Copper in PDB 9iq9: Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86

Enzymatic activity of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86

All present enzymatic activity of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86:
3.5.3.25;

Protein crystallography data

The structure of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86, PDB code: 9iq9 was solved by K.Oda, Y.Matoba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.65 / 1.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.502, 46.981, 59.559, 83.57, 84.69, 70.09
R / Rfree (%) 17.9 / 21.7

Other elements in 9iq9:

The structure of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Magnesium (Mg) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 (pdb code 9iq9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86, PDB code: 9iq9:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 9iq9

Go back to Copper Binding Sites List in 9iq9
Copper binding site 1 out of 3 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86


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 Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:25.7
occ:0.69
 O B:HOH405 1.9 21.6 0.5
OD2 B:ASP113 2.0 18.5 1.0
OD2 B:ASP109 2.0 16.4 0.2
OD2 B:ASP109 2.1 15.2 0.8
O B:HOH533 2.2 28.1 1.0
SG B:CYS86 2.7 19.7 0.7
CG B:ASP113 2.9 17.0 1.0
OD2 B:ASP198 3.0 33.8 1.0
CG B:ASP109 3.0 22.2 0.8
OD1 B:ASP113 3.1 20.3 1.0
CG B:ASP109 3.2 19.2 0.2
SG B:CYS86 3.2 18.5 0.3
OD1 B:ASP109 3.3 20.7 0.8
CU B:CU1303 3.4 18.0 0.5
CU B:CU1302 3.4 22.7 0.6
CB B:CYS86 3.7 18.1 0.7
CB B:CYS86 3.7 18.1 0.3
OD1 B:ASP109 3.8 19.0 0.2
OH B:TYR107 3.9 17.8 1.0
CG B:ASP198 4.0 20.5 1.0
CB B:ASP198 4.1 16.7 1.0
O B:HOH594 4.2 28.1 1.0
O B:HOH551 4.3 25.8 1.0
CB B:ASP113 4.3 17.4 1.0
CE1 B:TYR107 4.3 15.3 1.0
CB B:ASP109 4.3 17.9 0.8
CB B:ASP109 4.4 17.6 0.2
O B:GLY126 4.4 22.8 1.0
CZ B:TYR107 4.6 19.1 1.0
ND1 B:HIS111 4.8 20.7 0.8
OD2 B:ASP200 4.8 23.7 1.0
CB B:HIS111 4.9 18.6 0.8

Copper binding site 2 out of 3 in 9iq9

Go back to Copper Binding Sites List in 9iq9
Copper binding site 2 out of 3 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86


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 Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:22.7
occ:0.58
 O B:HOH405 1.9 21.6 0.5
ND1 B:HIS111 2.0 20.7 0.8
OD2 B:ASP200 2.0 23.7 1.0
OD1 B:ASP109 2.1 20.7 0.8
OD1 B:ASP200 2.6 19.9 1.0
CG B:ASP200 2.6 23.5 1.0
CD2 B:HIS111 2.8 21.7 0.2
OD2 B:ASP198 2.8 33.8 1.0
CE1 B:HIS111 2.8 22.5 0.8
OD1 B:ASP109 3.1 19.0 0.2
CG B:HIS111 3.1 18.0 0.8
CG B:ASP109 3.2 22.2 0.8
OD2 B:ASP109 3.2 16.4 0.2
CG B:ASP109 3.4 19.2 0.2
CU B:CU1301 3.4 25.7 0.7
OD2 B:ASP109 3.5 15.2 0.8
CB B:HIS111 3.6 18.6 0.8
CG B:HIS111 3.6 19.2 0.2
CG B:ASP198 3.6 20.5 1.0
N B:HIS111 3.7 15.0 0.8
CB B:HIS111 3.8 19.5 0.2
NE2 B:HIS111 3.8 20.1 0.2
N B:GLY110 4.0 17.4 0.8
NE2 B:HIS111 4.0 22.3 0.8
N B:GLY110 4.1 17.5 0.2
N B:HIS111 4.1 15.7 0.2
CB B:ASP200 4.1 17.5 1.0
CD2 B:HIS111 4.2 20.9 0.8
OD1 B:ASP198 4.2 22.5 1.0
CA B:HIS111 4.2 19.4 0.8
C B:GLY110 4.4 15.8 0.8
CB B:ASP198 4.4 16.7 1.0
O B:HOH533 4.4 28.1 1.0
O B:HOH594 4.4 28.1 1.0
CA B:GLY110 4.4 15.0 0.8
CB B:ASP109 4.5 17.9 0.8
OD1 B:ASP113 4.6 20.3 1.0
CA B:HIS111 4.6 18.4 0.2
CB B:ASP109 4.7 17.6 0.2
CA B:GLY110 4.7 15.4 0.2
C B:GLY110 4.7 16.3 0.2
C B:ASP109 4.7 16.0 0.8
O B:HOH466 4.8 21.3 1.0
C B:ASP109 4.8 16.2 0.2
ND1 B:HIS111 4.8 20.6 0.2
CA B:ASP109 4.8 15.6 0.8
CA B:ASP109 4.9 15.8 0.2
OD2 B:ASP113 4.9 18.5 1.0
CE1 B:HIS111 4.9 22.3 0.2

Copper binding site 3 out of 3 in 9iq9

Go back to Copper Binding Sites List in 9iq9
Copper binding site 3 out of 3 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86


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 Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu303

b:18.0
occ:0.52
 NE2 B:HIS196 1.9 17.6 1.0
SG B:CYS86 2.1 19.7 0.7
SG B:CYS86 2.4 18.5 0.3
CE1 B:HIS196 2.8 20.4 1.0
CB B:CYS86 3.0 18.1 0.7
CB B:CYS86 3.0 18.1 0.3
CD2 B:HIS196 3.1 16.7 1.0
OH B:TYR107 3.3 17.8 1.0
CU B:CU1301 3.4 25.7 0.7
OD2 B:ASP109 3.4 15.2 0.8
CA B:CYS86 3.7 17.1 0.7
CA B:CYS86 3.7 17.1 0.3
CB B:ASP198 3.7 16.7 1.0
CZ B:TYR107 3.8 19.1 1.0
OD2 B:ASP109 3.8 16.4 0.2
ND1 B:HIS196 4.0 17.2 1.0
OD2 B:ASP113 4.0 18.5 1.0
CG B:HIS196 4.1 15.9 1.0
CE1 B:TYR107 4.1 15.3 1.0
OD2 B:ASP198 4.3 33.8 1.0
CE2 B:TYR107 4.5 19.6 1.0
CG B:ASP198 4.5 20.5 1.0
CB B:ALA240 4.5 15.6 1.0
CG B:ASP109 4.6 22.2 0.8
N B:ASP198 4.6 15.3 1.0
CA B:ASP198 4.6 15.2 1.0
O B:CYS86 4.6 18.0 1.0
C B:CYS86 4.6 16.2 1.0
O B:HOH533 4.7 28.1 1.0
N B:CYS86 4.7 15.5 1.0
O B:HOH509 4.7 19.6 1.0
O B:HOH405 4.9 21.6 0.5
CG B:ASP109 4.9 19.2 0.2
C B:ILE197 5.0 15.4 1.0

Reference:

K.Oda, K.Komaguchi, Y.Matoba. Copper Inactivates Dcsb By Oxidation of the CYS86 to Cysteine Sulfinic Aicd To Be Published.
Page generated: Wed Jul 31 10:30:36 2024

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