Atomistry » Calcium » PDB 2vk5-2vuz » 2vr0
Atomistry »
  Calcium »
    PDB 2vk5-2vuz »
      2vr0 »

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

Go back to Calcium Binding Sites List in 2vr0
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

Go back to Calcium Binding Sites List in 2vr0
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

Go back to Calcium Binding Sites List in 2vr0
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

Go back to Calcium Binding Sites List in 2vr0
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

Go back to Calcium Binding Sites List in 2vr0
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

Go back to Calcium Binding Sites List in 2vr0
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: Tue Jul 8 08:42:56 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy