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Copper in PDB 5d4h: High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography

Enzymatic activity of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography

All present enzymatic activity of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography:
1.7.2.1;

Protein crystallography data

The structure of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography, PDB code: 5d4h was solved by Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, T.Masuda, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, M.E.P.Murphy, T.Inoue, S.Iwata, E.Mizohata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.51 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.419, 102.174, 145.791, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 16.5

Copper Binding Sites:

The binding sites of Copper atom in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography (pdb code 5d4h). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography, PDB code: 5d4h:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5d4h

Go back to Copper Binding Sites List in 5d4h
Copper binding site 1 out of 6 in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:16.1
occ:1.00
 ND1 A:HIS95 2.1 15.1 1.0
ND1 A:HIS145 2.1 14.6 1.0
SG A:CYS136 2.2 15.9 1.0
SD A:MET150 2.5 14.9 1.0
CE1 A:HIS145 3.0 15.0 1.0
CE1 A:HIS95 3.0 15.5 1.0
CG A:HIS95 3.1 16.4 1.0
CG A:HIS145 3.2 13.8 1.0
CB A:CYS136 3.2 14.2 1.0
CE A:MET150 3.3 16.1 1.0
CB A:HIS95 3.5 14.7 1.0
CB A:HIS145 3.5 13.9 1.0
CA A:HIS95 3.8 15.1 1.0
CG A:MET150 3.9 14.2 1.0
NE2 A:HIS145 4.2 16.0 1.0
NE2 A:HIS95 4.2 15.8 1.0
CG A:PRO138 4.2 17.6 1.0
CD2 A:HIS95 4.2 16.7 1.0
CD2 A:HIS145 4.2 14.9 1.0
O A:MET94 4.3 16.8 1.0
CB A:MET150 4.3 14.5 1.0
SD A:MET62 4.4 16.5 1.0
CA A:CYS136 4.6 13.0 1.0
CD A:PRO138 4.6 15.3 1.0
N A:ASN96 4.7 15.3 1.0
CB A:MET62 4.7 15.9 1.0
CA A:HIS145 4.8 14.6 1.0
C A:HIS95 4.8 14.9 1.0
N A:HIS95 4.9 15.9 1.0

Copper binding site 2 out of 6 in 5d4h

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Copper binding site 2 out of 6 in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:13.2
occ:0.95
 O2 A:NO2503 2.0 27.9 0.9
NE2 A:HIS135 2.0 11.9 1.0
NE2 A:HIS100 2.0 12.3 1.0
NE2 C:HIS306 2.0 12.5 1.0
N A:NO2503 2.1 26.6 0.9
O1 A:NO2503 2.2 23.6 0.9
CE1 A:HIS100 2.9 12.8 1.0
CE1 C:HIS306 3.0 12.5 1.0
CD2 A:HIS135 3.0 12.8 1.0
CE1 A:HIS135 3.1 13.6 1.0
CD2 A:HIS100 3.1 12.8 1.0
CD2 C:HIS306 3.1 12.7 1.0
OD2 A:ASP98 3.6 22.8 1.0
NE2 C:HIS255 4.1 16.9 1.0
ND1 A:HIS100 4.1 11.7 1.0
ND1 C:HIS306 4.1 11.2 1.0
ND1 A:HIS135 4.2 13.2 1.0
CG A:HIS135 4.2 12.2 1.0
CG A:HIS100 4.2 11.9 1.0
O A:HOH603 4.2 34.0 1.0
CG C:HIS306 4.2 10.7 1.0
CE1 C:HIS255 4.3 16.6 1.0
CG A:ASP98 4.3 19.8 1.0
CD2 C:HIS255 4.4 19.1 1.0
ND1 C:HIS255 4.7 16.4 1.0
OD1 A:ASP98 4.8 18.2 1.0
CG C:HIS255 4.9 13.3 1.0
CD2 C:LEU308 4.9 15.8 1.0
O C:HOH780 5.0 19.8 1.0

