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Copper in PDB 5d4i: Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography

Enzymatic activity of Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography

All present enzymatic activity of Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography:
1.7.2.1;

Protein crystallography data

The structure of Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography, PDB code: 5d4i 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) 28.97 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.000, 103.000, 147.400, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.6

Copper Binding Sites:

The binding sites of Copper atom in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography (pdb code 5d4i). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography, PDB code: 5d4i:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5d4i

Go back to Copper Binding Sites List in 5d4i
Copper binding site 1 out of 6 in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography


Mono view


Stereo pair view

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

b:35.2
occ:1.00
 ND1 A:HIS145 1.9 31.9 1.0
ND1 A:HIS95 2.0 29.4 1.0
SG A:CYS136 2.2 32.4 1.0
SD A:MET150 2.6 32.0 1.0
CE1 A:HIS145 2.8 32.8 1.0
CE1 A:HIS95 3.0 29.9 1.0
CG A:HIS145 3.0 35.0 1.0
CG A:HIS95 3.1 31.0 1.0
CB A:CYS136 3.2 31.9 1.0
CE A:MET150 3.3 34.7 1.0
CB A:HIS95 3.4 33.9 1.0
CB A:HIS145 3.5 28.4 1.0
CA A:HIS95 3.8 33.1 1.0
NE2 A:HIS145 4.0 33.1 1.0
CG A:MET150 4.0 28.5 1.0
CD2 A:HIS145 4.1 30.7 1.0
NE2 A:HIS95 4.1 34.3 1.0
CD2 A:HIS95 4.2 31.5 1.0
O A:MET94 4.2 35.9 1.0
CG A:PRO138 4.4 40.0 1.0
CB A:MET150 4.4 27.2 1.0
SD A:MET62 4.4 34.1 1.0
CA A:CYS136 4.6 28.8 1.0
N A:ASN96 4.6 30.7 1.0
CD A:PRO138 4.7 31.6 1.0
CA A:HIS145 4.7 30.6 1.0
C A:HIS95 4.8 35.9 1.0
CB A:MET62 4.8 30.8 1.0
N A:HIS95 4.9 34.2 1.0
C A:MET94 4.9 33.7 1.0

Copper binding site 2 out of 6 in 5d4i

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Copper binding site 2 out of 6 in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography


Mono view


Stereo pair view

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

b:31.1
occ:1.00
 O2 A:NO2503 1.9 43.9 1.0
NE2 C:HIS306 2.0 26.4 1.0
NE2 A:HIS100 2.0 27.4 1.0
NE2 A:HIS135 2.1 30.7 1.0
O1 A:NO2503 2.1 36.4 1.0
N A:NO2503 2.3 39.4 1.0
CE1 A:HIS100 2.9 29.2 1.0
CE1 C:HIS306 3.0 27.2 1.0
CD2 C:HIS306 3.0 29.6 1.0
CD2 A:HIS135 3.0 31.7 1.0
CE1 A:HIS135 3.1 31.4 1.0
CD2 A:HIS100 3.1 28.4 1.0
OD2 A:ASP98 3.9 43.7 1.0
NE2 C:HIS255 4.0 34.1 1.0
ND1 A:HIS100 4.1 27.4 1.0
ND1 C:HIS306 4.1 27.0 1.0
CG C:HIS306 4.1 28.7 1.0
ND1 A:HIS135 4.2 29.8 1.0
CG A:HIS100 4.2 28.5 1.0
CD2 C:HIS255 4.2 36.7 1.0
CG A:HIS135 4.2 30.3 1.0
CE1 C:HIS255 4.5 38.7 1.0
CG A:ASP98 4.6 40.9 1.0
OD1 A:ASP98 4.8 38.3 1.0
CG C:HIS255 4.8 32.3 1.0
O C:HOH701 4.9 36.6 1.0
ND1 C:HIS255 4.9 35.4 1.0

Copper binding site 3 out of 6 in 5d4i

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Copper binding site 3 out of 6 in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography


Mono view


Stereo pair view

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

b:35.3
occ:1.00
 ND1 B:HIS95 2.0 33.7 1.0
ND1 B:HIS145 2.0 33.6 1.0
SG B:CYS136 2.1 32.9 1.0
SD B:MET150 2.6 32.6 1.0
CE1 B:HIS95 2.9 32.9 1.0
CE1 B:HIS145 3.0 34.4 1.0
CG B:HIS95 3.0 32.9 1.0
CG B:HIS145 3.1 32.3 1.0
CB B:CYS136 3.2 29.4 1.0
CE B:MET150 3.4 33.1 1.0
CB B:HIS95 3.4 28.6 1.0
CB B:HIS145 3.5 29.6 1.0
CA B:HIS95 3.8 30.0 1.0
CG B:MET150 4.0 28.9 1.0
NE2 B:HIS95 4.1 34.9 1.0
NE2 B:HIS145 4.1 30.8 1.0
CG B:PRO138 4.1 39.6 1.0
CD2 B:HIS95 4.2 30.1 1.0
CD2 B:HIS145 4.2 35.7 1.0
O B:MET94 4.2 38.0 1.0
CB B:MET150 4.4 30.1 1.0
SD B:MET62 4.4 34.1 1.0
CA B:CYS136 4.6 30.6 1.0
N B:ASN96 4.6 29.9 1.0
CD B:PRO138 4.7 33.2 1.0
CA B:HIS145 4.7 29.2 1.0
C B:HIS95 4.8 36.9 1.0
N B:HIS95 4.9 34.8 1.0
CB B:MET62 4.9 26.7 1.0
C B:MET94 4.9 38.2 1.0
O B:ASN96 5.0 33.8 1.0

