Atomistry » Copper » PDB 2aps-2cg1 » 2b08
Atomistry »
  Copper »
    PDB 2aps-2cg1 »
      2b08 »

Copper in PDB 2b08: Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis

Enzymatic activity of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis

All present enzymatic activity of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis:
1.7.2.1;

Protein crystallography data

The structure of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis, PDB code: 2b08 was solved by H.J.Wijma, I.S.Macpherson, O.Farver, E.I.Tocheva, I.Pecht, M.Ph.Verbeet, M.E.P.Murphy, G.W.Canters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.52 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.972, 102.047, 146.423, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22

Copper Binding Sites:

The binding sites of Copper atom in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis (pdb code 2b08). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis, PDB code: 2b08:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 1 out of 9 in the Reduced Acetamide-Bound M150G 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 Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:30.0
occ:1.00
 ND1 A:HIS145 2.1 19.4 1.0
ND1 A:HIS95 2.2 19.5 1.0
SG A:CYS136 2.3 20.6 1.0
SD A:MET62 2.3 27.5 1.0
CE1 A:HIS145 3.0 21.1 1.0
CE A:MET62 3.0 25.3 1.0
CE1 A:HIS95 3.1 20.6 1.0
CG A:MET62 3.2 25.8 1.0
CG A:HIS145 3.2 19.7 1.0
CG A:HIS95 3.2 19.6 1.0
CB A:CYS136 3.2 19.4 1.0
CB A:HIS95 3.6 20.3 1.0
CB A:HIS145 3.6 17.0 1.0
CA A:HIS95 4.1 19.9 1.0
NE2 A:HIS145 4.1 21.4 1.0
CB A:MET62 4.2 22.6 1.0
NE2 A:HIS95 4.2 21.0 1.0
CD2 A:HIS145 4.3 18.4 1.0
CD2 A:HIS95 4.3 18.9 1.0
CG A:PRO138 4.4 19.6 1.0
O A:MET94 4.4 19.9 1.0
CA A:CYS136 4.7 19.2 1.0
CA A:HIS145 4.7 17.7 1.0
CD A:PRO138 4.7 19.6 1.0
O A:ACM1503 4.8 34.4 1.0
C2 A:ACM1503 4.9 33.0 1.0
N A:ASN96 5.0 19.5 1.0

Copper binding site 2 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 2 out of 9 in the Reduced Acetamide-Bound M150G 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 Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:21.0
occ:1.00
 NE2 A:HIS135 2.0 20.9 1.0
NE2 B:HIS306 2.0 18.7 1.0
NE2 A:HIS100 2.1 18.3 1.0
CD2 A:HIS135 2.9 18.1 1.0
CE1 B:HIS306 2.9 15.1 1.0
CE1 A:HIS100 2.9 19.7 1.0
CE1 A:HIS135 3.1 20.2 1.0
CD2 B:HIS306 3.2 17.4 1.0
CD2 A:HIS100 3.2 17.8 1.0
OD1 A:ASP98 3.7 24.7 1.0
CG A:HIS135 4.1 20.0 1.0
ND1 B:HIS306 4.1 16.0 1.0
ND1 A:HIS100 4.1 20.0 1.0
ND1 A:HIS135 4.1 18.8 1.0
CG B:HIS306 4.2 17.6 1.0
NE2 B:HIS255 4.2 20.0 1.0
CG A:HIS100 4.2 16.9 1.0
CE1 B:HIS255 4.3 18.8 1.0
CG A:ASP98 4.4 18.7 1.0
O A:HOH1808 4.4 28.4 1.0
CD2 B:HIS255 4.7 20.5 1.0
ND1 B:HIS255 4.8 21.4 1.0
OD2 A:ASP98 4.8 20.9 1.0
CD2 B:LEU308 4.8 17.3 1.0
CG B:HIS255 5.0 19.4 1.0

