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Calcium in PDB 2j7a: Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris

Protein crystallography data

The structure of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris, PDB code: 2j7a was solved by M.L.Rodrigues, T.F.Oliveira, I.A.C.Pereira, M.Archer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 288.67 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.664, 258.117, 580.742, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24

Other elements in 2j7a:

The structure of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Iron (Fe) 84 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris (pdb code 2j7a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris, PDB code: 2j7a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in 2j7a

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Calcium binding site 1 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:13.2
occ:1.00
 OE2 A:GLU235 2.3 10.1 1.0
OE1 A:GLN297 2.4 16.0 1.0
O A:LYS295 2.4 11.5 1.0
O A:TYR236 2.5 10.0 1.0
O A:HOH2098 2.6 8.8 1.0
OE1 A:GLU235 2.7 10.3 1.0
O A:HOH2101 2.8 13.0 1.0
CD A:GLU235 2.8 10.1 1.0
CD A:GLN297 3.5 14.2 1.0
C A:LYS295 3.5 10.8 1.0
C A:TYR236 3.7 9.4 1.0
OH A:TYR266 4.0 12.0 1.0
NE2 A:GLN297 4.0 15.5 1.0
CA A:ALA296 4.1 10.3 1.0
N A:TYR236 4.1 9.2 1.0
N A:ALA296 4.2 10.3 1.0
CG A:GLU235 4.3 8.1 1.0
OD2 A:ASP283 4.3 13.2 1.0
N A:GLN297 4.4 10.5 1.0
C A:ALA296 4.4 10.5 1.0
N A:TYR237 4.6 9.5 1.0
CA A:LYS295 4.6 11.4 1.0
CA A:TYR236 4.6 9.4 1.0
CA A:TYR237 4.6 9.5 1.0
CB A:LYS295 4.6 11.2 1.0
CB A:TYR237 4.7 9.1 1.0
CG A:GLN297 4.7 11.6 1.0
OD1 A:ASP283 4.7 16.9 1.0
CB A:GLN297 4.8 11.0 1.0
N A:LYS295 4.9 12.3 1.0
CG A:ASP283 4.9 15.6 1.0
CG2 A:ILE294 5.0 13.1 1.0

Calcium binding site 2 out of 24 in 2j7a

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Calcium binding site 2 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:11.1
occ:1.00
 O2A A:HEC1004 2.2 11.3 1.0
O A:ALA118 2.2 11.5 1.0
O A:GLY78 2.3 15.7 1.0
OE2 A:GLU117 2.3 14.6 1.0
O1A A:HEC1003 2.3 12.1 1.0
O A:HOH2195 2.7 47.1 1.0
CGA A:HEC1004 3.3 10.7 1.0
CD A:GLU117 3.3 15.1 1.0
C A:ALA118 3.4 11.6 1.0
C A:GLY78 3.4 15.0 1.0
CGA A:HEC1003 3.6 9.8 1.0
O1A A:HEC1004 3.7 14.4 1.0
CG A:GLU117 3.7 13.6 1.0
CAA A:HEC1003 4.0 6.1 1.0
N A:GLY78 4.0 16.0 1.0
CA A:ALA118 4.2 11.7 1.0
N A:ALA118 4.3 12.0 1.0
O A:HOH2194 4.3 19.6 1.0
CA A:GLY78 4.3 15.6 1.0
N A:ARG119 4.4 11.4 1.0
N A:SER79 4.4 14.6 1.0
CBA A:HEC1003 4.4 7.4 1.0
OE1 A:GLU117 4.4 13.9 1.0
CB A:ALA118 4.4 11.5 1.0
CA A:SER79 4.4 13.8 1.0
O2A A:HEC1003 4.4 10.9 1.0
CE A:LYS77 4.5 13.7 1.0
CA A:ARG119 4.5 11.0 1.0
CBA A:HEC1004 4.5 8.9 1.0
NZ A:LYS77 4.7 13.9 1.0
C A:GLU117 4.8 12.5 1.0
CB A:LYS77 4.9 15.9 1.0
OG A:SER79 5.0 12.2 1.0

Calcium binding site 3 out of 24 in 2j7a

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Calcium binding site 3 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1006

