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Copper in PDB 1npn: Crystal Structure of A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis

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

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

Protein crystallography data

The structure of Crystal Structure of A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis, PDB code: 1npn 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) 33.28 / 1.80
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 (%) 15.6 / 19.5

Other elements in 1npn:

The structure of Crystal Structure of A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis (pdb code 1npn). 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 A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis, PDB code: 1npn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1npn

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

b:17.8
occ:1.00
 ND1 A:HIS95 2.0 12.8 1.0
SG A:CYS136 2.2 10.9 1.0
CL A:CL498 2.3 21.1 1.0
SD A:MET150 2.7 13.9 1.0
CE1 A:HIS95 2.9 13.3 1.0
CG A:HIS95 3.1 11.8 1.0
CB A:CYS136 3.1 8.6 1.0
CE A:MET150 3.4 10.6 1.0
CB A:HIS95 3.5 10.5 1.0
CA A:HIS95 3.8 11.8 1.0
CG A:MET150 4.0 9.9 1.0
NE2 A:HIS95 4.1 13.2 1.0
CB A:ALA145 4.2 9.2 1.0
CD2 A:HIS95 4.2 10.5 1.0
O A:MET94 4.2 12.2 1.0
O A:HOH5498 4.3 29.9 1.0
CB A:MET150 4.4 9.1 1.0
CA A:CYS136 4.6 8.9 1.0
N A:ASN96 4.6 10.4 1.0
CD A:PRO138 4.7 11.9 1.0
CB A:MET62 4.7 15.9 1.0
CG A:PRO138 4.8 13.8 1.0
C A:HIS95 4.8 9.9 1.0
N A:HIS95 4.8 10.3 1.0
C A:MET94 4.9 12.5 1.0

Copper binding site 2 out of 6 in 1npn

Go back to Copper Binding Sites List in 1npn
Copper binding site 2 out of 6 in the Crystal Structure of A Copper Reconstituted 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 A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:12.2
occ:1.00
 NE2 A:HIS100 2.0 8.1 1.0
NE2 B:HIS306 2.1 9.9 1.0
NE2 A:HIS135 2.1 10.3 1.0
O B:HOH503 2.2 14.8 1.0
CE1 A:HIS100 2.9 8.8 1.0
CE1 B:HIS306 3.0 8.9 1.0
CD2 A:HIS135 3.0 10.8 1.0
CD2 A:HIS100 3.1 8.9 1.0
CE1 A:HIS135 3.1 10.6 1.0
CD2 B:HIS306 3.2 10.0 1.0
OD2 A:ASP98 3.7 19.2 1.0
ND1 A:HIS100 4.1 8.2 1.0
ND1 B:HIS306 4.1 9.1 1.0
CG A:HIS100 4.2 6.6 1.0
CG A:HIS135 4.2 9.7 1.0
ND1 A:HIS135 4.2 9.8 1.0
O A:HOH5497 4.2 31.4 1.0
NE2 B:HIS255 4.2 13.0 1.0
CE1 B:HIS255 4.2 7.5 1.0
CG B:HIS306 4.3 9.3 1.0
CG A:ASP98 4.4 13.0 1.0
ND1 B:HIS255 4.7 11.9 1.0
CD2 B:HIS255 4.7 6.0 1.0
OD1 A:ASP98 4.8 13.7 1.0
CD1 B:LEU308 4.9 10.8 1.0
CG B:HIS255 4.9 8.5 1.0
CD2 B:LEU308 4.9 11.7 1.0
O B:HOH1097 4.9 9.7 1.0

Copper binding site 3 out of 6 in 1npn

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

b:20.3
occ:1.00
 ND1 B:HIS95 2.0 11.2 1.0
SG B:CYS136 2.2 14.6 1.0
CL B:CL499 2.4 25.1 1.0
SD B:MET150 2.6 13.5 1.0
CE1 B:HIS95 3.0 13.4 1.0
CG B:HIS95 3.0 13.6 1.0
CB B:CYS136 3.2 12.5 1.0
CE B:MET150 3.2 13.4 1.0
CB B:HIS95 3.4 14.7 1.0
CA B:HIS95 3.8 14.1 1.0
CG B:MET150 4.0 10.5 1.0
NE2 B:HIS95 4.1 12.3 1.0
CD2 B:HIS95 4.1 10.7 1.0
CG B:PRO138 4.2 19.2 1.0
O B:MET94 4.3 15.6 1.0
CB B:ALA145 4.3 12.8 1.0
CB B:MET150 4.5 10.9 1.0
CA B:CYS136 4.6 12.8 1.0
N B:ASN96 4.6 12.1 1.0
CE B:MET62 4.7 33.0 1.0
CB B:MET62 4.7 17.2 1.0
C B:HIS95 4.8 14.1 1.0
N B:HIS95 4.8 14.9 1.0
CD B:PRO138 4.8 15.2 1.0
C B:MET94 5.0 15.6 1.0

