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Copper in PDB 4yse: High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis

Enzymatic activity of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis

All present enzymatic activity of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis:
1.7.2.1;

Protein crystallography data

The structure of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis, PDB code: 4yse was solved by Y.Fukuda, K.M.Tse, M.Suzuki, K.Diederichs, K.Hirata, T.Nakane, M.Sugahara, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, H.Matsumura, 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) 49.65 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.871, 101.149, 146.238, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 16.8

Copper Binding Sites:

The binding sites of Copper atom in the High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis (pdb code 4yse). 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 Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis, PDB code: 4yse:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4yse

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Copper binding site 1 out of 6 in the High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:13.1
occ:0.95
 ND1 A:HIS145 2.0 12.3 1.0
ND1 A:HIS95 2.1 12.1 1.0
SG A:CYS136 2.2 13.5 1.0
SD A:MET150 2.5 12.8 1.0
CE1 A:HIS145 2.9 12.3 1.0
CE1 A:HIS95 3.0 12.8 1.0
CG A:HIS145 3.1 12.4 1.0
CG A:HIS95 3.1 12.3 1.0
CB A:CYS136 3.2 12.6 1.0
CE A:MET150 3.3 15.0 1.0
CB A:HIS95 3.5 13.1 1.0
CB A:HIS145 3.5 13.4 1.0
CA A:HIS95 3.8 13.2 1.0
CG A:MET150 3.9 12.6 1.0
NE2 A:HIS145 4.1 14.3 1.0
NE2 A:HIS95 4.2 14.3 1.0
CG A:PRO138 4.2 15.6 1.0
O A:MET94 4.2 14.5 0.3
CD2 A:HIS145 4.2 13.0 1.0
CD2 A:HIS95 4.3 13.0 1.0
O A:MET94 4.3 14.8 0.7
CB A:MET150 4.4 12.2 1.0
SD A:MET62 4.5 14.4 1.0
CA A:CYS136 4.6 11.7 1.0
CD A:PRO138 4.6 13.0 1.0
N A:ASN96 4.7 13.0 1.0
CB A:MET62 4.8 13.0 1.0
C A:HIS95 4.8 13.1 1.0
N A:HIS95 4.8 12.6 1.0
CA A:HIS145 4.8 12.5 1.0
C A:MET94 4.9 13.5 0.3
C A:MET94 5.0 12.8 0.7

Copper binding site 2 out of 6 in 4yse

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Copper binding site 2 out of 6 in the High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:11.9
occ:0.95
 NE2 A:HIS100 2.0 12.6 1.0
NE2 A:HIS135 2.0 11.6 1.0
NE2 C:HIS306 2.0 11.3 1.0
O C:HOH842 2.3 15.8 0.5
O A:HOH505 2.3 12.2 1.0
CE1 A:HIS100 2.9 11.7 1.0
CD2 A:HIS135 3.0 12.3 1.0
CE1 C:HIS306 3.0 12.0 1.0
CE1 A:HIS135 3.0 11.6 1.0
CD2 A:HIS100 3.1 11.5 1.0
CD2 C:HIS306 3.1 12.1 1.0
OD2 A:ASP98 3.6 15.6 0.3
O C:HOH842 3.6 16.5 0.3
OD2 A:ASP98 3.8 14.2 0.7
ND1 A:HIS100 4.1 11.7 1.0
O A:HOH540 4.1 16.6 0.3
NE2 C:HIS255 4.1 13.3 1.0
CG A:HIS135 4.1 11.4 1.0
ND1 A:HIS135 4.1 12.0 1.0
ND1 C:HIS306 4.1 11.4 1.0
CG A:HIS100 4.2 11.9 1.0
CG C:HIS306 4.2 11.0 1.0
CE1 C:HIS255 4.4 14.6 1.0
CG A:ASP98 4.4 11.6 0.7
CG A:ASP98 4.4 13.5 0.3
CD2 C:HIS255 4.4 15.1 1.0
OD1 A:ASP98 4.6 13.7 0.7
ND1 C:HIS255 4.8 15.0 1.0
CG C:HIS255 4.8 11.6 1.0
CD2 C:LEU308 4.9 13.9 1.0
CD1 C:LEU308 5.0 14.8 1.0
O A:HOH692 5.0 14.6 1.0

Copper binding site 3 out of 6 in 4yse

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Copper binding site 3 out of 6 in the High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:13.4
occ:1.00
 NE2 A:HIS306 2.0 11.8 1.0
NE2 B:HIS100 2.0 12.3 1.0
NE2 B:HIS135 2.0 12.4 1.0
O B:HOH509 2.3 12.4 1.0
O A:HOH718 2.3 18.8 0.7
CE1 B:HIS100 2.9 12.8 1.0
CE1 A:HIS306 2.9 12.1 1.0
CD2 B:HIS135 3.0 12.5 1.0
CD2 A:HIS306 3.1 12.0 1.0
CE1 B:HIS135 3.1 12.4 1.0
CD2 B:HIS100 3.1 11.6 1.0
OD2 B:ASP98 3.5 16.7 0.3
O A:HOH718 3.6 18.3 0.3
OD2 B:ASP98 3.9 15.5 0.7
ND1 B:HIS100 4.1 12.1 1.0
O B:HOH505 4.1 17.1 0.3
NE2 A:HIS255 4.1 15.5 1.0
ND1 A:HIS306 4.1 12.2 1.0
CG B:HIS135 4.2 11.4 1.0
ND1 B:HIS135 4.2 12.2 1.0
CG B:HIS100 4.2 11.3 1.0
CG A:HIS306 4.2 11.3 1.0
CE1 A:HIS255 4.4 16.0 1.0
CG B:ASP98 4.4 10.2 0.3
CD2 A:HIS255 4.4 15.9 1.0
CG B:ASP98 4.4 13.5 0.7
OD1 B:ASP98 4.6 13.3 0.7
ND1 A:HIS255 4.8 15.4 1.0
CG A:HIS255 4.9 12.6 1.0
O A:HOH691 4.9 14.8 1.0
CD2 A:LEU308 4.9 15.8 1.0
CD1 A:LEU308 5.0 15.6 1.0

Copper binding site 4 out of 6 in 4yse

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Copper binding site 4 out of 6 in the High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:12.9
occ:0.95
 ND1 B:HIS145 2.0 13.7 1.0
ND1 B:HIS95 2.0 12.9 1.0
SG B:CYS136 2.2 13.5 1.0
SD B:MET150 2.5 13.1 1.0
CE1 B:HIS145 2.9 12.7 1.0
CE1 B:HIS95 3.0 13.1 1.0
CG B:HIS145 3.1 12.8 1.0
CG B:HIS95 3.1 11.9 1.0
CB B:CYS136 3.2 13.3 1.0
CE B:MET150 3.3 14.0 1.0
CB B:HIS95 3.5 13.8 1.0
CB B:HIS145 3.6 12.5 1.0
CA B:HIS95 3.8 13.3 1.0
CG B:MET150 3.9 12.2 1.0
NE2 B:HIS145 4.1 12.8 1.0
NE2 B:HIS95 4.1 12.5 1.0
CD2 B:HIS145 4.2 13.1 1.0
CG B:PRO138 4.2 16.4 1.0
O B:MET94 4.2 14.9 0.3
CD2 B:HIS95 4.2 12.4 1.0
O B:MET94 4.3 15.0 0.7
SD B:MET62 4.3 15.1 1.0
CB B:MET150 4.4 11.5 1.0
CA B:CYS136 4.6 11.9 1.0
CD B:PRO138 4.6 15.5 1.0
N B:ASN96 4.7 12.9 1.0
C B:HIS95 4.8 14.3 1.0
CA B:HIS145 4.8 11.8 1.0
N B:HIS95 4.8 14.4 1.0
CB B:MET62 4.9 13.0 1.0
C B:MET94 4.9 14.0 0.3
C B:MET94 5.0 12.7 0.7

