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Calcium in PDB 2rdz: High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.

Enzymatic activity of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.

All present enzymatic activity of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.:
1.7.2.2;

Protein crystallography data

The structure of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase., PDB code: 2rdz was solved by T.A.Clarke, A.M.Hemmings, D.J.Richardson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.65 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.460, 79.300, 137.580, 90.00, 101.57, 90.00
R / Rfree (%) 15.4 / 18.9

Other elements in 2rdz:

The structure of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. (pdb code 2rdz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase., PDB code: 2rdz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2rdz

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Calcium binding site 1 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:10.1
occ:1.00
 O A:LYS261 2.3 8.7 1.0
O A:TYR216 2.4 10.0 1.0
O A:HOH489 2.4 8.4 1.0
O A:HOH499 2.4 8.7 1.0
OE1 A:GLN263 2.4 10.5 1.0
OE1 A:GLU215 2.5 9.3 1.0
OE2 A:GLU215 2.5 7.4 1.0
CD A:GLU215 2.9 7.0 1.0
C A:LYS261 3.5 9.2 1.0
C A:TYR216 3.6 11.2 1.0
CD A:GLN263 3.6 12.9 1.0
OH A:TYR242 4.1 12.0 1.0
N A:TYR216 4.1 9.3 1.0
CA A:ALA262 4.1 9.0 1.0
NE2 A:GLN263 4.3 13.4 1.0
N A:GLN263 4.3 9.2 1.0
N A:ALA262 4.3 9.0 1.0
OD2 A:ASP249 4.3 10.9 1.0
C A:ALA262 4.3 9.4 1.0
CG A:GLU215 4.4 8.7 1.0
N A:TYR217 4.5 10.6 1.0
CA A:TYR217 4.5 12.0 1.0
CB A:TYR217 4.5 12.2 1.0
CA A:TYR216 4.5 10.4 1.0
CA A:LYS261 4.6 8.2 1.0
OD1 A:ASP249 4.6 10.4 1.0
CB A:LYS261 4.6 8.7 1.0
CG A:ASP249 4.8 9.4 1.0
CG A:GLN263 4.8 11.0 1.0
CB A:GLN263 4.8 8.8 1.0
N A:LYS261 4.9 8.8 1.0
CZ3 A:TRP379 4.9 9.6 1.0

Calcium binding site 2 out of 8 in 2rdz

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Calcium binding site 2 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:28.3
occ:1.00
 O1A A:HEC3 2.3 11.2 1.0
O1A A:HEC4 2.4 26.1 1.0
O A:HOH650 2.5 28.8 1.0
O A:PRO91 2.5 9.8 1.0
O A:HOH908 2.6 33.0 1.0
O A:HOH936 2.6 33.4 1.0
O A:HOH623 2.8 33.4 1.0
CGA A:HEC3 3.4 13.6 1.0
CGA A:HEC4 3.5 24.6 1.0
C A:PRO91 3.6 9.7 1.0
O2A A:HEC3 4.0 13.4 1.0
O2A A:HEC4 4.0 26.4 1.0
CA A:ARG92 4.2 9.5 1.0
O A:HOH556 4.3 19.1 1.0
N A:ARG92 4.3 9.4 1.0
O A:HOH898 4.3 37.0 1.0
O A:HOH721 4.5 26.9 1.0
CA A:PRO91 4.6 9.4 1.0
CAA A:HEC3 4.6 8.7 1.0
CG A:PRO91 4.6 10.1 1.0
CBA A:HEC3 4.6 8.5 1.0
N A:PRO91 4.6 9.6 1.0
CBA A:HEC4 4.7 18.5 1.0
O A:HOH747 4.7 28.1 1.0
CB A:PRO91 4.8 10.3 1.0
CD A:PRO91 4.8 9.4 1.0
O A:HOH814 4.9 39.6 1.0
CB A:ARG92 5.0 8.5 1.0

Calcium binding site 3 out of 8 in 2rdz

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Calcium binding site 3 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1501

b:10.6
occ:1.00
 O B:TYR216 2.4 8.7 1.0
O B:LYS261 2.4 9.0 1.0
O B:HOH504 2.4 10.4 1.0
O B:HOH528 2.4 9.2 1.0
OE1 B:GLN263 2.4 11.8 1.0
OE1 B:GLU215 2.5 8.7 1.0
OE2 B:GLU215 2.6 9.6 1.0
CD B:GLU215 2.9 8.4 1.0
C B:LYS261 3.5 9.2 1.0
C B:TYR216 3.6 9.1 1.0
CD B:GLN263 3.6 12.6 1.0
OH B:TYR242 4.0 12.2 1.0
N B:TYR216 4.1 8.1 1.0
NE2 B:GLN263 4.1 11.0 1.0
CA B:ALA262 4.1 9.3 1.0
N B:GLN263 4.2 9.2 1.0
N B:ALA262 4.3 10.1 1.0
C B:ALA262 4.3 9.9 1.0
OD2 B:ASP249 4.4 11.0 1.0
CG B:GLU215 4.4 7.2 1.0
N B:TYR217 4.5 9.7 1.0
CA B:TYR216 4.5 8.6 1.0
CA B:TYR217 4.5 10.7 1.0
OD1 B:ASP249 4.6 11.3 1.0
CA B:LYS261 4.6 9.4 1.0
CB B:TYR217 4.6 11.3 1.0
CB B:LYS261 4.7 8.9 1.0
O B:HOH656 4.8 28.7 1.0
CG B:GLN263 4.8 9.7 1.0
CG B:ASP249 4.8 11.4 1.0
CB B:GLN263 4.9 9.4 1.0
N B:LYS261 4.9 9.6 1.0
CZ3 B:TRP379 4.9 8.8 1.0
CZ B:TYR242 5.0 12.5 1.0