Copper binding site 4 out of 6 in 1npn

Go back to Copper Binding Sites List in 1npn
Copper binding site 4 out of 6 in the Crystal Structure of A Copper Reconstituted 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 A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:14.2
occ:1.00
 NE2 B:HIS135 2.0 12.8 1.0
NE2 B:HIS100 2.1 10.3 1.0
NE2 C:HIS306 2.1 12.9 1.0
O C:HOH504 2.2 19.1 1.0
CD2 B:HIS135 2.9 12.4 1.0
CE1 B:HIS100 3.0 11.3 1.0
CE1 C:HIS306 3.1 13.3 1.0
CE1 B:HIS135 3.1 12.2 1.0
CD2 B:HIS100 3.1 11.8 1.0
CD2 C:HIS306 3.1 13.8 1.0
OD2 B:ASP98 3.7 18.7 1.0
CG B:HIS135 4.1 10.9 1.0
ND1 B:HIS100 4.1 9.5 1.0
ND1 B:HIS135 4.2 11.3 1.0
CE1 C:HIS255 4.2 10.8 1.0
ND1 C:HIS306 4.2 11.4 1.0
CG B:HIS100 4.2 10.9 1.0
CG C:HIS306 4.3 11.9 1.0
NE2 C:HIS255 4.3 13.0 1.0
CG B:ASP98 4.4 15.3 1.0
O B:HOH5489 4.4 31.7 1.0
ND1 C:HIS255 4.5 12.8 1.0
CD2 C:HIS255 4.7 10.1 1.0
OD1 B:ASP98 4.8 14.0 1.0
CD1 C:LEU308 4.9 11.8 1.0
CG C:HIS255 4.9 10.3 1.0
CD2 C:LEU308 5.0 13.6 1.0

Copper binding site 5 out of 6 in 1npn

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

b:22.0
occ:1.00
 ND1 C:HIS95 2.1 16.9 1.0
CL C:CL500 2.2 30.1 1.0
SG C:CYS136 2.2 16.0 1.0
SD C:MET150 2.7 16.9 1.0
CE1 C:HIS95 3.0 17.3 1.0
CG C:HIS95 3.1 17.7 1.0
CB C:CYS136 3.1 14.4 1.0
CE C:MET150 3.4 13.8 1.0
CB C:HIS95 3.4 17.8 1.0
CA C:HIS95 3.7 18.1 1.0
CG C:MET150 4.0 13.4 1.0
NE2 C:HIS95 4.1 15.9 1.0
CB C:ALA145 4.2 15.8 1.0
CD2 C:HIS95 4.2 17.0 1.0
O C:MET94 4.2 20.1 1.0
CB C:MET150 4.5 14.4 1.0
CG C:PRO138 4.6 21.1 1.0
CA C:CYS136 4.6 15.1 1.0
N C:ASN96 4.6 18.0 1.0
CB C:MET62 4.6 21.5 1.0
CD C:PRO138 4.6 18.5 1.0
C C:HIS95 4.8 17.6 1.0
N C:HIS95 4.8 18.4 1.0
C C:MET94 4.9 20.0 1.0
CG C:MET62 5.0 26.7 1.0

Copper binding site 6 out of 6 in 1npn

Go back to Copper Binding Sites List in 1npn
Copper binding site 6 out of 6 in the Crystal Structure of A Copper Reconstituted 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 A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:15.2
occ:1.00
 NE2 C:HIS100 2.0 11.3 1.0
NE2 A:HIS306 2.1 11.5 1.0
NE2 C:HIS135 2.1 13.5 1.0
O A:HOH505 2.2 13.3 1.0
CE1 C:HIS100 2.9 13.7 1.0
CD2 C:HIS135 3.0 13.7 1.0
CE1 A:HIS306 3.0 9.7 1.0
CD2 C:HIS100 3.1 11.9 1.0
CD2 A:HIS306 3.2 8.8 1.0
CE1 C:HIS135 3.2 13.3 1.0
OD2 C:ASP98 3.7 20.4 1.0
ND1 C:HIS100 4.0 12.0 1.0
CE1 A:HIS255 4.1 13.0 1.0
ND1 A:HIS306 4.2 8.9 1.0
CG C:HIS135 4.2 11.9 1.0
CG C:HIS100 4.2 11.6 1.0
ND1 C:HIS135 4.3 11.9 1.0
NE2 A:HIS255 4.3 18.0 1.0
CG A:HIS306 4.3 9.5 1.0
O C:HOH5488 4.3 24.1 1.0
CG C:ASP98 4.4 19.6 1.0
CD1 A:ILE257 4.5 22.5 1.0
ND1 A:HIS255 4.5 16.1 1.0
CD2 A:HIS255 4.7 13.7 1.0
OD1 C:ASP98 4.8 19.8 1.0
CD1 A:LEU308 4.9 11.8 1.0
CG A:HIS255 4.9 14.3 1.0
CD2 A:LEU308 5.0 11.8 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 145G/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: Sun Dec 13 11:00:54 2020

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