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Calcium in PDB 2rf7: Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E

Enzymatic activity of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E

All present enzymatic activity of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E:
1.7.2.2;

Protein crystallography data

The structure of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E, PDB code: 2rf7 was solved by T.A.Clarke, D.J.Richardson, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.31 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.292, 91.201, 295.486, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.6

Other elements in 2rf7:

The structure of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E (pdb code 2rf7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E, PDB code: 2rf7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2rf7

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Calcium binding site 1 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


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 the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:17.5
occ:1.00
 O A:LYS261 2.4 10.6 1.0
OE1 A:GLU263 2.4 18.5 1.0
O A:TYR216 2.4 14.7 1.0
O A:HOH516 2.4 21.2 1.0
OE2 A:GLU215 2.4 9.2 1.0
O A:HOH535 2.5 16.9 1.0
OE1 A:GLU215 2.6 13.7 1.0
CD A:GLU215 2.9 12.3 1.0
C A:LYS261 3.5 11.8 1.0
CD A:GLU263 3.6 19.7 1.0
C A:TYR216 3.6 15.8 1.0
OH A:TYR242 4.0 11.2 1.0
N A:TYR216 4.1 14.3 1.0
OE2 A:GLU263 4.2 24.5 1.0
CA A:ALA262 4.2 11.3 1.0
OD2 A:ASP249 4.3 14.8 1.0
N A:GLU263 4.3 12.2 1.0
N A:ALA262 4.3 11.3 1.0
CG A:GLU215 4.4 12.5 1.0
N A:TYR217 4.5 15.6 1.0
C A:ALA262 4.5 12.0 1.0
CA A:TYR217 4.5 16.0 1.0
CA A:TYR216 4.5 15.6 1.0
CA A:LYS261 4.6 11.9 1.0
CB A:TYR217 4.6 15.7 1.0
CB A:LYS261 4.6 11.2 1.0
OD1 A:ASP249 4.7 16.9 1.0
CG A:GLU263 4.8 16.9 1.0
CB A:GLU263 4.8 13.3 1.0
CG A:ASP249 4.8 15.3 1.0
N A:LYS261 4.8 12.1 1.0
O A:HOH584 4.9 29.4 1.0
CZ3 A:TRP379 4.9 12.1 1.0
CZ A:TYR242 5.0 12.6 1.0

Calcium binding site 2 out of 8 in 2rf7

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Calcium binding site 2 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


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 the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:64.5
occ:1.00
 O2A A:HEC4 2.4 34.3 1.0
O A:PRO91 2.6 17.2 1.0
O1A A:HEC3 2.8 23.1 1.0
O A:HOH799 3.2 38.7 1.0
O A:HOH784 3.3 27.2 1.0
CGA A:HEC4 3.5 32.2 1.0
C A:PRO91 3.6 16.8 1.0
CG A:PRO91 3.9 15.4 1.0
O A:HOH821 3.9 44.5 1.0
CGA A:HEC3 4.1 19.3 1.0
N A:PRO91 4.1 15.7 1.0
CD A:PRO91 4.2 15.7 1.0
CA A:PRO91 4.2 16.6 1.0
O1A A:HEC4 4.3 35.9 1.0
CB A:PRO91 4.3 15.9 1.0
CBA A:HEC4 4.4 27.2 1.0
CB A:LYS90 4.4 16.7 1.0
O A:HOH622 4.5 24.7 1.0
N A:ARG92 4.5 16.6 1.0
CAA A:HEC3 4.7 12.3 1.0
C A:LYS90 4.7 16.5 1.0
CA A:ARG92 4.7 16.6 1.0
O A:HOH646 4.7 38.2 1.0
O A:HOH800 4.8 36.9 1.0
O2A A:HEC3 4.8 24.2 1.0
CBA A:HEC3 5.0 15.6 1.0

Calcium binding site 3 out of 8 in 2rf7

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Calcium binding site 3 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


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 the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1501