Calcium binding site 4 out of 8 in 2rdz

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Calcium binding site 4 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1502

b:25.8
occ:1.00
 O1A B:HEC3 2.4 11.5 1.0
O B:HOH676 2.4 27.0 1.0
O B:PRO91 2.4 8.7 1.0
O B:HOH716 2.5 31.3 1.0
O B:HOH955 2.6 32.7 1.0
O1A B:HEC4 2.6 25.5 1.0
O B:HOH661 3.0 31.2 1.0
CGA B:HEC3 3.5 11.7 1.0
C B:PRO91 3.5 9.0 1.0
CGA B:HEC4 3.6 23.0 1.0
O2A B:HEC4 3.9 23.3 1.0
O2A B:HEC3 4.0 11.9 1.0
CA B:ARG92 4.2 8.3 1.0
O B:HOH525 4.3 13.0 1.0
N B:ARG92 4.3 8.2 1.0
O B:HOH902 4.5 29.1 1.0
CA B:PRO91 4.5 9.4 1.0
N B:PRO91 4.5 9.6 1.0
O B:HOH658 4.5 22.5 1.0
CD B:PRO91 4.7 10.3 1.0
CG B:PRO91 4.7 11.0 1.0
CAA B:HEC3 4.7 7.8 1.0
CBA B:HEC3 4.7 10.2 1.0
CBA B:HEC4 4.8 17.8 1.0
CB B:PRO91 4.8 9.7 1.0
O B:HOH720 4.8 34.6 1.0

Calcium binding site 5 out of 8 in 2rdz

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Calcium binding site 5 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1501

b:11.3
occ:1.00
 O C:TYR216 2.3 11.6 1.0
O C:LYS261 2.4 10.8 1.0
O C:HOH495 2.4 9.8 1.0
OE1 C:GLN263 2.4 13.0 1.0
O C:HOH514 2.4 12.1 1.0
OE1 C:GLU215 2.5 10.2 1.0
OE2 C:GLU215 2.6 12.2 1.0
CD C:GLU215 2.9 11.3 1.0
CD C:GLN263 3.5 14.3 1.0
C C:LYS261 3.6 10.6 1.0
C C:TYR216 3.6 13.1 1.0
OH C:TYR242 4.0 13.6 1.0
NE2 C:GLN263 4.1 15.8 1.0
N C:TYR216 4.1 11.7 1.0
CA C:ALA262 4.2 9.9 1.0
OD2 C:ASP249 4.3 12.3 1.0
N C:ALA262 4.3 10.2 1.0
N C:GLN263 4.4 10.6 1.0
CG C:GLU215 4.4 10.9 1.0
C C:ALA262 4.4 10.8 1.0
N C:TYR217 4.5 12.9 1.0
CA C:TYR216 4.5 12.3 1.0
CA C:TYR217 4.5 13.8 1.0
OD1 C:ASP249 4.6 11.9 1.0
CA C:LYS261 4.6 10.3 1.0
CB C:TYR217 4.6 14.0 1.0
CB C:LYS261 4.7 10.6 1.0
CG C:ASP249 4.7 12.3 1.0
CG C:GLN263 4.8 10.4 1.0
N C:LYS261 4.9 10.5 1.0
CB C:GLN263 4.9 10.4 1.0
CZ3 C:TRP379 4.9 10.3 1.0
CZ C:TYR242 5.0 12.5 1.0