Copper binding site 3 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 3 out of 9 in the Reduced Acetamide-Bound M150G 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 Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1506

b:37.0
occ:0.30
 O A:HOH1655 2.0 24.4 1.0
NE2 A:HIS145 2.0 21.4 1.0
SD A:MET141 2.7 31.4 1.0
CE A:MET141 2.9 31.0 1.0
CD2 A:HIS145 3.0 18.4 1.0
CE1 A:HIS145 3.0 21.1 1.0
CB A:MET141 3.5 22.9 1.0
CG A:MET141 3.8 25.9 1.0
CZ3 A:TRP144 3.9 23.5 1.0
CE3 A:TRP144 4.1 20.2 1.0
CG A:PRO138 4.1 19.6 1.0
CG A:HIS145 4.1 19.7 1.0
ND1 A:HIS145 4.1 19.4 1.0
CB A:PRO138 4.2 19.8 1.0
O A:HOH1542 4.3 23.1 1.0
O A:MET94 4.3 19.9 1.0
CD2 A:LEU93 4.3 23.1 1.0
CB A:LEU93 4.6 22.7 1.0
CD1 A:LEU93 4.6 22.8 1.0
CG A:LEU93 4.7 23.0 1.0
O A:MET141 4.9 19.5 1.0
CA A:MET141 5.0 23.1 1.0

Copper binding site 4 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 4 out of 9 in the Reduced Acetamide-Bound M150G 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 Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2501

b:35.5
occ:1.00
 CU B:CU12505 2.1 33.7 0.3
ND1 B:HIS95 2.2 27.2 1.0
SD B:MET62 2.2 33.3 1.0
SG B:CYS136 2.3 25.1 1.0
ND1 B:HIS145 2.5 28.0 1.0
CE1 B:HIS95 3.1 25.7 1.0
CB B:CYS136 3.1 23.7 1.0
CG B:HIS95 3.2 26.3 1.0
CE B:MET62 3.2 29.5 1.0
CG B:MET62 3.2 30.1 1.0
CE1 B:HIS145 3.3 29.9 1.0
CG B:HIS145 3.5 26.8 1.0
CB B:HIS95 3.5 26.8 1.0
O B:ACM2503 3.8 48.1 1.0
CB B:HIS145 3.8 24.7 1.0
CA B:HIS95 4.0 26.7 1.0
NE2 B:HIS95 4.2 26.4 1.0
CB B:MET62 4.3 27.7 1.0
CD2 B:HIS95 4.3 26.5 1.0
O B:MET94 4.4 26.0 1.0
CG B:PRO138 4.5 30.4 1.0
NE2 B:HIS145 4.5 28.4 1.0
CA B:CYS136 4.6 24.1 1.0
CD2 B:HIS145 4.6 28.8 1.0
CD B:PRO138 4.8 29.6 1.0
CA B:HIS145 4.9 24.6 1.0
N B:ASN96 4.9 26.3 1.0
C1 B:ACM2503 5.0 47.8 1.0

Copper binding site 5 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 5 out of 9 in the Reduced Acetamide-Bound M150G 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 Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2502

b:26.0
occ:1.00
 NE2 B:HIS135 2.0 21.9 1.0
NE2 B:HIS100 2.0 21.2 1.0
NE2 C:HIS306 2.1 21.4 1.0
CE1 B:HIS100 2.8 21.9 1.0
CD2 B:HIS135 2.9 20.4 1.0
CE1 C:HIS306 3.0 20.6 1.0
CD2 C:HIS306 3.1 20.4 1.0
CE1 B:HIS135 3.1 22.2 1.0
CD2 B:HIS100 3.2 21.0 1.0
OD1 B:ASP98 3.8 25.8 1.0
ND1 B:HIS100 4.0 22.8 1.0
CG B:HIS135 4.1 21.4 1.0
ND1 B:HIS135 4.1 22.7 1.0
ND1 C:HIS306 4.1 19.8 1.0
CG B:HIS100 4.2 21.0 1.0
CG C:HIS306 4.2 21.3 1.0
NE2 C:HIS255 4.2 24.3 1.0
CG B:ASP98 4.3 24.7 1.0
CE1 C:HIS255 4.4 24.6 1.0
CD2 C:HIS255 4.6 23.1 1.0
O B:HOH2649 4.6 41.5 1.0
OD2 B:ASP98 4.8 25.6 1.0
ND1 C:HIS255 4.8 25.9 1.0
CD2 C:LEU308 4.9 20.9 1.0
CG C:HIS255 5.0 22.3 1.0
O B:HOH2709 5.0 23.3 1.0
CG1 C:ILE257 5.0 26.7 1.0