Copper binding site 5 out of 6 in 4yse

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Copper binding site 5 out of 6 in the High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu405

b:10.8
occ:1.00
 NE2 C:HIS135 2.0 10.5 1.0
NE2 B:HIS306 2.0 10.1 1.0
NE2 C:HIS100 2.0 9.9 1.0
O B:HOH746 2.2 13.2 0.5
O C:HOH602 2.3 9.8 1.0
CE1 C:HIS100 3.0 10.9 1.0
CE1 B:HIS306 3.0 10.2 1.0
CD2 C:HIS135 3.0 10.4 1.0
CE1 C:HIS135 3.0 9.7 1.0
CD2 C:HIS100 3.1 10.1 1.0
CD2 B:HIS306 3.1 10.4 1.0
OD2 C:ASP98 3.5 12.8 0.3
O B:HOH746 3.5 11.4 0.2
OD2 C:ASP98 3.8 12.2 0.7
O C:HOH612 4.1 14.5 0.3
ND1 B:HIS306 4.1 9.8 1.0
ND1 C:HIS100 4.1 10.1 1.0
CG C:HIS135 4.1 9.7 1.0
NE2 B:HIS255 4.1 13.0 1.0
ND1 C:HIS135 4.1 10.3 1.0
CG C:HIS100 4.2 9.3 1.0
CG B:HIS306 4.2 9.5 1.0
CE1 B:HIS255 4.3 13.5 1.0
CG C:ASP98 4.3 11.1 0.3
CG C:ASP98 4.4 11.7 0.7
CD2 B:HIS255 4.5 12.6 1.0
OD1 C:ASP98 4.6 12.3 0.7
ND1 B:HIS255 4.7 13.4 1.0
CG B:HIS255 4.9 10.1 1.0
CD2 B:LEU308 4.9 13.3 1.0
OD1 C:ASP98 4.9 12.9 0.3
O B:HOH709 4.9 12.6 1.0
CD1 B:LEU308 5.0 14.5 1.0

Copper binding site 6 out of 6 in 4yse

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Copper binding site 6 out of 6 in the High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of High Resolution Synchrotron Structure of Copper Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:11.2
occ:1.00
 ND1 C:HIS145 2.0 10.8 1.0
ND1 C:HIS95 2.1 10.3 1.0
SG C:CYS136 2.2 11.4 1.0
SD C:MET150 2.5 11.2 1.0
CE1 C:HIS145 2.9 10.9 1.0
CE1 C:HIS95 3.0 10.3 1.0
CG C:HIS145 3.1 10.7 1.0
CG C:HIS95 3.1 10.5 1.0
CB C:CYS136 3.2 10.2 1.0
CE C:MET150 3.2 12.5 1.0
CB C:HIS95 3.5 11.3 1.0
CB C:HIS145 3.5 11.2 1.0
CA C:HIS95 3.8 10.9 1.0
CG C:MET150 3.9 11.2 1.0
NE2 C:HIS145 4.1 10.8 1.0
NE2 C:HIS95 4.2 11.3 1.0
CD2 C:HIS145 4.2 11.5 1.0
CD2 C:HIS95 4.2 11.9 1.0
CG C:PRO138 4.3 12.6 1.0
CB C:MET150 4.3 9.8 1.0
O C:MET94 4.3 12.1 1.0
SD C:MET62 4.4 10.9 0.8
CA C:CYS136 4.6 9.7 1.0
CD C:PRO138 4.6 12.4 1.0
N C:ASN96 4.7 10.4 1.0
CA C:HIS145 4.8 10.2 1.0
CB C:MET62 4.8 11.0 0.8
CB C:MET62 4.8 12.9 0.2
C C:HIS95 4.8 10.6 1.0
N C:HIS95 4.9 11.5 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: Wed Jul 31 03:36:56 2024

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