Calcium binding site 6 out of 8 in 2rdz

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Calcium binding site 6 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1502

b:31.9
occ:1.00
 O1A C:HEC3 2.3 14.1 1.0
O C:PRO91 2.4 13.2 1.0
O C:HOH609 2.6 30.6 1.0
O C:HOH769 2.7 38.4 1.0
O1A C:HEC4 2.8 27.5 1.0
O C:HOH712 2.8 32.6 1.0
CGA C:HEC3 3.5 15.8 1.0
C C:PRO91 3.5 13.8 1.0
CGA C:HEC4 3.6 25.3 1.0
O2A C:HEC4 4.0 28.0 1.0
O2A C:HEC3 4.0 15.5 1.0
CA C:ARG92 4.2 13.5 1.0
O C:HOH568 4.2 19.1 1.0
N C:ARG92 4.3 13.4 1.0
O C:HOH660 4.4 29.4 1.0
O C:HOH718 4.5 39.5 1.0
CA C:PRO91 4.5 13.3 1.0
N C:PRO91 4.6 13.5 1.0
CG C:PRO91 4.6 13.7 1.0
CAA C:HEC3 4.6 12.9 1.0
CBA C:HEC3 4.6 14.6 1.0
CD C:PRO91 4.8 13.6 1.0
O C:HOH640 4.8 30.0 1.0
CB C:PRO91 4.8 13.9 1.0
CBA C:HEC4 4.8 20.6 1.0
CB C:ARG92 5.0 12.8 1.0

Calcium binding site 7 out of 8 in 2rdz

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Calcium binding site 7 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1501

b:8.8
occ:1.00
 O D:TYR216 2.3 6.8 1.0
O D:LYS261 2.3 7.8 1.0
O D:HOH497 2.4 6.2 1.0
OE1 D:GLN263 2.4 11.6 1.0
O D:HOH520 2.4 7.1 1.0
OE2 D:GLU215 2.5 7.2 1.0
OE1 D:GLU215 2.5 7.5 1.0
CD D:GLU215 2.9 8.3 1.0
C D:LYS261 3.5 8.1 1.0
C D:TYR216 3.6 8.1 1.0
CD D:GLN263 3.6 12.3 1.0
OH D:TYR242 4.0 9.4 1.0
N D:TYR216 4.1 6.7 1.0
CA D:ALA262 4.2 8.0 1.0
NE2 D:GLN263 4.2 10.7 1.0
N D:GLN263 4.3 8.7 1.0
N D:ALA262 4.3 7.5 1.0
OD2 D:ASP249 4.3 11.4 1.0
CG D:GLU215 4.4 7.4 1.0
C D:ALA262 4.4 8.6 1.0
N D:TYR217 4.5 7.8 1.0
CA D:TYR216 4.5 7.0 1.0
CA D:TYR217 4.5 8.8 1.0
CB D:TYR217 4.6 9.3 1.0
CA D:LYS261 4.6 7.2 1.0
OD1 D:ASP249 4.6 9.0 1.0
CB D:LYS261 4.7 8.1 1.0
CG D:GLN263 4.8 9.0 1.0
CB D:GLN263 4.8 8.0 1.0
CG D:ASP249 4.8 8.2 1.0
N D:LYS261 4.9 8.2 1.0
CZ D:TYR242 4.9 9.3 1.0
CZ3 D:TRP379 5.0 6.8 1.0

Calcium binding site 8 out of 8 in 2rdz

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Calcium binding site 8 out of 8 in the High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of High Resolution Crystal Structure of the Escherichia Coli Cytochrome C Nitrite Reductase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1502

b:16.3
occ:0.50
 O D:PRO91 2.3 10.9 1.0
O1A D:HEC3 2.3 12.1 1.0
O D:HOH707 2.6 27.7 1.0
O D:HOH758 2.8 36.2 1.0
C D:PRO91 3.4 10.5 1.0
O1A D:HEC4 3.4 26.5 1.0
CGA D:HEC3 3.4 12.8 1.0
O2A D:HEC3 3.8 10.8 1.0
O D:HOH974 3.8 29.5 1.0
CA D:ARG92 3.9 11.3 1.0
N D:ARG92 4.1 10.7 1.0
O D:HOH973 4.3 33.2 1.0
CA D:PRO91 4.4 10.2 1.0
CB D:ARG92 4.5 11.8 1.0
N D:PRO91 4.6 10.3 1.0
CGA D:HEC4 4.6 22.5 1.0
O D:HOH776 4.6 32.5 1.0
CB D:PRO91 4.7 10.8 1.0
O D:HOH709 4.7 34.4 1.0
CBA D:HEC3 4.7 9.0 1.0
CD D:PRO91 4.8 11.0 1.0
O D:HOH700 4.8 25.3 1.0
CAA D:HEC3 4.8 8.2 1.0
C D:ARG92 4.9 10.6 1.0
O D:GLU64 5.0 17.0 1.0

Reference:

T.A.Clarke, G.L.Kemp, J.H.Wonderen, R.M.Doyle, J.A.Cole, N.Tovell, M.R.Cheesman, J.N.Butt, D.J.Richardson, A.M.Hemmings. Role of A Conserved Glutamine Residue in Tuning the Catalytic Activity of Escherichia Coli Cytochrome C Nitrite Reductase. Biochemistry V. 47 3789 2008.
ISSN: ISSN 0006-2960
PubMed: 18311941
DOI: 10.1021/BI702175W
Page generated: Tue Jul 8 08:11:58 2025

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