Copper binding site 6 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 6 out of 9 in the Reduced Acetamide-Bound M150G 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 Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2505

b:33.7
occ:0.30
 ND1 B:HIS145 2.0 28.0 1.0
SG B:CYS136 2.0 25.1 1.0
CU B:CU12501 2.1 35.5 1.0
CG B:PRO138 2.4 30.4 1.0
CG B:HIS145 2.7 26.8 1.0
CD B:PRO138 2.8 29.6 1.0
CE1 B:HIS145 2.8 29.9 1.0
CB B:HIS145 3.2 24.7 1.0
CB B:CYS136 3.3 23.7 1.0
CD2 B:HIS145 3.5 28.8 1.0
NE2 B:HIS145 3.6 28.4 1.0
ND1 B:HIS95 3.6 27.2 1.0
CB B:PRO138 3.9 30.1 1.0
O B:MET94 3.9 26.0 1.0
N B:PRO138 4.0 29.3 1.0
CA B:HIS95 4.0 26.7 1.0
SD B:MET62 4.1 33.3 1.0
CB B:HIS95 4.2 26.8 1.0
CA B:CYS136 4.3 24.1 1.0
N B:ALA137 4.3 25.9 1.0
CG B:HIS95 4.3 26.3 1.0
C B:CYS136 4.3 24.9 1.0
OD1 B:ASN96 4.4 27.1 1.0
CE1 B:HIS95 4.5 25.7 1.0
N B:ASN96 4.5 26.3 1.0
CA B:PRO138 4.6 30.0 1.0
CA B:HIS145 4.6 24.6 1.0
O B:ACM2503 4.7 48.1 1.0
C B:MET94 4.8 27.4 1.0
C B:HIS95 4.8 26.7 1.0
O B:HOH2648 4.9 43.7 1.0
C B:ALA137 4.9 28.4 1.0
N B:HIS95 4.9 26.9 1.0
CA B:ALA137 4.9 27.2 1.0
O B:CYS136 5.0 24.9 1.0

Copper binding site 7 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 7 out of 9 in the Reduced Acetamide-Bound M150G 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 7 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3501

b:42.9
occ:1.00
 CU C:CU13505 1.9 44.3 0.4
SD C:MET62 2.1 40.6 1.0
ND1 C:HIS95 2.3 34.2 1.0
ND1 C:HIS145 2.3 32.2 1.0
SG C:CYS136 2.3 32.8 1.0
CE1 C:HIS145 3.2 34.0 1.0
CE1 C:HIS95 3.2 32.8 1.0
CG C:MET62 3.2 38.9 1.0
CB C:CYS136 3.3 30.5 1.0
CE C:MET62 3.3 41.8 1.0
CG C:HIS95 3.3 33.0 1.0
CG C:HIS145 3.3 29.8 1.0
CB C:HIS95 3.6 32.6 1.0
CB C:HIS145 3.7 27.9 1.0
CA C:HIS95 4.0 31.9 1.0
CB C:MET62 4.3 36.5 1.0
NE2 C:HIS95 4.3 32.8 1.0
NE2 C:HIS145 4.3 33.4 1.0
O C:MET94 4.3 33.0 1.0
CD2 C:HIS95 4.4 33.7 1.0
CD2 C:HIS145 4.4 31.1 1.0
CG C:PRO138 4.6 33.5 1.0
CA C:CYS136 4.7 30.4 1.0
CA C:HIS145 4.8 27.7 1.0
CD C:PRO138 4.8 33.2 1.0
N C:ASN96 4.9 30.8 1.0
N C:HIS95 5.0 32.3 1.0

