2 1.0 CG B:ASP249 4.8 19.1 1.0 CG B:GLN263 4.9 22.5 1.0 N B:LYS261 4.9 16.3 1.0 CB B:GLN263 4.9 19.7 1.0 CZ B:TYR242 4.9 14.3 1.0 CZ3 B:TRP379 5.0 16.3 1.0

Calcium binding site 4 out of 4 in the Esherichia Coli Nitrite Reductase Nrfa H264N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Esherichia Coli Nitrite Reductase Nrfa H264N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca507 b:30.8 occ:1.00 O1A B:HEM504 2.2 36.4 1.0 O B:HOH653 2.3 30.7 1.0 O1A B:HEM503 2.3 24.4 1.0 O B:PRO91 2.4 19.4 1.0 O B:HOH901 2.5 51.3 1.0 O B:HOH701 2.6 34.1 1.0 CGA B:HEM504 3.4 30.8 1.0 CGA B:HEM503 3.4 22.0 1.0 C B:PRO91 3.5 19.2 1.0 O2A B:HEM503 3.8 24.3 1.0 O2A B:HEM504 3.9 32.6 1.0 CA B:ARG92 4.2 19.3 1.0 N B:ARG92 4.3 18.9 1.0 CG B:PRO91 4.3 20.2 1.0 O B:HOH856 4.4 32.1 1.0 O B:HOH688 4.5 18.7 1.0 CA B:PRO91 4.5 20.4 1.0 N B:PRO91 4.5 19.9 1.0 CBA B:HEM504 4.6 20.0 1.0 CBA B:HEM503 4.7 18.2 1.0 CAA B:HEM503 4.7 14.9 1.0 CB B:PRO91 4.7 20.6 1.0 CD B:PRO91 4.7 19.9 1.0 O B:HOH878 4.8 39.7 1.0 CB B:LYS90 5.0 21.2 1.0

C.W.Lockwood, B.Burlat, M.R.Cheesman, M.Kern, J.Simon, T.A.Clarke, D.J.Richardson, J.N.Butt. Resolution of Key Roles For the Distal Pocket Histidine in Cytochrome C Nitrite Reductases. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25658043
DOI: 10.1021/JA512941J