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Calcium in PDB 2vr0: Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor

Enzymatic activity of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor

All present enzymatic activity of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor:
1.7.2.2;

Protein crystallography data

The structure of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor, PDB code: 2vr0 was solved by M.L.Rodrigues, M.Archer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 154.30 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.102, 189.115, 263.460, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.1

Other elements in 2vr0:

The structure of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor also contains other interesting chemical elements:

Iron (Fe) 28 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor (pdb code 2vr0). 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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor, PDB code: 2vr0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2vr0

Go back to Calcium Binding Sites List in 2vr0
Calcium binding site 1 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:19.4
occ:1.00
 O A:LYS295 2.0 23.3 1.0
O A:HOH2014 2.2 2.0 1.0
OE1 A:GLN297 2.5 26.4 1.0
OE1 A:GLU235 2.5 23.4 1.0
OE2 A:GLU235 2.6 23.3 1.0
O A:TYR236 2.7 24.4 1.0
CD A:GLU235 2.9 24.0 1.0
C A:LYS295 3.2 23.4 1.0
CD A:GLN297 3.6 25.9 1.0
C A:TYR236 3.9 24.4 1.0
CA A:ALA296 3.9 23.4 1.0
N A:ALA296 3.9 23.4 1.0
OD2 A:ASP283 3.9 22.8 1.0
NE2 A:GLN297 4.1 26.7 1.0
C A:ALA296 4.2 23.7 1.0
CA A:LYS295 4.2 23.2 1.0
OH A:TYR266 4.2 24.5 1.0
N A:GLN297 4.2 23.6 1.0
CB A:LYS295 4.3 23.3 1.0
N A:TYR236 4.3 24.0 1.0
CG A:GLU235 4.4 23.4 1.0
OD1 A:ASP283 4.5 25.8 1.0
N A:LYS295 4.5 23.1 1.0
CG A:ASP283 4.6 24.3 1.0
CG A:LYS295 4.7 23.3 1.0
CA A:TYR236 4.8 24.4 1.0
CB A:TYR237 4.8 24.3 1.0
N A:TYR237 4.8 24.3 1.0
CG A:GLN297 4.8 24.8 1.0
CA A:TYR237 4.9 24.4 1.0
O A:ALA296 4.9 24.1 1.0

Calcium binding site 2 out of 8 in 2vr0

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Calcium binding site 2 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:36.5
occ:1.00
 OE2 A:GLU117 2.2 25.2 1.0
O1A A:HEC1004 2.3 21.9 1.0
O A:ALA118 2.4 23.7 1.0
O1A A:HEC1003 2.4 21.4 1.0
O2A A:HEC1004 2.5 21.1 1.0
O A:GLY78 2.5 24.5 1.0
CGA A:HEC1004 2.7 20.1 1.0
CD A:GLU117 3.3 25.5 1.0
C A:ALA118 3.5 23.9 1.0
C A:GLY78 3.6 24.4 1.0
CG A:GLU117 3.6 24.6 1.0
CGA A:HEC1003 3.6 21.2 1.0
N A:GLY78 4.0 25.1 1.0
CAA A:HEC1003 4.1 15.8 1.0
CBA A:HEC1004 4.2 14.5 1.0
N A:ALA118 4.2 24.0 1.0
CA A:ALA118 4.3 23.9 1.0
CE A:LYS77 4.3 24.9 1.0
CA A:GLY78 4.3 24.6 1.0
CBA A:HEC1003 4.4 19.4 1.0
OE1 A:GLU117 4.4 24.3 1.0
CB A:ALA118 4.5 23.8 1.0
N A:SER79 4.5 24.0 1.0
N A:ARG119 4.5 23.6 1.0
NZ A:LYS77 4.5 23.4 1.0
O2A A:HEC1003 4.6 21.7 1.0
CA A:SER79 4.6 23.9 1.0
CA A:ARG119 4.7 23.5 1.0
CB A:LYS77 4.8 26.1 1.0
C A:GLU117 4.8 24.1 1.0
C A:LYS77 5.0 25.5 1.0
CB A:GLU117 5.0 24.0 1.0

Calcium binding site 3 out of 8 in 2vr0

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Calcium binding site 3 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1006

b:20.0
occ:1.00
 OE1 B:GLN297 2.3 27.5 1.0
O B:TYR236 2.4 25.6 1.0
O B:LYS295 2.4 23.3 1.0
O B:HOH2016 2.4 16.2 1.0
OE1 B:GLU235 2.5 25.9 1.0
OE2 B:GLU235 2.6 25.3 1.0
CD B:GLU235 2.9 25.2 1.0
CD B:GLN297 3.4 27.3 1.0
C B:LYS295 3.5 23.3 1.0
C B:TYR236 3.6 25.3 1.0
NE2 B:GLN297 3.9 27.5 1.0
N B:TYR236 4.1 24.9 1.0
CA B:ALA296 4.2 23.4 1.0
N B:GLN297 4.2 23.1 1.0
OD2 B:ASP283 4.2 23.4 1.0
N B:ALA296 4.3 23.1 1.0
OH B:TYR266 4.3 22.5 1.0
C B:ALA296 4.4 22.9 1.0
CG B:GLU235 4.4 24.1 1.0
CA B:TYR236 4.5 25.1 1.0
CA B:LYS295 4.5 23.4 1.0
CB B:LYS295 4.5 23.5 1.0
N B:TYR237 4.5 24.8 1.0
CG B:GLN297 4.6 26.1 1.0
CA B:TYR237 4.7 24.9 1.0
OD1 B:ASP283 4.7 24.1 1.0
CB B:GLN297 4.7 24.1 1.0
CG B:ASP283 4.8 24.5 1.0
CB B:TYR237 4.8 24.8 1.0
CG B:LYS295 4.9 23.4 1.0
N B:LYS295 4.9 23.3 1.0
CD1 B:TYR236 4.9 25.1 1.0
CG B:TYR236 4.9 24.7 1.0
C B:GLU235 5.0 24.5 1.0

Calcium binding site 4 out of 8 in 2vr0

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Calcium binding site 4 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1007

b:19.8
occ:1.00
 O2A B:HEC1004 2.2 14.4 1.0
O B:GLY78 2.2 23.9 1.0
O B:ALA118 2.3 24.2 1.0
O1A B:HEC1003 2.3 18.4 1.0
OE2 B:GLU117 2.5 27.4 1.0
CGA B:HEC1004 2.9 13.7 1.0
O1A B:HEC1004 2.9 15.7 1.0
CD B:GLU117 3.4 26.4 1.0
C B:GLY78 3.4 24.0 1.0
C B:ALA118 3.5 24.5 1.0
CG B:GLU117 3.6 25.1 1.0
CGA B:HEC1003 3.6 18.5 1.0
O B:HOH2029 4.0 26.4 1.0
N B:GLY78 4.1 24.6 1.0
CAA B:HEC1003 4.1 13.2 1.0
N B:SER79 4.3 23.9 1.0
CBA B:HEC1004 4.3 11.3 1.0
CA B:GLY78 4.4 24.1 1.0
CA B:ALA118 4.4 24.3 1.0
N B:ALA118 4.4 24.4 1.0
O2A B:HEC1003 4.4 18.6 1.0
N B:ARG119 4.4 24.3 1.0
CA B:SER79 4.4 23.7 1.0
CE B:LYS77 4.4 25.5 1.0
CA B:ARG119 4.5 23.7 1.0
CBA B:HEC1003 4.6 16.2 1.0
OE1 B:GLU117 4.6 26.0 1.0
CB B:ALA118 4.6 24.0 1.0
C B:GLU117 4.8 24.5 1.0
OG B:SER79 4.9 23.1 1.0
NZ B:LYS77 4.9 26.4 1.0
CB B:GLU117 5.0 24.3 1.0

Calcium binding site 5 out of 8 in 2vr0

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Calcium binding site 5 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1006

b:30.6
occ:1.00
 O D:TYR236 2.3 24.2 1.0
O D:LYS295 2.3 23.1 1.0
OE2 D:GLU235 2.5 23.2 1.0
OE1 D:GLN297 2.8 26.4 1.0
OE1 D:GLU235 2.9 22.9 1.0
CD D:GLU235 3.1 23.6 1.0
C D:LYS295 3.5 23.2 1.0
C D:TYR236 3.5 24.4 1.0
OD2 D:ASP283 3.6 22.6 1.0
CD D:GLN297 3.9 26.3 1.0
OH D:TYR266 4.0 24.4 1.0
OD1 D:ASP283 4.2 25.8 1.0
NE2 D:GLN297 4.2 27.0 1.0
N D:TYR236 4.3 24.1 1.0
CG D:ASP283 4.3 24.3 1.0
CB D:TYR237 4.3 24.1 1.0
N D:ALA296 4.4 23.4 1.0
CA D:TYR237 4.4 24.4 1.0
CA D:LYS295 4.4 23.3 1.0
N D:TYR237 4.4 24.3 1.0
CA D:ALA296 4.4 23.5 1.0
CB D:LYS295 4.4 23.3 1.0
CG D:GLU235 4.5 23.5 1.0
CA D:TYR236 4.6 24.4 1.0
N D:LYS295 4.6 23.1 1.0
N D:GLN297 4.8 23.6 1.0
C D:ALA296 4.8 23.5 1.0
CZ D:TYR266 5.0 24.1 1.0

Calcium binding site 6 out of 8 in 2vr0

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Calcium binding site 6 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1007

b:29.1
occ:1.00
 O D:ALA118 2.2 23.5 1.0
O D:GLY78 2.3 24.2 1.0
O1A D:HEC1003 2.3 27.2 1.0
OE2 D:GLU117 2.3 25.7 1.0
O2A D:HEC1004 2.3 20.6 1.0
CGA D:HEC1004 3.1 21.8 1.0
O1A D:HEC1004 3.1 23.0 1.0
CD D:GLU117 3.3 25.8 1.0
C D:ALA118 3.4 23.8 1.0
C D:GLY78 3.4 24.3 1.0
CGA D:HEC1003 3.5 26.3 1.0
CG D:GLU117 3.6 24.8 1.0
N D:GLY78 4.0 25.1 1.0
CAA D:HEC1003 4.2 21.1 1.0
CA D:ALA118 4.2 23.8 1.0
N D:ALA118 4.2 24.1 1.0
N D:SER79 4.3 24.2 1.0
CA D:GLY78 4.3 24.5 1.0
N D:ARG119 4.4 23.5 1.0
CA D:SER79 4.4 23.8 1.0
CBA D:HEC1003 4.4 24.7 1.0
CB D:ALA118 4.4 23.7 1.0
O2A D:HEC1003 4.4 27.1 1.0
OE1 D:GLU117 4.5 24.6 1.0
CA D:ARG119 4.5 23.4 1.0
CBA D:HEC1004 4.5 18.8 1.0
CE D:LYS77 4.7 25.0 1.0
NZ D:LYS77 4.8 22.9 1.0
C D:GLU117 4.8 24.1 1.0
CB D:LYS77 4.9 25.9 1.0

Calcium binding site 7 out of 8 in 2vr0

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Calcium binding site 7 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1006

b:24.7
occ:1.00
 O E:TYR236 2.3 25.4 1.0
O E:LYS295 2.4 23.2 1.0
OE2 E:GLU235 2.5 25.1 1.0
OE1 E:GLN297 2.6 27.4 1.0
OE1 E:GLU235 2.8 25.9 1.0
CD E:GLU235 3.0 25.3 1.0
C E:TYR236 3.6 25.2 1.0
C E:LYS295 3.6 23.3 1.0
CD E:GLN297 3.6 27.4 1.0
OD2 E:ASP283 3.8 23.4 1.0
NE2 E:GLN297 4.1 27.6 1.0
OH E:TYR266 4.1 22.3 1.0
OD1 E:ASP283 4.3 24.0 1.0
N E:TYR236 4.3 24.7 1.0
CG E:ASP283 4.4 24.5 1.0
N E:TYR237 4.4 25.0 1.0
CA E:TYR237 4.4 24.9 1.0
CA E:ALA296 4.4 23.2 1.0
CB E:TYR237 4.5 24.5 1.0
N E:ALA296 4.5 23.1 1.0
CA E:LYS295 4.5 23.5 1.0
CG E:GLU235 4.5 24.2 1.0
CB E:LYS295 4.6 23.5 1.0
CA E:TYR236 4.6 25.0 1.0
N E:GLN297 4.6 23.4 1.0
C E:ALA296 4.7 22.9 1.0
N E:LYS295 4.8 23.3 1.0
CG E:GLN297 5.0 25.7 1.0

Calcium binding site 8 out of 8 in 2vr0

Go back to Calcium Binding Sites List in 2vr0
Calcium binding site 8 out of 8 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor


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 Cytochrome C Nitrite Reductase Nrfha Complex Bound to the Hqno Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1007

b:25.5
occ:1.00
 O2A E:HEC1004 2.1 27.1 1.0
O E:GLY78 2.2 23.9 1.0
O E:ALA118 2.4 24.5 1.0
O2A E:HEC1003 2.4 36.2 1.0
OE2 E:GLU117 2.5 27.2 1.0
CGA E:HEC1004 2.9 26.2 1.0
O1A E:HEC1004 2.9 25.9 1.0
C E:GLY78 3.4 23.9 1.0
CD E:GLU117 3.5 26.4 1.0
C E:ALA118 3.5 24.4 1.0
CGA E:HEC1003 3.6 36.8 1.0
CG E:GLU117 3.6 25.0 1.0
CAA E:HEC1003 3.9 34.7 1.0
N E:GLY78 4.1 24.4 1.0
CBA E:HEC1004 4.3 27.5 1.0
CBA E:HEC1003 4.3 35.4 1.0
N E:SER79 4.3 23.7 1.0
CA E:GLY78 4.4 24.1 1.0
CA E:SER79 4.4 23.6 1.0
CA E:ALA118 4.4 24.4 1.0
N E:ARG119 4.4 24.1 1.0
N E:ALA118 4.4 24.5 1.0
CA E:ARG119 4.4 23.8 1.0
CE E:LYS77 4.6 25.6 1.0
O1A E:HEC1003 4.6 38.8 1.0
CB E:ALA118 4.6 24.2 1.0
OE1 E:GLU117 4.6 26.3 1.0
C E:GLU117 4.9 24.6 1.0
OG E:SER79 4.9 23.4 1.0
CAA E:HEC1004 5.0 29.2 1.0

Reference:

M.L.Rodrigues, K.A.Scott, M.S.P.Sansom, I.A.C.Pereira, M.Archer. Quinol Oxidation By C-Type Cytochromes: Structural Characterization of the Menaquinol Binding Site of Nrfha. J.Mol.Biol. V. 381 341 2008.
ISSN: ISSN 0022-2836
PubMed: 18597779
DOI: 10.1016/J.JMB.2008.05.066
Page generated: Fri Jul 12 18:09:00 2024

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