b:16.5
occ:1.00
 OE1 B:GLU263 2.3 18.6 1.0
O B:LYS261 2.3 10.9 1.0
O B:HOH583 2.4 20.1 1.0
O B:TYR216 2.5 11.1 1.0
O B:HOH494 2.5 11.4 1.0
OE2 B:GLU215 2.5 11.1 1.0
OE1 B:GLU215 2.5 9.2 1.0
CD B:GLU215 2.9 12.6 1.0
CD B:GLU263 3.5 19.7 1.0
C B:LYS261 3.5 11.4 1.0
C B:TYR216 3.6 11.0 1.0
OE2 B:GLU263 4.0 22.5 1.0
OH B:TYR242 4.1 9.9 1.0
CA B:ALA262 4.1 10.9 1.0
N B:TYR216 4.2 9.9 1.0
N B:ALA262 4.3 10.9 1.0
N B:GLU263 4.3 10.9 1.0
OD2 B:ASP249 4.4 15.0 1.0
CG B:GLU215 4.4 11.1 1.0
C B:ALA262 4.5 10.7 1.0
N B:TYR217 4.5 11.4 1.0
O B:HOH922 4.5 34.2 1.0
CA B:TYR216 4.6 10.8 1.0
CA B:TYR217 4.6 11.6 1.0
CA B:LYS261 4.6 12.2 1.0
OD1 B:ASP249 4.7 16.0 1.0
CB B:LYS261 4.7 12.7 1.0
CB B:TYR217 4.7 11.0 1.0
CG B:GLU263 4.7 14.8 1.0
CB B:GLU263 4.8 12.4 1.0
N B:LYS261 4.8 12.3 1.0
CG B:ASP249 4.9 15.0 1.0
CZ3 B:TRP379 5.0 8.9 1.0

Calcium binding site 4 out of 8 in 2rf7

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Calcium binding site 4 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


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 the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1502

b:64.4
occ:1.00
 O B:PRO91 2.5 14.4 1.0
O1A B:HEC3 2.8 22.1 1.0
O1A B:HEC4 3.0 34.1 1.0
O B:HOH822 3.1 32.4 1.0
O B:HOH681 3.3 34.1 1.0
C B:PRO91 3.5 14.7 1.0
CGA B:HEC4 3.6 30.3 1.0
O2A B:HEC4 3.7 34.1 1.0
CGA B:HEC3 4.0 18.5 1.0
O B:HOH514 4.0 24.9 1.0
CG B:PRO91 4.1 15.6 1.0
N B:PRO91 4.1 15.5 1.0
CD B:PRO91 4.1 15.1 1.0
CA B:PRO91 4.3 14.9 1.0
CB B:LYS90 4.4 16.5 1.0
N B:ARG92 4.5 13.7 1.0
CA B:ARG92 4.5 13.5 1.0
O2A B:HEC3 4.5 20.7 1.0
C B:LYS90 4.6 16.1 1.0
CB B:PRO91 4.6 15.1 1.0
O B:HOH695 4.7 26.5 1.0
CBA B:HEC4 4.8 24.6 1.0
O B:HOH748 4.8 36.2 1.0
CAA B:HEC3 4.9 11.8 1.0

Calcium binding site 5 out of 8 in 2rf7

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Calcium binding site 5 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1501

b:13.7
occ:1.00
 OE1 C:GLU263 2.4 16.7 1.0
O C:TYR216 2.4 11.3 1.0
O C:HOH886 2.4 14.7 1.0
OE2 C:GLU215 2.5 8.0 1.0
O C:LYS261 2.5 11.5 1.0
O C:HOH913 2.5 12.9 1.0
OE1 C:GLU215 2.6 10.2 1.0
CD C:GLU215 2.9 12.3 1.0
CD C:GLU263 3.5 15.3 1.0
C C:TYR216 3.6 11.2 1.0
C C:LYS261 3.6 10.3 1.0
OH C:TYR242 4.0 9.5 1.0
OE2 C:GLU263 4.0 18.8 1.0
N C:TYR216 4.2 10.4 1.0
OD2 C:ASP249 4.2 13.6 1.0
CA C:ALA262 4.3 9.0 1.0
CG C:GLU215 4.4 10.4 1.0
N C:ALA262 4.4 9.4 1.0
N C:TYR217 4.4 11.5 1.0
N C:GLU263 4.5 9.9 1.0
CA C:TYR217 4.5 11.9 1.0
C C:ALA262 4.6 9.9 1.0
CA C:TYR216 4.6 10.5 1.0
CB C:TYR217 4.6 11.7 1.0
OD1 C:ASP249 4.6 13.3 1.0
CA C:LYS261 4.6 10.7 1.0
CB C:LYS261 4.7 11.1 1.0
CG C:GLU263 4.8 13.6 1.0
CG C:ASP249 4.8 13.8 1.0
CB C:GLU263 4.8 11.2 1.0
N C:LYS261 4.8 11.1 1.0
CZ C:TYR242 4.9 12.2 1.0
CZ3 C:TRP379 4.9 7.8 1.0
O C:HOH867 5.0 23.5 1.0