b:11.3
occ:1.00
 OE1 B:GLN297 2.3 13.8 1.0
O B:HOH2105 2.3 8.9 1.0
O B:TYR236 2.4 9.2 1.0
OE1 B:GLU235 2.5 12.1 1.0
O B:LYS295 2.5 12.2 1.0
O B:HOH2101 2.6 12.8 1.0
OE2 B:GLU235 2.6 7.5 1.0
CD B:GLU235 2.9 9.6 1.0
CD B:GLN297 3.3 12.8 1.0
C B:TYR236 3.6 9.4 1.0
C B:LYS295 3.6 11.0 1.0
NE2 B:GLN297 3.8 13.2 1.0
N B:TYR236 4.0 9.1 1.0
OH B:TYR266 4.0 11.1 1.0
CA B:ALA296 4.2 9.4 1.0
N B:GLN297 4.3 9.1 1.0
N B:ALA296 4.3 10.4 1.0
CG B:GLU235 4.4 8.4 1.0
C B:ALA296 4.4 9.2 1.0
OD2 B:ASP283 4.4 17.5 1.0
CA B:TYR236 4.5 9.9 1.0
N B:TYR237 4.5 10.2 1.0
CA B:TYR237 4.6 10.5 1.0
CG B:GLN297 4.6 10.8 1.0
CB B:TYR237 4.7 10.9 1.0
CA B:LYS295 4.7 10.7 1.0
CB B:LYS295 4.8 10.4 1.0
CB B:GLN297 4.8 9.0 1.0
OD1 B:ASP283 4.9 17.2 1.0
N B:LYS295 4.9 11.6 1.0
CG B:TYR236 5.0 13.0 1.0
CD2 B:TYR236 5.0 13.2 1.0
C B:GLU235 5.0 7.9 1.0

Calcium binding site 4 out of 24 in 2j7a

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Calcium binding site 4 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1007

b:13.2
occ:1.00
 O2A B:HEC1004 2.2 12.4 1.0
OE2 B:GLU117 2.3 13.8 1.0
O B:ALA118 2.3 11.4 1.0
O1A B:HEC1003 2.4 8.1 1.0
O B:GLY78 2.4 12.9 1.0
CGA B:HEC1004 2.9 8.9 1.0
O1A B:HEC1004 2.9 5.2 1.0
CD B:GLU117 3.4 17.3 1.0
C B:ALA118 3.4 11.6 1.0
C B:GLY78 3.5 12.8 1.0
CGA B:HEC1003 3.6 8.0 1.0
CG B:GLU117 3.8 15.9 1.0
CAA B:HEC1003 3.9 7.1 1.0
O B:HOH2182 4.0 10.9 1.0
N B:GLY78 4.1 13.9 1.0
CA B:ALA118 4.3 11.8 1.0
CBA B:HEC1004 4.3 7.9 1.0
N B:ALA118 4.3 12.5 1.0
N B:ARG119 4.3 10.9 1.0
CBA B:HEC1003 4.4 7.0 1.0
CA B:GLY78 4.4 13.1 1.0
OE1 B:GLU117 4.4 19.4 1.0
N B:SER79 4.4 12.5 1.0
CB B:ALA118 4.5 11.8 1.0
CA B:ARG119 4.5 10.8 1.0
CA B:SER79 4.5 12.3 1.0
CE B:LYS77 4.5 10.5 1.0
O2A B:HEC1003 4.5 8.7 1.0
NZ B:LYS77 4.8 11.7 1.0
C B:GLU117 4.9 13.2 1.0
CAA B:HEC1004 5.0 7.0 1.0

Calcium binding site 5 out of 24 in 2j7a

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Calcium binding site 5 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1006

b:16.1
occ:1.00
 O D:HOH2095 2.3 13.9 1.0
O D:LYS295 2.4 13.1 1.0
OE1 D:GLN297 2.4 10.8 1.0
OE2 D:GLU235 2.5 12.1 1.0
O D:TYR236 2.5 11.5 1.0
O D:HOH2092 2.5 19.2 1.0
OE1 D:GLU235 2.6 14.7 1.0
CD D:GLU235 2.9 12.5 1.0
CD D:GLN297 3.6 10.0 1.0
C D:LYS295 3.6 12.7 1.0
C D:TYR236 3.6 11.7 1.0
OH D:TYR266 4.0 14.6 1.0
N D:TYR236 4.1 11.6 1.0
CA D:ALA296 4.1 12.1 1.0
NE2 D:GLN297 4.2 9.9 1.0
OD2 D:ASP283 4.2 18.7 1.0
N D:ALA296 4.3 12.0 1.0
CG D:GLU235 4.3 12.6 1.0
N D:GLN297 4.4 11.6 1.0
C D:ALA296 4.5 12.2 1.0
CA D:TYR236 4.5 11.4 1.0
N D:TYR237 4.5 12.1 1.0
CA D:TYR237 4.6 12.3 1.0
CA D:LYS295 4.7 12.7 1.0
CG D:GLN297 4.8 10.4 1.0
OD1 D:ASP283 4.8 20.8 1.0
CB D:TYR237 4.8 12.2 1.0
CB D:GLN297 4.8 11.4 1.0
O D:HOH2034 4.9 16.6 1.0
CG D:ASP283 4.9 17.1 1.0
CB D:LYS295 4.9 11.6 1.0
N D:LYS295 4.9 13.3 1.0