Copper binding site 8 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 8 out of 9 in the Reduced Acetamide-Bound M150G 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 8 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3502

b:26.8
occ:1.00
 NE2 C:HIS100 2.1 23.7 1.0
NE2 C:HIS135 2.1 25.9 1.0
NE2 A:HIS306 2.1 24.2 1.0
CD2 C:HIS135 2.9 26.4 1.0
CE1 A:HIS306 3.0 25.3 1.0
CE1 C:HIS100 3.0 22.8 1.0
CD2 C:HIS100 3.1 24.3 1.0
CD2 A:HIS306 3.2 23.8 1.0
CE1 C:HIS135 3.3 25.0 1.0
OD1 C:ASP98 3.7 29.8 1.0
CG C:HIS135 4.1 26.6 1.0
ND1 C:HIS100 4.1 24.1 1.0
ND1 A:HIS306 4.1 23.8 1.0
NE2 A:HIS255 4.2 24.1 1.0
CG C:HIS100 4.2 24.0 1.0
ND1 C:HIS135 4.3 24.7 1.0
CG A:HIS306 4.3 23.2 1.0
CE1 A:HIS255 4.3 24.5 1.0
CG C:ASP98 4.3 26.7 1.0
O C:HOH3636 4.5 34.3 1.0
CD2 A:HIS255 4.6 22.8 1.0
ND1 A:HIS255 4.7 22.7 1.0
OD2 C:ASP98 4.7 24.2 1.0
CG1 A:ILE257 4.8 23.0 1.0
CG A:HIS255 4.9 22.5 1.0
O A:HOH1543 5.0 24.9 1.0

Copper binding site 9 out of 9 in 2b08

Go back to Copper Binding Sites List in 2b08
Copper binding site 9 out of 9 in the Reduced Acetamide-Bound M150G 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 9 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3505

b:44.3
occ:0.40
 CU C:CU13501 1.9 42.9 1.0
SG C:CYS136 2.0 32.8 1.0
ND1 C:HIS145 2.0 32.2 1.0
CG C:PRO138 2.7 33.5 1.0
CG C:HIS145 2.7 29.8 1.0
CE1 C:HIS145 2.8 34.0 1.0
CD C:PRO138 3.0 33.2 1.0
CB C:HIS145 3.2 27.9 1.0
CB C:CYS136 3.2 30.5 1.0
ND1 C:HIS95 3.6 34.2 1.0
CD2 C:HIS145 3.6 31.1 1.0
NE2 C:HIS145 3.6 33.4 1.0
O C:MET94 3.8 33.0 1.0
SD C:MET62 3.8 40.6 1.0
CA C:HIS95 3.8 31.9 1.0
CB C:PRO138 3.9 34.0 1.0
N C:PRO138 4.1 33.0 1.0
CB C:HIS95 4.2 32.6 1.0
N C:ALA137 4.3 30.8 1.0
CG C:HIS95 4.3 33.0 1.0
CA C:CYS136 4.3 30.4 1.0
C C:CYS136 4.4 31.1 1.0
OD1 C:ASN96 4.4 28.3 1.0
N C:ASN96 4.4 30.8 1.0
CE1 C:HIS95 4.5 32.8 1.0
C C:HIS95 4.7 31.8 1.0
CA C:HIS145 4.7 27.7 1.0
C C:MET94 4.7 32.6 1.0
CA C:PRO138 4.7 33.7 1.0
N C:HIS95 4.8 32.3 1.0
CE C:MET62 4.9 41.8 1.0
C C:ALA137 5.0 32.3 1.0

Reference:

H.J.Wijma, I.Macpherson, O.Farver, E.I.Tocheva, I.Pecht, M.P.Verbeet, M.E.P.Murphy, G.W.Canters. Effect of the Methionine Ligand on the Reorganization Energy of the Type-1 Copper Site of Nitrite Reductase. J.Am.Chem.Soc. V. 129 519 2007.
ISSN: ISSN 0002-7863
PubMed: 17227014
DOI: 10.1021/JA064763J
Page generated: Tue Jul 30 23:13:48 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy