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Calcium in PDB 3tor: Crystal Structure of Escherichia Coli Nrfa with Europium Bound

Enzymatic activity of Crystal Structure of Escherichia Coli Nrfa with Europium Bound

All present enzymatic activity of Crystal Structure of Escherichia Coli Nrfa with Europium Bound:
1.7.2.2;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Nrfa with Europium Bound, PDB code: 3tor was solved by C.W.J.Lockwood, T.A.Clarke, J.N.Butt, 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) 146.10 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.884, 90.489, 292.196, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 22.2

Other elements in 3tor:

The structure of Crystal Structure of Escherichia Coli Nrfa with Europium Bound also contains other interesting chemical elements:

Iron (Fe) 20 atoms
Europium (Eu) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound (pdb code 3tor). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound, PDB code: 3tor:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3tor

Go back to Calcium Binding Sites List in 3tor
Calcium binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Escherichia Coli Nrfa with Europium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:12.9
occ:1.00
 O A:TYR216 2.4 12.8 1.0
OE1 A:GLN263 2.4 13.5 1.0
O A:LYS261 2.4 13.3 1.0
O A:HOH21 2.4 12.7 1.0
OE2 A:GLU215 2.4 11.1 1.0
O A:HOH583 2.5 13.0 1.0
OE1 A:GLU215 2.5 11.5 1.0
CD A:GLU215 2.8 13.9 1.0
CD A:GLN263 3.5 16.5 1.0
C A:LYS261 3.5 11.4 1.0
C A:TYR216 3.6 12.6 1.0
OH A:TYR242 4.0 14.1 1.0
NE2 A:GLN263 4.0 14.2 1.0
N A:TYR216 4.1 11.5 1.0
CA A:ALA262 4.1 10.3 1.0
N A:GLN263 4.3 10.0 1.0
N A:ALA262 4.3 11.3 1.0
CG A:GLU215 4.3 11.5 1.0
C A:ALA262 4.4 10.9 1.0
OD2 A:ASP249 4.4 14.7 1.0
N A:TYR217 4.5 13.4 1.0
CA A:TYR216 4.5 12.0 1.0
CA A:LYS261 4.6 12.5 1.0
CA A:TYR217 4.6 12.7 1.0
OD1 A:ASP249 4.6 15.3 1.0
CB A:TYR217 4.7 12.1 1.0
CB A:LYS261 4.7 13.9 1.0
CG A:GLN263 4.8 15.8 1.0
CG A:ASP249 4.8 14.4 1.0
N A:LYS261 4.8 11.9 1.0
CZ A:TYR242 4.8 16.3 1.0
CZ3 A:TRP379 4.9 15.7 1.0
CB A:GLN263 5.0 12.9 1.0

Calcium binding site 2 out of 4 in 3tor

Go back to Calcium Binding Sites List in 3tor
Calcium binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Escherichia Coli Nrfa with Europium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:13.7
occ:1.00
 OE1 B:GLN263 2.3 15.9 1.0
O B:HOH635 2.3 18.8 1.0
OE2 B:GLU215 2.3 11.7 1.0
O B:TYR216 2.4 17.4 1.0
O B:LYS261 2.4 14.0 1.0
O B:HOH566 2.4 19.2 1.0
OE1 B:GLU215 2.5 12.9 1.0
CD B:GLU215 2.8 10.7 1.0
CD B:GLN263 3.5 18.3 1.0
C B:TYR216 3.5 15.9 1.0
C B:LYS261 3.6 13.4 1.0
OH B:TYR242 4.0 11.9 1.0
NE2 B:GLN263 4.0 19.0 1.0
N B:TYR216 4.1 13.5 1.0
CA B:ALA262 4.2 12.4 1.0
OD2 B:ASP249 4.2 18.3 1.0
CG B:GLU215 4.3 13.8 1.0
N B:TYR217 4.3 16.1 1.0
N B:ALA262 4.3 12.7 1.0
N B:GLN263 4.3 12.3 1.0
C B:ALA262 4.4 12.5 1.0
CA B:TYR217 4.4 14.3 1.0
CA B:TYR216 4.4 15.5 1.0
OD1 B:ASP249 4.5 15.1 1.0
CB B:TYR217 4.6 14.4 1.0
CA B:LYS261 4.6 14.1 1.0
CB B:LYS261 4.7 13.6 1.0
CG B:ASP249 4.7 17.6 1.0
CG B:GLN263 4.8 14.5 1.0
CZ3 B:TRP379 4.9 16.2 1.0
CZ B:TYR242 4.9 13.0 1.0
N B:LYS261 4.9 13.5 1.0
C B:GLU215 5.0 14.5 1.0
CB B:GLN263 5.0 13.1 1.0