Calcium binding site 6 out of 24 in 2j7a

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Calcium binding site 6 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1007

b:11.7
occ:1.00
 O2A D:HEC1004 2.0 13.0 1.0
OE2 D:GLU117 2.2 13.7 1.0
O D:GLY78 2.3 15.1 1.0
O D:ALA118 2.3 11.5 1.0
O1A D:HEC1003 2.3 8.8 1.0
CGA D:HEC1004 3.2 12.1 1.0
CD D:GLU117 3.2 16.8 1.0
C D:GLY78 3.4 14.6 1.0
C D:ALA118 3.5 12.1 1.0
CG D:GLU117 3.6 13.3 1.0
CGA D:HEC1003 3.6 8.3 1.0
O1A D:HEC1004 3.7 16.1 1.0
N D:GLY78 3.9 15.2 1.0
CAA D:HEC1003 4.1 3.1 1.0
O D:HOH2164 4.2 19.3 1.0
CA D:GLY78 4.2 14.9 1.0
N D:ALA118 4.3 12.5 1.0
N D:SER79 4.3 14.3 1.0
CBA D:HEC1004 4.4 10.9 1.0
CA D:ALA118 4.4 12.0 1.0
CA D:SER79 4.4 13.9 1.0
OE1 D:GLU117 4.4 17.3 1.0
N D:ARG119 4.4 12.3 1.0
CBA D:HEC1003 4.4 5.9 1.0
O2A D:HEC1003 4.5 11.9 1.0
CA D:ARG119 4.5 12.0 1.0
CE D:LYS77 4.6 14.8 1.0
CB D:ALA118 4.6 11.8 1.0
C D:GLU117 4.9 12.5 1.0
CB D:GLU117 4.9 13.1 1.0
CB D:LYS77 5.0 15.7 1.0
C D:LYS77 5.0 15.5 1.0

Calcium binding site 7 out of 24 in 2j7a

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Calcium binding site 7 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1006

b:17.1
occ:1.00
 O E:LYS295 2.3 13.6 1.0
O E:HOH2085 2.3 11.0 1.0
O E:TYR236 2.4 15.1 1.0
OE1 E:GLN297 2.4 17.2 1.0
OE1 E:GLU235 2.6 9.1 1.0
OE2 E:GLU235 2.6 13.3 1.0
CD E:GLU235 2.9 10.1 1.0
C E:LYS295 3.5 13.7 1.0
C E:TYR236 3.6 14.8 1.0
CD E:GLN297 3.6 15.3 1.0
OH E:TYR266 4.0 12.1 1.0
N E:TYR236 4.0 13.1 1.0
NE2 E:GLN297 4.1 14.8 1.0
CA E:ALA296 4.2 13.3 1.0
N E:ALA296 4.3 13.4 1.0
N E:GLN297 4.3 13.4 1.0
CG E:GLU235 4.4 10.9 1.0
N E:TYR237 4.4 15.4 1.0
CA E:TYR236 4.5 14.3 1.0
C E:ALA296 4.5 13.3 1.0
OD2 E:ASP283 4.5 19.9 1.0
CA E:TYR237 4.5 15.5 1.0
CA E:LYS295 4.6 13.8 1.0
OD1 E:ASP283 4.6 18.5 1.0
CB E:TYR237 4.7 15.3 1.0
CB E:LYS295 4.8 13.5 1.0
CG E:GLN297 4.8 14.2 1.0
N E:LYS295 4.9 14.0 1.0
CB E:GLN297 4.9 13.5 1.0
CG E:ASP283 4.9 18.4 1.0
CZ E:TYR266 5.0 13.8 1.0

Calcium binding site 8 out of 24 in 2j7a

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Calcium binding site 8 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


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 From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1007

b:18.1
occ:1.00
 O2A E:HEC1004 2.2 21.2 1.0
O E:ALA118 2.2 15.8 1.0
OE2 E:GLU117 2.3 16.7 1.0
O1A E:HEC1003 2.3 12.6 1.0
O E:GLY78 2.4 17.9 1.0
CGA E:HEC1004 3.1 18.0 1.0
O1A E:HEC1004 3.2 20.9 1.0
CD E:GLU117 3.3 17.0 1.0
C E:ALA118 3.4 15.9 1.0
CGA E:HEC1003 3.5 13.2 1.0
C E:GLY78 3.5 18.4 1.0
CG E:GLU117 3.7 17.1 1.0
CAA E:HEC1003 3.9 13.4 1.0
N E:GLY78 4.2 19.1 1.0
O E:HOH2153 4.2 14.7 1.0
N E:ARG119 4.3 15.7 1.0
N E:ALA118 4.3 15.9 1.0
CBA E:HEC1003 4.3 12.8 1.0
CA E:ALA118 4.3 15.5 1.0
CA E:ARG119 4.3 15.6 1.0
OE1 E:GLU117 4.4 17.9 1.0
CA E:GLY78 4.4 18.7 1.0
N E:SER79 4.4 18.6 1.0
O2A E:HEC1003 4.5 15.9 1.0
CBA E:HEC1004 4.5 14.9 1.0
CA E:SER79 4.5 19.0 1.0
CB E:ALA118 4.6 15.5 1.0
CE E:LYS77 4.6 16.9 1.0
C E:GLU117 4.9 16.3 1.0
CAA E:HEC1004 5.0 13.2 1.0