Calcium binding site 6 out of 8 in 2rf7

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Calcium binding site 6 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1502

b:61.5
occ:1.00
 O1A C:HEC4 2.3 31.7 1.0
O C:PRO91 2.4 12.1 1.0
O1A C:HEC3 2.6 19.5 1.0
CGA C:HEC4 3.4 29.2 1.0
O C:HOH916 3.5 28.9 1.0
C C:PRO91 3.5 13.1 1.0
CGA C:HEC3 3.8 13.8 1.0
O2A C:HEC4 3.9 33.5 1.0
CG C:PRO91 4.2 11.8 1.0
N C:PRO91 4.2 12.5 1.0
O C:HOH881 4.3 16.6 1.0
CD C:PRO91 4.3 11.8 1.0
CA C:PRO91 4.3 12.0 1.0
N C:ARG92 4.4 12.7 1.0
O2A C:HEC3 4.4 13.4 1.0
CB C:PRO91 4.5 13.2 1.0
CA C:ARG92 4.5 12.2 1.0
CB C:LYS90 4.6 14.2 1.0
O C:HOH1115 4.6 30.8 1.0
O C:HOH1319 4.6 43.9 1.0
CBA C:HEC4 4.6 21.8 1.0
C C:LYS90 4.7 12.8 1.0
CAA C:HEC3 4.7 11.4 1.0
CBA C:HEC3 4.9 10.8 1.0

Calcium binding site 7 out of 8 in 2rf7

Go back to Calcium Binding Sites List in 2rf7
Calcium binding site 7 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1501

b:22.4
occ:1.00
 OE1 D:GLU263 2.3 20.6 1.0
O D:TYR216 2.3 22.0 1.0
O D:LYS261 2.4 18.5 1.0
O D:HOH507 2.4 15.8 1.0
O D:HOH666 2.5 30.6 1.0
OE1 D:GLU215 2.5 18.7 1.0
OE2 D:GLU215 2.6 17.0 1.0
CD D:GLU215 2.9 19.2 1.0
CD D:GLU263 3.5 22.3 1.0
C D:TYR216 3.5 22.2 1.0
C D:LYS261 3.6 18.4 1.0
OE2 D:GLU263 4.0 27.6 1.0
OH D:TYR242 4.1 19.8 1.0
N D:TYR216 4.1 21.1 1.0
CA D:ALA262 4.2 18.2 1.0
OD2 D:ASP249 4.3 19.7 1.0
N D:GLU263 4.3 18.5 1.0
N D:ALA262 4.3 18.6 1.0
CG D:GLU215 4.4 18.4 1.0
N D:TYR217 4.4 22.4 1.0
CA D:TYR216 4.5 21.7 1.0
C D:ALA262 4.5 18.6 1.0
CA D:TYR217 4.5 23.2 1.0
CA D:LYS261 4.6 17.6 1.0
CB D:TYR217 4.6 22.0 1.0
CB D:LYS261 4.7 17.4 1.0
CG D:GLU263 4.8 19.2 1.0
OD1 D:ASP249 4.8 22.6 1.0
O D:HOH758 4.8 34.0 1.0
N D:LYS261 4.9 18.1 1.0
CB D:GLU263 4.9 18.8 1.0
CZ3 D:TRP379 4.9 13.1 1.0
CG D:ASP249 4.9 21.8 1.0
CZ D:TYR242 5.0 20.9 1.0

Calcium binding site 8 out of 8 in 2rf7

Go back to Calcium Binding Sites List in 2rf7
Calcium binding site 8 out of 8 in the Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Escherichia Coli Nrfa Mutant Q263E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1502

b:87.7
occ:1.00
 O1A D:HEC4 2.6 38.6 1.0
O D:PRO91 2.6 22.2 1.0
O1A D:HEC3 2.9 25.2 1.0
CGA D:HEC4 3.5 36.0 1.0
O D:HOH624 3.6 40.3 1.0
O2A D:HEC4 3.6 38.7 1.0
C D:PRO91 3.7 22.1 1.0
CGA D:HEC3 4.1 23.9 1.0
O D:HOH607 4.3 32.2 1.0
O D:HOH651 4.4 38.3 1.0
N D:PRO91 4.5 22.4 1.0
CA D:PRO91 4.6 21.7 1.0
CD D:PRO91 4.6 21.4 1.0
CB D:LYS90 4.7 22.6 1.0
N D:ARG92 4.7 21.9 1.0
O2A D:HEC3 4.7 25.8 1.0
CA D:ARG92 4.7 21.4 1.0
CG D:PRO91 4.8 21.2 1.0
C D:LYS90 4.9 22.8 1.0
CBA D:HEC4 4.9 31.4 1.0
CB D:PRO91 4.9 21.8 1.0
O D:HOH595 5.0 45.0 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: Fri Jul 12 15:56:46 2024

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