Copper binding site 3 out of 6 in 5d4h

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Copper binding site 3 out of 6 in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:13.8
occ:0.95
 ND1 B:HIS95 2.0 13.7 1.0
ND1 B:HIS145 2.0 12.5 1.0
SG B:CYS136 2.2 14.6 1.0
SD B:MET150 2.5 13.9 1.0
CE1 B:HIS145 2.9 13.2 1.0
CE1 B:HIS95 3.0 15.2 1.0
CG B:HIS95 3.1 14.1 1.0
CG B:HIS145 3.1 13.0 1.0
CB B:CYS136 3.2 14.0 1.0
CE B:MET150 3.3 13.1 1.0
CB B:HIS95 3.4 14.4 1.0
CB B:HIS145 3.5 13.5 1.0
CA B:HIS95 3.8 13.6 1.0
CG B:MET150 3.9 13.1 1.0
NE2 B:HIS145 4.1 14.6 1.0
NE2 B:HIS95 4.1 14.2 1.0
CG B:PRO138 4.2 16.8 1.0
CD2 B:HIS145 4.2 13.4 1.0
CD2 B:HIS95 4.2 13.4 1.0
O B:MET94 4.2 16.1 1.0
SD B:MET62 4.4 16.0 1.0
CB B:MET150 4.4 12.9 1.0
CD B:PRO138 4.6 14.7 1.0
CA B:CYS136 4.6 12.8 1.0
N B:ASN96 4.7 13.7 1.0
CA B:HIS145 4.8 13.5 1.0
C B:HIS95 4.8 13.8 1.0
CB B:MET62 4.8 14.5 1.0
N B:HIS95 4.8 13.6 1.0
C B:MET94 5.0 15.3 1.0

Copper binding site 4 out of 6 in 5d4h

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Copper binding site 4 out of 6 in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:12.8
occ:0.95
 NE2 B:HIS100 2.0 11.7 1.0
NE2 A:HIS306 2.0 11.9 1.0
NE2 B:HIS135 2.0 11.5 1.0
O2 A:NO2504 2.1 19.5 0.5
O A:HOH710 2.1 28.0 0.5
N A:NO2504 2.2 21.0 0.5
O1 A:NO2504 2.2 21.6 0.5
CE1 B:HIS100 3.0 11.3 1.0
CE1 A:HIS306 3.0 10.7 1.0
CD2 B:HIS135 3.0 12.6 1.0
CD2 B:HIS100 3.0 11.7 1.0
CE1 B:HIS135 3.1 11.9 1.0
CD2 A:HIS306 3.1 11.7 1.0
OD2 B:ASP98 3.6 23.1 1.0
ND1 B:HIS100 4.1 10.8 1.0
NE2 A:HIS255 4.1 18.4 1.0
ND1 A:HIS306 4.2 11.2 1.0
CG B:HIS135 4.2 11.6 1.0
CG B:HIS100 4.2 11.2 1.0
ND1 B:HIS135 4.2 12.6 1.0
CG A:HIS306 4.2 10.4 1.0
O B:HOH606 4.3 31.3 1.0
CE1 A:HIS255 4.3 18.8 1.0
CG B:ASP98 4.4 15.6 1.0
CD2 A:HIS255 4.4 20.1 1.0
OD1 B:ASP98 4.8 17.2 1.0
ND1 A:HIS255 4.8 17.2 1.0
CD2 A:LEU308 4.8 15.9 1.0
CG A:HIS255 4.9 13.9 1.0
O A:HOH807 4.9 17.4 1.0
CD1 A:LEU308 5.0 15.2 1.0