Calcium binding site 9 out of 24 in 2j7a

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Calcium binding site 9 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1006

b:13.2
occ:1.00
 OE2 G:GLU235 2.3 12.1 1.0
OE1 G:GLN297 2.3 8.5 1.0
O G:LYS295 2.3 12.1 1.0
O G:TYR236 2.4 11.0 1.0
O G:HOH2080 2.4 20.3 1.0
O G:HOH2074 2.5 16.7 1.0
OE1 G:GLU235 2.6 10.0 1.0
CD G:GLU235 2.8 10.3 1.0
CD G:GLN297 3.5 10.1 1.0
C G:LYS295 3.6 11.6 1.0
C G:TYR236 3.6 9.8 1.0
OH G:TYR266 3.9 12.8 1.0
NE2 G:GLN297 4.0 10.6 1.0
N G:TYR236 4.0 9.0 1.0
CG G:GLU235 4.2 7.4 1.0
CA G:ALA296 4.2 10.5 1.0
N G:ALA296 4.3 11.3 1.0
OD2 G:ASP283 4.3 13.9 1.0
N G:GLN297 4.4 10.1 1.0
C G:ALA296 4.5 10.5 1.0
CA G:TYR236 4.5 9.8 1.0
N G:TYR237 4.6 9.4 1.0
CA G:TYR237 4.6 9.0 1.0
CA G:LYS295 4.6 11.7 1.0
CG G:GLN297 4.7 8.8 1.0
CB G:TYR237 4.8 8.3 1.0
OD1 G:ASP283 4.8 13.1 1.0
CB G:LYS295 4.8 11.2 1.0
CB G:GLN297 4.8 10.2 1.0
N G:LYS295 4.9 12.1 1.0
CZ G:TYR266 4.9 15.3 1.0
CG G:ASP283 5.0 13.4 1.0
CG2 G:ILE294 5.0 11.3 1.0
C G:GLU235 5.0 8.4 1.0

Calcium binding site 10 out of 24 in 2j7a

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Calcium binding site 10 out of 24 in the Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Cytochrome C Nitrite Reductase Nrfha Complex From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1007

b:16.4
occ:1.00
 O2A G:HEC1004 2.2 12.2 1.0
OE2 G:GLU117 2.2 16.4 1.0
O G:GLY78 2.3 14.7 1.0
O G:ALA118 2.3 11.5 1.0
O1A G:HEC1003 2.4 11.2 1.0
O G:HOH2155 2.8 28.0 1.0
CGA G:HEC1004 3.2 12.6 1.0
CD G:GLU117 3.3 16.8 1.0
O1A G:HEC1004 3.4 14.8 1.0
C G:GLY78 3.4 14.6 1.0
C G:ALA118 3.4 11.4 1.0
CGA G:HEC1003 3.6 6.6 1.0
CG G:GLU117 3.7 14.3 1.0
N G:GLY78 4.0 15.0 1.0
CAA G:HEC1003 4.1 4.9 1.0
O G:HOH2154 4.2 22.4 1.0
CA G:GLY78 4.3 14.8 1.0
CA G:ALA118 4.3 11.7 1.0
N G:ALA118 4.3 12.4 1.0
OE1 G:GLU117 4.4 18.8 1.0
N G:SER79 4.4 14.4 1.0
N G:ARG119 4.4 11.3 1.0
CE G:LYS77 4.4 13.0 1.0
CBA G:HEC1003 4.4 5.6 1.0
O2A G:HEC1003 4.4 7.6 1.0
CA G:SER79 4.5 14.4 1.0
CA G:ARG119 4.5 10.8 1.0
CB G:ALA118 4.5 11.6 1.0
CBA G:HEC1004 4.5 9.8 1.0
NZ G:LYS77 4.8 15.9 1.0
C G:GLU117 4.8 12.3 1.0
CB G:LYS77 4.9 15.4 1.0

Reference:

M.L.Rodrigues, T.F.Oliveira, I.A.C.Pereira, M.Archer. X-Ray Structure of the Membrane-Bound Cytochrome C Quinol Dehydrogenase Nrfh Reveals Novel Haem Coordination. Embo J. V. 25 5951 2006.
ISSN: ISSN 0261-4189
PubMed: 17139260
DOI: 10.1038/SJ.EMBOJ.7601439
Page generated: Fri Jul 12 13:30:30 2024

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