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Copper in PDB 5d4j: Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals

Enzymatic activity of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals

All present enzymatic activity of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals:
1.7.2.1;

Protein crystallography data

The structure of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals, PDB code: 5d4j was solved by Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, 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) 24.79 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.395, 102.207, 144.506, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.2

Other elements in 5d4j:

The structure of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals (pdb code 5d4j). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals, PDB code: 5d4j:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 1 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:30.5
occ:1.00
 ND1 A:HIS145 2.0 23.4 1.0
SG A:CYS136 2.1 28.8 1.0
ND1 A:HIS95 2.3 40.4 1.0
SD A:MET150 2.4 32.7 1.0
CE1 A:HIS145 2.9 25.9 1.0
CG A:HIS145 3.1 25.0 1.0
CB A:CYS136 3.1 26.1 1.0
CE A:MET150 3.2 26.9 1.0
CG A:HIS95 3.3 38.1 1.0
CE1 A:HIS95 3.3 39.2 1.0
CB A:HIS95 3.5 33.9 1.0
CB A:HIS145 3.5 22.2 1.0
CA A:HIS95 3.8 35.0 1.0
CG A:MET150 3.9 32.1 1.0
NE2 A:HIS145 4.0 25.1 1.0
CD2 A:HIS145 4.1 25.4 1.0
CG A:PRO138 4.1 29.0 1.0
O A:MET94 4.3 34.7 1.0
CB A:MET150 4.4 29.1 1.0
CD2 A:HIS95 4.4 40.5 1.0
NE2 A:HIS95 4.4 37.9 1.0
N A:ASN96 4.5 30.7 1.0
SD A:MET62 4.5 34.5 1.0
CA A:CYS136 4.5 28.6 1.0
CD A:PRO138 4.6 27.4 1.0
C A:HIS95 4.7 31.8 1.0
CA A:HIS145 4.8 25.2 1.0
CB A:MET62 4.8 28.9 1.0
N A:HIS95 4.9 35.2 1.0

Copper binding site 2 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 2 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:31.0
occ:1.00
 NE2 A:HIS135 2.1 26.0 1.0
NE2 A:HIS100 2.1 23.5 1.0
NE2 C:HIS306 2.1 26.4 1.0
CL C:CL601 2.3 53.2 1.0
CD2 A:HIS135 2.9 27.0 1.0
CE1 A:HIS100 2.9 24.6 1.0
CE1 C:HIS306 3.0 26.7 1.0
CD2 C:HIS306 3.2 25.7 1.0
CE1 A:HIS135 3.2 26.5 1.0
CD2 A:HIS100 3.2 25.8 1.0
OD2 A:ASP98 3.9 44.2 1.0
NE2 C:HIS255 4.1 31.7 1.0
CG A:HIS135 4.1 25.8 1.0
ND1 A:HIS100 4.1 25.4 1.0
ND1 C:HIS306 4.2 26.6 1.0
ND1 A:HIS135 4.2 28.4 1.0
CG A:HIS100 4.3 27.5 1.0
CG C:HIS306 4.3 26.4 1.0
CE1 C:HIS255 4.3 34.5 1.0
CG A:ASP98 4.3 35.3 1.0
CD2 C:HIS255 4.4 35.8 1.0
OD1 A:ASP98 4.6 29.6 1.0
ND1 C:HIS255 4.7 31.4 1.0
CD2 C:LEU308 4.8 23.5 1.0
CG C:HIS255 4.8 34.3 1.0

Copper binding site 3 out of 6 in 5d4j

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Copper binding site 3 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:32.1
occ:1.00
 ND1 B:HIS145 2.1 28.8 1.0
SG B:CYS136 2.1 31.7 1.0
ND1 B:HIS95 2.2 28.7 1.0
SD B:MET150 2.4 31.5 1.0
CE1 B:HIS145 2.9 30.5 1.0
CG B:HIS145 3.1 29.3 1.0
CG B:HIS95 3.2 29.8 1.0
CE1 B:HIS95 3.2 28.3 1.0
CB B:CYS136 3.2 31.2 1.0
CE B:MET150 3.2 27.1 1.0
CB B:HIS95 3.4 29.8 1.0
CB B:HIS145 3.6 26.9 1.0
CA B:HIS95 3.8 29.7 1.0
CG B:MET150 3.8 28.1 1.0
NE2 B:HIS145 4.0 27.2 1.0
CD2 B:HIS145 4.1 28.2 1.0
CG B:PRO138 4.2 31.4 1.0
O B:MET94 4.2 34.4 1.0
NE2 B:HIS95 4.3 29.0 1.0
CD2 B:HIS95 4.3 28.3 1.0
CB B:MET150 4.4 26.2 1.0
SD B:MET62 4.4 30.8 1.0
CD B:PRO138 4.5 27.8 1.0
CA B:CYS136 4.6 29.4 1.0
N B:ASN96 4.7 32.2 1.0
N B:HIS95 4.7 31.5 1.0
C B:HIS95 4.8 36.2 1.0
CA B:HIS145 4.8 27.0 1.0
CB B:MET62 4.9 31.0 1.0
C B:MET94 4.9 32.4 1.0

