Atomistry » Copper » PDB 1jxd-1mfm » 1l9t
Atomistry »
  Copper »
    PDB 1jxd-1mfm »
      1l9t »

Copper in PDB 1l9t: Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6

Enzymatic activity of Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6

All present enzymatic activity of Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6:
1.7.99.3;

Protein crystallography data

The structure of Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9t was solved by M.J.Boulanger, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.730, 102.340, 145.900, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.8

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 (pdb code 1l9t). 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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9t:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1l9t

Go back to Copper Binding Sites List in 1l9t
Copper binding site 1 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6


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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:20.4
occ:1.00
ND1 A:HIS145 2.0 16.9 1.0
ND1 A:HIS95 2.1 18.6 1.0
SG A:CYS136 2.2 17.2 1.0
SD A:MET150 2.4 17.5 1.0
CE1 A:HIS145 2.9 16.9 1.0
CE1 A:HIS95 3.0 19.5 1.0
CG A:HIS145 3.1 15.3 1.0
CG A:HIS95 3.1 18.6 1.0
CB A:CYS136 3.2 17.4 1.0
CE A:MET150 3.3 16.3 1.0
CB A:HIS95 3.5 16.1 1.0
CB A:HIS145 3.6 15.5 1.0
CG A:MET150 3.8 16.2 1.0
CA A:HIS95 3.9 17.9 1.0
NE2 A:HIS145 4.1 17.7 1.0
NE2 A:HIS95 4.2 19.4 1.0
CD2 A:HIS145 4.2 18.1 1.0
CD2 A:HIS95 4.2 18.5 1.0
CB A:MET150 4.3 16.0 1.0
SD A:MET62 4.3 19.5 1.0
CG A:PRO138 4.3 19.7 1.0
O A:MET94 4.4 18.1 1.0
CA A:CYS136 4.6 17.1 1.0
N A:ASN96 4.7 17.4 1.0
CB A:MET62 4.7 18.3 1.0
CD A:PRO138 4.7 17.6 1.0
CA A:HIS145 4.7 16.0 1.0
C A:HIS95 4.9 17.5 1.0
N A:HIS95 5.0 18.2 1.0

Copper binding site 2 out of 6 in 1l9t

Go back to Copper Binding Sites List in 1l9t
Copper binding site 2 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6


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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:21.1
occ:1.00
O2 B:NO2504 2.0 35.6 1.0
NE2 A:HIS100 2.1 16.6 1.0
NE2 B:HIS306 2.1 17.7 1.0
N B:NO2504 2.1 35.4 1.0
NE2 A:HIS135 2.1 18.7 1.0
O1 B:NO2504 2.3 30.9 1.0
CE1 A:HIS100 3.0 18.5 1.0
CE1 B:HIS306 3.0 16.6 1.0
CE1 A:HIS135 3.1 17.3 1.0
CD2 A:HIS135 3.1 18.1 1.0
CD2 A:HIS100 3.1 17.4 1.0
CD2 B:HIS306 3.1 17.2 1.0
OD2 A:ASP98 3.5 26.9 1.0
NE2 B:HIS255 4.0 20.6 1.0
ND1 A:HIS100 4.1 16.7 1.0
ND1 B:HIS306 4.2 15.6 1.0
O A:HOH5296 4.2 45.1 1.0
ND1 A:HIS135 4.2 16.0 1.0
CG A:HIS100 4.2 15.6 1.0
CG A:HIS135 4.2 18.1 1.0
CG B:HIS306 4.3 16.7 1.0
CD2 B:HIS255 4.3 21.2 1.0
CG A:ASP98 4.3 23.2 1.0
CE1 B:HIS255 4.4 23.9 1.0
CG B:HIS255 4.8 20.6 1.0
ND1 B:HIS255 4.8 22.8 1.0
OD1 A:ASP98 4.9 23.7 1.0
O B:HOH6001 4.9 19.6 1.0
CD2 B:LEU308 4.9 17.1 1.0

Copper binding site 3 out of 6 in 1l9t

Go back to Copper Binding Sites List in 1l9t
Copper binding site 3 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6


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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:22.9
occ:1.00
ND1 B:HIS145 2.0 20.6 1.0
ND1 B:HIS95 2.0 18.5 1.0
SG B:CYS136 2.2 20.4 1.0
SD B:MET150 2.5 19.3 1.0
CE1 B:HIS145 2.9 23.3 1.0
CE1 B:HIS95 3.0 19.9 1.0
CG B:HIS95 3.1 19.7 1.0
CG B:HIS145 3.1 21.8 1.0
CB B:CYS136 3.2 18.5 1.0
CE B:MET150 3.3 21.6 1.0
CB B:HIS95 3.4 20.3 1.0
CB B:HIS145 3.5 20.4 1.0
CG B:MET150 3.8 17.8 1.0
CA B:HIS95 3.9 21.3 1.0
NE2 B:HIS145 4.1 22.9 1.0
NE2 B:HIS95 4.1 18.6 1.0
CD2 B:HIS95 4.2 18.8 1.0
CD2 B:HIS145 4.2 22.2 1.0
CG B:PRO138 4.2 20.8 1.0
SD B:MET62 4.3 21.9 1.0
O B:MET94 4.3 22.3 1.0
CB B:MET150 4.4 17.4 1.0
CA B:CYS136 4.6 19.7 1.0
CD B:PRO138 4.6 19.1 1.0
N B:ASN96 4.7 20.6 1.0
CA B:HIS145 4.8 19.5 1.0
CB B:MET62 4.8 20.7 1.0
C B:HIS95 4.9 21.7 1.0
N B:HIS95 4.9 21.5 1.0