Copper binding site 4 out of 6 in 5d4i

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Copper binding site 4 out of 6 in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography


Mono view


Stereo pair view

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

b:32.2
occ:1.00
 NE2 A:HIS306 2.0 28.4 1.0
O2 A:NO2504 2.0 47.6 1.0
NE2 B:HIS100 2.0 27.6 1.0
NE2 B:HIS135 2.1 30.6 1.0
O1 A:NO2504 2.2 37.7 1.0
N A:NO2504 2.3 44.4 1.0
CE1 B:HIS100 2.9 29.2 1.0
CE1 A:HIS306 3.0 29.0 1.0
CD2 A:HIS306 3.0 29.1 1.0
CD2 B:HIS135 3.1 29.4 1.0
CD2 B:HIS100 3.1 30.8 1.0
CE1 B:HIS135 3.1 28.9 1.0
NE2 A:HIS255 3.9 37.7 1.0
OD2 B:ASP98 3.9 44.3 1.0
CD2 A:HIS255 4.1 34.6 1.0
ND1 A:HIS306 4.1 28.2 1.0
ND1 B:HIS100 4.1 29.0 1.0
CG A:HIS306 4.2 26.4 1.0
CG B:HIS100 4.2 29.5 1.0
CG B:HIS135 4.2 24.6 1.0
ND1 B:HIS135 4.2 29.8 1.0
CG B:ASP98 4.5 36.4 1.0
CE1 A:HIS255 4.5 35.5 1.0
CG A:HIS255 4.7 31.4 1.0
OD1 B:ASP98 4.7 35.7 1.0
O A:HOH673 4.8 35.6 1.0
ND1 A:HIS255 4.9 37.1 1.0
CD2 A:LEU308 5.0 31.3 1.0

Copper binding site 5 out of 6 in 5d4i

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Copper binding site 5 out of 6 in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography


Mono view


Stereo pair view

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

b:26.6
occ:1.00
 ND1 C:HIS145 2.0 26.6 1.0
ND1 C:HIS95 2.0 23.9 1.0
SG C:CYS136 2.2 25.0 1.0
SD C:MET150 2.5 25.6 1.0
CE1 C:HIS145 2.9 24.4 1.0
CE1 C:HIS95 2.9 26.0 1.0
CG C:HIS145 3.0 26.2 1.0
CG C:HIS95 3.1 25.3 1.0
CB C:CYS136 3.2 25.4 1.0
CE C:MET150 3.3 26.9 1.0
CB C:HIS145 3.4 22.1 1.0
CB C:HIS95 3.5 24.0 1.0
CA C:HIS95 3.8 25.2 1.0
CG C:MET150 4.0 24.6 1.0
NE2 C:HIS145 4.0 25.2 1.0
NE2 C:HIS95 4.1 26.5 1.0
CD2 C:HIS145 4.1 27.2 1.0
CD2 C:HIS95 4.1 27.3 1.0
O C:MET94 4.3 28.4 1.0
CB C:MET150 4.3 23.8 1.0
CG C:PRO138 4.4 27.6 1.0
SD C:MET62 4.4 29.0 1.0
N C:ASN96 4.6 24.1 1.0
CA C:CYS136 4.6 22.5 1.0
CD C:PRO138 4.7 23.6 1.0
CA C:HIS145 4.7 22.8 1.0
C C:HIS95 4.8 26.4 1.0
CB C:MET62 4.9 26.1 1.0
N C:HIS95 4.9 24.3 1.0

Copper binding site 6 out of 6 in 5d4i

Go back to Copper Binding Sites List in 5d4i
Copper binding site 6 out of 6 in the Intact Nitrite Complex of A Copper Nitrite Reductase Determined By Serial Femtosecond Crystallography


Mono view


Stereo pair view

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

b:25.9
occ:1.00
 NE2 C:HIS100 2.0 21.9 1.0
NE2 B:HIS306 2.0 22.9 1.0
NE2 C:HIS135 2.0 24.4 1.0
O2 C:NO2503 2.1 37.7 1.0
O1 C:NO2503 2.1 31.4 1.0
N C:NO2503 2.3 42.3 1.0
CE1 C:HIS100 2.9 21.8 1.0
CE1 B:HIS306 3.0 22.5 1.0
CD2 C:HIS135 3.0 23.1 1.0
CD2 B:HIS306 3.0 24.6 1.0
CD2 C:HIS100 3.1 24.3 1.0
CE1 C:HIS135 3.1 23.6 1.0
OD2 C:ASP98 3.9 36.8 1.0
NE2 B:HIS255 4.1 30.5 1.0
ND1 C:HIS100 4.1 22.6 1.0
ND1 B:HIS306 4.1 22.6 1.0
CG B:HIS306 4.1 21.9 1.0
CG C:HIS100 4.1 22.1 1.0
CG C:HIS135 4.2 21.6 1.0
ND1 C:HIS135 4.2 21.0 1.0
CD2 B:HIS255 4.3 27.7 1.0
CE1 B:HIS255 4.5 30.0 1.0
CG C:ASP98 4.5 31.9 1.0
OD1 C:ASP98 4.7 29.3 1.0
O B:HOH682 4.8 29.5 1.0
CG B:HIS255 4.8 25.7 1.0
ND1 B:HIS255 4.9 29.4 1.0
CD2 B:LEU308 4.9 26.2 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 04:00:53 2024

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