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Copper in PDB 1npj: Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis

Enzymatic activity of Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis

All present enzymatic activity of Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis:
1.7.99.3;

Protein crystallography data

The structure of Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis, PDB code: 1npj was solved by H.J.Wijma, M.J.Boulanger, A.Molon, M.Fittipaldi, M.Huber, M.E.Murphy, M.P.Verbeet, G.W.Canters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.41 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.600, 102.520, 146.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.5

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis (pdb code 1npj). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis, PDB code: 1npj:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1npj

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Copper binding site 1 out of 6 in the Crystal Structure of H145A Mutant of 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 Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:25.6
occ:1.00
ND1 A:HIS95 2.1 19.2 1.0
SG A:CYS136 2.2 19.8 1.0
SD A:MET150 2.5 20.6 1.0
CB A:CYS136 3.0 19.7 1.0
CG A:HIS95 3.0 20.5 1.0
CE A:MET150 3.1 20.2 1.0
CE1 A:HIS95 3.1 22.0 1.0
CB A:HIS95 3.3 17.3 1.0
CA A:HIS95 3.7 17.9 1.0
CG A:MET150 3.8 17.9 1.0
CD2 A:HIS95 4.2 19.1 1.0
CB A:ALA145 4.2 17.6 1.0
NE2 A:HIS95 4.2 21.7 1.0
N A:ASN96 4.3 16.9 1.0
O A:MET94 4.4 18.8 1.0
CB A:MET150 4.4 17.0 1.0
CA A:CYS136 4.5 17.4 1.0
SD A:MET62 4.5 24.4 1.0
C A:HIS95 4.6 16.1 1.0
N A:HIS95 4.8 16.6 1.0
O A:ASN96 4.8 18.5 1.0
CD A:PRO138 4.8 24.0 1.0
CB A:MET62 4.8 19.7 1.0
C A:MET94 5.0 19.6 1.0

Copper binding site 2 out of 6 in 1npj

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Copper binding site 2 out of 6 in the Crystal Structure of H145A Mutant of 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 Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:19.3
occ:1.00
NE2 A:HIS100 2.0 14.9 1.0
NE2 A:HIS135 2.0 14.3 1.0
NE2 B:HIS306 2.2 14.8 1.0
O A:HOH503 2.2 26.9 1.0
CE1 A:HIS100 2.9 15.7 1.0
CD2 A:HIS135 3.0 15.4 1.0
CE1 A:HIS135 3.0 16.3 1.0
CE1 B:HIS306 3.0 13.6 1.0
CD2 A:HIS100 3.1 15.1 1.0
CD2 B:HIS306 3.2 14.9 1.0
OD2 A:ASP98 3.7 25.5 1.0
ND1 A:HIS100 4.0 16.2 1.0
CG A:HIS135 4.1 14.5 1.0
ND1 A:HIS135 4.1 14.0 1.0
CG A:HIS100 4.1 12.7 1.0
CE1 B:HIS255 4.2 15.1 1.0
ND1 B:HIS306 4.2 16.1 1.0
NE2 B:HIS255 4.3 20.9 1.0
CG B:HIS306 4.3 15.2 1.0
CG A:ASP98 4.4 22.7 1.0
ND1 B:HIS255 4.5 20.4 1.0
CD2 B:HIS255 4.7 16.6 1.0
OD1 A:ASP98 4.9 21.3 1.0
CG B:HIS255 4.9 18.2 1.0
O B:HOH1097 4.9 17.2 1.0
CD2 B:LEU308 4.9 16.5 1.0
CD1 B:LEU308 4.9 16.2 1.0

Copper binding site 3 out of 6 in 1npj

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Copper binding site 3 out of 6 in the Crystal Structure of H145A Mutant of 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 Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:27.6
occ:1.00
ND1 B:HIS95 2.0 18.9 1.0
SG B:CYS136 2.2 23.1 1.0
SD B:MET150 2.6 20.2 1.0
CG B:HIS95 3.0 21.5 1.0
CE B:MET150 3.1 19.4 1.0
CE1 B:HIS95 3.1 19.9 1.0
CB B:CYS136 3.1 20.4 1.0
CB B:HIS95 3.2 22.4 1.0
CA B:HIS95 3.7 23.2 1.0
CG B:MET150 3.9 18.0 1.0
CD2 B:HIS95 4.1 18.4 1.0
NE2 B:HIS95 4.1 21.8 1.0
CB B:ALA145 4.1 26.4 1.0
O B:MET94 4.4 23.2 1.0
N B:ASN96 4.4 22.4 1.0
CB B:MET150 4.5 18.1 1.0
SD B:MET62 4.6 27.4 1.0
CA B:CYS136 4.6 21.0 1.0
C B:HIS95 4.6 23.5 1.0
CD B:PRO138 4.7 29.8 1.0
N B:HIS95 4.7 24.6 1.0
O B:ASN96 4.8 22.8 1.0
CB B:MET62 4.9 21.6 1.0
C B:MET94 5.0 23.2 1.0