Copper binding site 4 out of 6 in 1l9t

Go back to Copper Binding Sites List in 1l9t
Copper binding site 4 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6


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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:23.9
occ:1.00
O2 C:NO2604 1.9 37.3 1.0
NE2 B:HIS100 2.1 19.0 1.0
NE2 B:HIS135 2.1 20.5 1.0
NE2 C:HIS306 2.1 18.4 1.0
N C:NO2604 2.2 35.8 1.0
O1 C:NO2604 2.4 34.2 1.0
CE1 B:HIS100 2.9 19.4 1.0
CE1 B:HIS135 3.1 19.7 1.0
CE1 C:HIS306 3.1 19.3 1.0
CD2 B:HIS135 3.1 19.5 1.0
CD2 C:HIS306 3.1 21.1 1.0
CD2 B:HIS100 3.2 19.7 1.0
OD2 B:ASP98 3.6 28.4 1.0
NE2 C:HIS255 3.9 26.0 1.0
ND1 B:HIS100 4.1 18.4 1.0
O B:HOH6004 4.1 39.9 1.0
ND1 B:HIS135 4.2 18.7 1.0
ND1 C:HIS306 4.2 18.9 1.0
CG B:HIS135 4.2 19.0 1.0
CD2 C:HIS255 4.2 25.0 1.0
CG B:HIS100 4.2 19.2 1.0
CG C:HIS306 4.3 19.4 1.0
CE1 C:HIS255 4.3 25.0 1.0
CG B:ASP98 4.4 24.7 1.0
CG C:HIS255 4.8 23.1 1.0
ND1 C:HIS255 4.8 25.6 1.0
OD1 B:ASP98 4.8 22.9 1.0
O C:HOH6003 4.9 21.7 1.0

Copper binding site 5 out of 6 in 1l9t

Go back to Copper Binding Sites List in 1l9t
Copper binding site 5 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6


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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:27.2
occ:1.00
ND1 C:HIS145 2.0 25.1 1.0
ND1 C:HIS95 2.1 24.8 1.0
SG C:CYS136 2.2 24.6 1.0
SD C:MET150 2.5 23.4 1.0
CE1 C:HIS145 2.8 26.4 1.0
CE1 C:HIS95 3.1 24.3 1.0
CG C:HIS145 3.1 25.1 1.0
CG C:HIS95 3.1 23.2 1.0
CB C:CYS136 3.2 23.3 1.0
CE C:MET150 3.3 22.5 1.0
CB C:HIS95 3.4 24.9 1.0
CB C:HIS145 3.5 23.4 1.0
CA C:HIS95 3.8 25.6 1.0
CG C:MET150 3.8 23.0 1.0
NE2 C:HIS145 4.0 24.5 1.0
CD2 C:HIS145 4.1 25.9 1.0
CG C:PRO138 4.2 27.1 1.0
NE2 C:HIS95 4.2 22.6 1.0
CD2 C:HIS95 4.2 24.2 1.0
O C:MET94 4.3 25.9 1.0
SD C:MET62 4.3 24.4 1.0
CB C:MET150 4.4 23.2 1.0
CA C:CYS136 4.6 23.7 1.0
CD C:PRO138 4.6 24.8 1.0
N C:ASN96 4.7 24.9 1.0
CB C:MET62 4.7 24.8 1.0
CA C:HIS145 4.8 23.1 1.0
C C:HIS95 4.8 26.2 1.0
N C:HIS95 4.9 25.6 1.0

Copper binding site 6 out of 6 in 1l9t

Go back to Copper Binding Sites List in 1l9t
Copper binding site 6 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6


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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:25.0
occ:1.00
O2 A:NO2704 2.0 39.4 1.0
NE2 C:HIS100 2.1 19.7 1.0
NE2 A:HIS306 2.1 20.4 1.0
NE2 C:HIS135 2.2 22.1 1.0
N A:NO2704 2.2 38.0 1.0
O1 A:NO2704 2.4 34.5 1.0
CE1 C:HIS100 2.9 21.0 1.0
CE1 A:HIS306 3.0 19.6 1.0
CD2 C:HIS135 3.1 21.5 1.0
CD2 A:HIS306 3.1 20.4 1.0
CD2 C:HIS100 3.2 20.7 1.0
CE1 C:HIS135 3.2 22.6 1.0
OD2 C:ASP98 3.6 30.8 1.0
NE2 A:HIS255 3.8 28.0 1.0
O C:HOH5309 4.0 44.6 1.0
ND1 C:HIS100 4.1 18.6 1.0
CD2 A:HIS255 4.1 26.9 1.0
ND1 A:HIS306 4.2 18.2 1.0
CG C:HIS100 4.2 18.8 1.0
CG C:HIS135 4.2 21.0 1.0
CG A:HIS306 4.3 18.8 1.0
ND1 C:HIS135 4.3 21.9 1.0
CE1 A:HIS255 4.3 26.7 1.0
CG C:ASP98 4.4 28.2 1.0
CG A:HIS255 4.7 24.8 1.0
ND1 A:HIS255 4.9 27.4 1.0
O A:HOH5326 4.9 47.4 1.0
OD1 C:ASP98 4.9 29.2 1.0
CD2 A:LEU308 5.0 20.0 1.0
CD1 A:LEU308 5.0 20.7 1.0

Reference:

M.J.Boulanger, M.E.P.Murphy. Directing the Mode of Nitrite Binding to A Copper-Containing Nitrite Reductase From Alcaligenes Faecalis S-6: Characterization of An Active Site Isoleucine Protein Sci. V. 12 248 2003.
ISSN: ISSN 0961-8368
PubMed: 12538888
DOI: 10.1110/PS.0224503
Page generated: Tue Jul 30 22:14:51 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