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

Enzymatic activity of Esherichia Coli Nitrite Reductase Nrfa H264N

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

Protein crystallography data

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

Other elements in 4wjy:

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

Iron (Fe) 10 atoms

Calcium Binding Sites:

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 4wjy

Go back to Calcium Binding Sites List in 4wjy
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 4wjy

Go back to Calcium Binding Sites List in 4wjy
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 4wjy

Go back to Calcium Binding Sites List in 4wjy
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 4wjy

Go back to Calcium Binding Sites List in 4wjy
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

Reference:

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
Page generated: Sun Jul 14 14:07:46 2024

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