Copper binding site 4 out of 6 in 5d4j

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Copper binding site 4 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:30.2
occ:1.00
 NE2 B:HIS100 2.0 22.3 1.0
NE2 A:HIS306 2.1 30.9 1.0
NE2 B:HIS135 2.1 30.1 1.0
CL A:CL503 2.3 63.3 1.0
CE1 B:HIS100 2.9 23.0 1.0
CE1 A:HIS306 2.9 30.6 1.0
CD2 B:HIS135 2.9 27.2 1.0
CD2 B:HIS100 3.1 24.7 1.0
CD2 A:HIS306 3.2 30.8 1.0
CE1 B:HIS135 3.2 28.9 1.0
OD2 B:ASP98 3.8 41.4 1.0
ND1 B:HIS100 4.0 21.4 1.0
ND1 A:HIS306 4.1 31.2 1.0
CG B:HIS135 4.1 28.3 1.0
NE2 A:HIS255 4.2 29.9 1.0
CG B:HIS100 4.2 23.9 1.0
ND1 B:HIS135 4.3 26.0 1.0
CG A:HIS306 4.3 29.9 1.0
CG B:ASP98 4.4 35.2 1.0
CE1 A:HIS255 4.4 30.9 1.0
CD2 A:HIS255 4.5 30.0 1.0
OD1 B:ASP98 4.7 33.9 1.0
O A:HOH664 4.8 29.6 1.0
CD2 A:LEU308 4.8 24.9 1.0
ND1 A:HIS255 4.9 29.9 1.0
CG A:HIS255 5.0 31.6 1.0

Copper binding site 5 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 5 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu602

b:29.2
occ:1.00
 ND1 C:HIS145 2.1 27.8 1.0
ND1 C:HIS95 2.1 26.8 1.0
SG C:CYS136 2.3 24.9 1.0
SD C:MET150 2.5 30.1 1.0
CE1 C:HIS145 2.9 26.4 1.0
CG C:HIS95 3.0 25.4 1.0
CE1 C:HIS95 3.1 26.2 1.0
CG C:HIS145 3.2 28.1 1.0
CB C:CYS136 3.2 26.3 1.0
CB C:HIS95 3.3 24.3 1.0
CE C:MET150 3.3 27.1 1.0
CB C:HIS145 3.6 25.7 1.0
CA C:HIS95 3.8 27.1 1.0
CG C:MET150 3.9 24.1 1.0
NE2 C:HIS145 4.1 27.3 1.0
CD2 C:HIS95 4.2 25.6 1.0
O C:MET94 4.2 29.8 1.0
CD2 C:HIS145 4.2 26.8 1.0
NE2 C:HIS95 4.2 27.9 1.0
CG C:PRO138 4.4 24.5 1.0
CB C:MET150 4.4 25.2 1.0
SD C:MET62 4.4 33.2 1.0
CD C:PRO138 4.6 24.4 1.0
N C:ASN96 4.7 26.4 1.0
CA C:CYS136 4.7 28.3 1.0
CA C:HIS145 4.8 27.2 1.0
N C:HIS95 4.8 28.9 1.0
C C:HIS95 4.8 25.5 1.0
CB C:MET62 4.9 28.5 1.0
C C:MET94 4.9 30.6 1.0

Copper binding site 6 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 6 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu603

b:27.8
occ:1.00
 NE2 C:HIS100 2.0 28.5 1.0
NE2 B:HIS306 2.1 24.5 1.0
NE2 C:HIS135 2.1 24.4 1.0
CL B:CL503 2.2 49.2 1.0
CE1 C:HIS100 2.9 25.7 1.0
CE1 B:HIS306 3.0 24.6 1.0
CD2 C:HIS135 3.0 24.7 1.0
CD2 B:HIS306 3.1 28.0 1.0
CE1 C:HIS135 3.1 27.1 1.0
CD2 C:HIS100 3.2 27.3 1.0
OD2 C:ASP98 3.7 32.1 1.0
ND1 C:HIS100 4.0 24.8 1.0
ND1 B:HIS306 4.1 24.1 1.0
NE2 B:HIS255 4.2 28.4 1.0
CG C:HIS135 4.2 26.4 1.0
ND1 C:HIS135 4.2 26.8 1.0
CG B:HIS306 4.2 23.4 1.0
CG C:HIS100 4.2 26.1 1.0
CG C:ASP98 4.4 30.1 1.0
CE1 B:HIS255 4.4 27.4 1.0
CD2 B:HIS255 4.5 28.7 1.0
OD1 C:ASP98 4.7 29.2 1.0
ND1 B:HIS255 4.8 28.4 1.0
CD2 B:LEU308 4.8 22.5 1.0
O C:HOH808 4.9 27.9 1.0
CG B:HIS255 4.9 29.6 1.0
CD1 B:LEU308 5.0 21.1 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 04:29:57 2025

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