Calcium binding site 3 out of 4 in 3tor

Go back to Calcium Binding Sites List in 3tor
Calcium binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Escherichia Coli Nrfa with Europium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:13.0
occ:1.00
 O C:LYS261 2.3 11.0 1.0
OE1 C:GLN263 2.3 17.9 1.0
OE1 C:GLU215 2.5 12.4 1.0
OE2 C:GLU215 2.5 12.2 1.0
O C:HOH509 2.5 14.2 1.0
O C:HOH583 2.5 16.5 1.0
O C:TYR216 2.5 13.2 1.0
CD C:GLU215 2.8 13.6 1.0
C C:LYS261 3.5 11.0 1.0
CD C:GLN263 3.5 18.9 1.0
C C:TYR216 3.7 13.2 1.0
OH C:TYR242 4.0 10.5 1.0
CA C:ALA262 4.0 12.3 1.0
NE2 C:GLN263 4.0 16.0 1.0
N C:TYR216 4.2 10.8 1.0
N C:ALA262 4.2 11.3 1.0
N C:GLN263 4.2 11.9 1.0
OD2 C:ASP249 4.3 11.4 1.0
C C:ALA262 4.3 12.5 1.0
CG C:GLU215 4.3 7.3 1.0
CA C:LYS261 4.5 10.8 1.0
N C:TYR217 4.6 11.5 1.0
CA C:TYR217 4.6 12.6 1.0
CB C:LYS261 4.6 9.6 1.0
CB C:TYR217 4.6 10.6 1.0
CA C:TYR216 4.6 12.9 1.0
OD1 C:ASP249 4.6 16.5 1.0
CG C:GLN263 4.7 14.8 1.0
CZ3 C:TRP379 4.7 12.4 1.0
N C:LYS261 4.8 10.5 1.0
CG C:ASP249 4.8 14.0 1.0
CB C:GLN263 4.9 11.8 1.0
CZ C:TYR242 4.9 12.9 1.0

Calcium binding site 4 out of 4 in 3tor

Go back to Calcium Binding Sites List in 3tor
Calcium binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Escherichia Coli Nrfa with Europium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1

b:19.4
occ:1.00
 O D:LYS261 2.3 13.3 1.0
OE1 D:GLN263 2.4 17.5 1.0
O D:HOH509 2.4 14.0 1.0
O D:TYR216 2.4 15.7 1.0
OE2 D:GLU215 2.5 12.3 1.0
O D:HOH543 2.5 14.8 1.0
OE1 D:GLU215 2.6 8.8 1.0
CD D:GLU215 2.9 15.2 1.0
C D:LYS261 3.6 14.4 1.0
CD D:GLN263 3.6 20.4 1.0
C D:TYR216 3.6 15.9 1.0
OH D:TYR242 3.9 17.7 1.0
NE2 D:GLN263 4.1 18.9 1.0
N D:TYR216 4.1 14.5 1.0
CA D:ALA262 4.2 14.7 1.0
N D:GLN263 4.2 15.2 1.0
OD2 D:ASP249 4.3 15.2 1.0
N D:ALA262 4.4 14.1 1.0
CG D:GLU215 4.4 12.7 1.0
C D:ALA262 4.4 15.0 1.0
N D:TYR217 4.5 14.8 1.0
CA D:TYR217 4.5 16.4 1.0
CA D:TYR216 4.6 15.6 1.0
CA D:LYS261 4.6 13.1 1.0
CB D:TYR217 4.6 16.5 1.0
OD1 D:ASP249 4.6 18.6 1.0
CB D:LYS261 4.6 13.0 1.0
N D:LYS261 4.8 13.2 1.0
CZ3 D:TRP379 4.8 14.4 1.0
CG D:ASP249 4.8 15.7 1.0
CG D:GLN263 4.8 20.4 1.0
CZ D:TYR242 4.9 18.9 1.0
O D:HOH629 4.9 35.8 1.0
CB D:GLN263 5.0 15.2 1.0

Reference:

C.W.Lockwood, T.A.Clarke, J.N.Butt, A.M.Hemmings, D.J.Richardson. Characterization of the Active Site and Calcium Binding in Cytochrome C Nitrite Reductases. Biochem.Soc.Trans. V. 39 1871 2011.
ISSN: ISSN 0300-5127
PubMed: 22103542
DOI: 10.1042/BST20110731
Page generated: Sat Jul 13 19:50:14 2024

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