Copper binding site 4 out of 6 in 1npj

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Copper binding site 4 out of 6 in the Crystal Structure of H145A Mutant of 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 Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:22.2
occ:1.00
NE2 B:HIS100 2.0 19.6 1.0
NE2 B:HIS135 2.0 19.4 1.0
NE2 C:HIS306 2.1 16.6 1.0
O B:HOH504 2.2 25.4 1.0
CE1 B:HIS100 2.9 17.2 1.0
CD2 B:HIS135 2.9 18.0 1.0
CE1 C:HIS306 3.0 17.9 1.0
CE1 B:HIS135 3.1 19.1 1.0
CD2 B:HIS100 3.1 19.2 1.0
CD2 C:HIS306 3.2 19.1 1.0
OD2 B:ASP98 3.8 27.9 1.0
ND1 B:HIS100 4.0 18.7 1.0
CG B:HIS135 4.1 17.8 1.0
CE1 C:HIS255 4.1 20.1 1.0
ND1 C:HIS306 4.2 17.0 1.0
ND1 B:HIS135 4.2 17.9 1.0
CG B:HIS100 4.2 18.1 1.0
NE2 C:HIS255 4.2 22.0 1.0
CG C:HIS306 4.3 20.1 1.0
O B:HOH5639 4.3 54.5 1.0
CG B:ASP98 4.4 24.7 1.0
ND1 C:HIS255 4.6 21.8 1.0
CD2 C:HIS255 4.7 19.2 1.0
OD1 B:ASP98 4.8 24.7 1.0
O B:HOH1098 4.9 20.0 1.0
CG C:HIS255 4.9 20.3 1.0
CD2 C:LEU308 4.9 21.9 1.0

Copper binding site 5 out of 6 in 1npj

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Copper binding site 5 out of 6 in the Crystal Structure of H145A Mutant of 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 Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:30.7
occ:1.00
SG C:CYS136 2.1 27.3 1.0
ND1 C:HIS95 2.2 30.0 1.0
SD C:MET150 2.6 28.3 1.0
CG C:HIS95 3.0 29.4 1.0
CB C:CYS136 3.1 27.5 1.0
CE C:MET150 3.1 26.0 1.0
CB C:HIS95 3.2 29.8 1.0
CE1 C:HIS95 3.2 30.1 1.0
CA C:HIS95 3.6 29.9 1.0
CG C:MET150 3.9 25.5 1.0
CB C:ALA145 4.1 29.8 1.0
CD2 C:HIS95 4.2 29.9 1.0
O C:MET94 4.2 30.6 1.0
NE2 C:HIS95 4.3 29.3 1.0
N C:ASN96 4.4 29.1 1.0
CA C:CYS136 4.5 26.8 1.0
CB C:MET150 4.5 25.8 1.0
C C:HIS95 4.6 29.3 1.0
SD C:MET62 4.6 32.1 1.0
N C:HIS95 4.7 29.4 1.0
CD C:PRO138 4.7 36.6 1.0
O C:ASN96 4.8 26.8 1.0
CB C:MET62 4.9 30.2 1.0
C C:MET94 4.9 30.5 1.0

Copper binding site 6 out of 6 in 1npj

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Copper binding site 6 out of 6 in the Crystal Structure of H145A Mutant of 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 Crystal Structure of H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:24.4
occ:1.00
NE2 C:HIS135 2.0 18.5 1.0
NE2 C:HIS100 2.0 22.1 1.0
NE2 A:HIS306 2.2 19.9 1.0
O C:HOH505 2.3 24.3 1.0
CE1 C:HIS100 2.9 24.7 1.0
CD2 C:HIS135 2.9 21.5 1.0
CE1 A:HIS306 3.0 18.1 1.0
CE1 C:HIS135 3.1 22.2 1.0
CD2 C:HIS100 3.1 23.3 1.0
CD2 A:HIS306 3.3 18.4 1.0
OD2 C:ASP98 3.9 32.6 1.0
CE1 A:HIS255 4.1 23.9 1.0
ND1 C:HIS100 4.1 23.6 1.0
CG C:HIS135 4.1 21.6 1.0
ND1 C:HIS135 4.1 23.4 1.0
ND1 A:HIS306 4.2 15.4 1.0
CG C:HIS100 4.2 22.5 1.0
NE2 A:HIS255 4.2 25.9 1.0
O C:HOH5593 4.2 38.5 1.0
CG A:HIS306 4.3 19.0 1.0
ND1 A:HIS255 4.5 23.4 1.0
CG C:ASP98 4.5 31.7 1.0
CD2 A:HIS255 4.7 21.9 1.0
CG A:HIS255 4.9 24.3 1.0
OD1 C:ASP98 4.9 31.5 1.0

Reference:

H.J.Wijma, M.J.Boulanger, A.Molon, M.Fittipaldi, M.Huber, M.E.Murphy, M.P.Verbeet, G.W.Canters. Reconstitution of the Type-1 Active Site of the H145G/A Variants of Nitrite Reductase By Ligand Insertion Biochemistry V. 42 4075 2003.
ISSN: ISSN 0006-2960
PubMed: 12680761
DOI: 10.1021/BI027270+
Page generated: Thu Sep 3 16:11:21 2020
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