Copper binding site 5 out of 6 in 5d4h

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Copper binding site 5 out of 6 in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:11.5
occ:0.95
 ND1 C:HIS145 2.0 11.6 1.0
ND1 C:HIS95 2.0 11.2 1.0
SG C:CYS136 2.2 12.4 1.0
SD C:MET150 2.5 11.6 1.0
CE1 C:HIS145 2.9 12.0 1.0
CE1 C:HIS95 3.0 11.1 1.0
CG C:HIS95 3.1 11.2 1.0
CG C:HIS145 3.1 11.8 1.0
CB C:CYS136 3.2 11.4 1.0
CE C:MET150 3.3 12.5 1.0
CB C:HIS95 3.4 11.9 1.0
CB C:HIS145 3.6 11.4 1.0
CA C:HIS95 3.8 11.4 1.0
CG C:MET150 3.9 11.9 1.0
NE2 C:HIS145 4.1 12.4 1.0
NE2 C:HIS95 4.2 12.5 1.0
CD2 C:HIS145 4.2 12.7 1.0
CD2 C:HIS95 4.2 11.8 1.0
CG C:PRO138 4.2 13.8 1.0
O C:MET94 4.3 13.7 1.0
CB C:MET150 4.3 11.9 1.0
SD C:MET62 4.4 13.8 1.0
CA C:CYS136 4.6 10.2 1.0
CD C:PRO138 4.6 11.1 1.0
N C:ASN96 4.7 11.8 1.0
CB C:MET62 4.7 12.7 1.0
CA C:HIS145 4.8 11.6 1.0
C C:HIS95 4.8 11.7 1.0
N C:HIS95 4.8 12.0 1.0
C C:MET94 5.0 11.8 1.0

Copper binding site 6 out of 6 in 5d4h

Go back to Copper Binding Sites List in 5d4h
Copper binding site 6 out of 6 in the High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of High-Resolution Nitrite Complex of A Copper Nitrite Reductase Determined By Synchrotron Radiation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:12.0
occ:1.00
 NE2 B:HIS306 2.0 10.4 1.0
NE2 C:HIS100 2.0 11.0 1.0
NE2 C:HIS135 2.0 11.5 1.0
O2 B:NO2503 2.1 19.6 0.5
O B:HOH706 2.2 24.1 0.5
O1 B:NO2503 2.2 19.6 0.5
N B:NO2503 2.2 20.4 0.5
CE1 C:HIS100 3.0 11.6 1.0
CE1 B:HIS306 3.0 10.7 1.0
CD2 C:HIS135 3.0 10.6 1.0
CE1 C:HIS135 3.1 12.1 1.0
CD2 C:HIS100 3.1 10.0 1.0
CD2 B:HIS306 3.1 10.9 1.0
OD2 C:ASP98 3.6 20.7 1.0
NE2 B:HIS255 4.0 16.9 1.0
ND1 C:HIS100 4.1 11.3 1.0
ND1 B:HIS306 4.2 10.2 1.0
ND1 C:HIS135 4.2 11.7 1.0
CG C:HIS135 4.2 11.0 1.0
CG C:HIS100 4.2 10.2 1.0
CG B:HIS306 4.2 10.3 1.0
CE1 B:HIS255 4.3 17.3 1.0
O C:HOH609 4.3 32.1 1.0
CG C:ASP98 4.4 13.6 1.0
CD2 B:HIS255 4.4 17.5 1.0
ND1 B:HIS255 4.7 15.3 1.0
OD1 C:ASP98 4.7 15.4 1.0
CG B:HIS255 4.8 11.6 1.0
O B:HOH819 4.9 16.6 1.0
CD2 B:LEU308 5.0 14.4 1.0

Reference:

Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, T.Masuda, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, M.E.Murphy, T.Inoue, S.Iwata, E.Mizohata. Redox-Coupled Proton Transfer Mechanism in Nitrite Reductase Revealed By Femtosecond Crystallography Proc.Natl.Acad.Sci.Usa V. 113 2928 2016.
ISSN: ESSN 1091-6490
PubMed: 26929369
DOI: 10.1073/PNAS.1517770113
Page generated: Mon Jul 14 04:29:35 2025

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