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Magnesium in PDB 8ius: Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86

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

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

Protein crystallography data

The structure of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86, PDB code: 8ius 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) 35.25 / 2.14
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.872, 46.756, 58.139, 84.98, 86.4, 70.57
R / Rfree (%) 15.8 / 21.9

Other elements in 8ius:

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

Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 (pdb code 8ius). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86, PDB code: 8ius:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8ius

Go back to Magnesium Binding Sites List in 8ius
Magnesium binding site 1 out of 3 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:11.7
occ:1.00
OD2 A:ASP200 2.0 16.1 1.0
OD1 A:ASP109 2.1 12.2 1.0
O A:HOH517 2.1 15.6 1.0
ND1 A:HIS111 2.2 18.3 1.0
OD2 A:ASP198 2.3 16.8 1.0
OD1 A:ASP200 2.3 17.0 1.0
CG A:ASP200 2.5 17.6 1.0
CE1 A:HIS111 3.0 16.9 1.0
CG A:ASP109 3.0 12.9 1.0
CG A:ASP198 3.2 16.1 1.0
CG A:HIS111 3.2 18.9 1.0
MN A:MN401 3.3 17.8 1.0
OD2 A:ASP109 3.4 16.2 1.0
CB A:HIS111 3.6 16.4 1.0
OD1 A:ASP198 3.7 13.7 1.0
N A:HIS111 3.8 14.2 1.0
O A:HOH502 4.0 21.5 1.0
CB A:ASP200 4.0 17.9 1.0
N A:GLY110 4.0 13.7 1.0
CB A:ASP198 4.1 14.5 1.0
NE2 A:HIS111 4.2 18.8 1.0
O A:HOH558 4.3 27.3 1.0
OD1 A:ASP113 4.3 19.4 1.0
CD2 A:HIS111 4.3 19.1 1.0
O A:HOH572 4.3 18.8 1.0
CA A:HIS111 4.3 18.0 1.0
CB A:ASP109 4.4 12.5 1.0
CA A:GLY110 4.6 13.8 1.0
C A:GLY110 4.6 18.3 1.0
C A:ASP109 4.8 14.2 1.0
CA A:ASP109 4.8 15.1 1.0
OD2 A:ASP113 4.8 16.8 1.0
CG A:ASP113 5.0 18.3 1.0

Magnesium binding site 2 out of 3 in 8ius

Go back to Magnesium Binding Sites List in 8ius
Magnesium binding site 2 out of 3 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:35.1
occ:1.00
OE2 B:GLU241 2.0 32.7 1.0
O B:HOH535 2.0 34.8 1.0
OD2 B:ASP198 2.1 26.9 1.0
OD2 B:ASP200 2.3 28.2 1.0
O B:HOH502 2.3 36.0 1.0
OD1 B:ASP198 2.4 22.8 1.0
CG B:ASP198 2.6 26.5 1.0
CD B:GLU241 3.2 32.9 1.0
CG B:ASP200 3.2 25.6 1.0
O B:HOH523 3.4 24.1 1.0
O B:HOH522 3.5 37.1 1.0
CB B:ASP200 3.7 28.2 1.0
MG B:MG402 3.9 25.8 1.0
CG B:GLU241 4.0 29.4 1.0
O B:ASP210 4.0 49.0 1.0
CB B:GLU241 4.0 26.6 1.0
OE1 B:GLU241 4.0 34.7 1.0
O B:HOH587 4.1 28.0 1.0
OD1 B:ASP200 4.1 23.8 1.0
CB B:ASP198 4.1 20.1 1.0
O B:HOH548 4.3 35.6 1.0
N B:ASP200 4.6 22.5 1.0
CA B:ASP200 4.8 25.0 1.0
OD1 B:ASP210 4.8 57.7 1.0
CB B:TYR211 4.9 48.0 1.0
OD2 B:ASP109 4.9 24.0 1.0
SG B:CYS86 5.0 35.3 1.0

Magnesium binding site 3 out of 3 in 8ius

Go back to Magnesium Binding Sites List in 8ius
Magnesium binding site 3 out of 3 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Reduced CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:25.8
occ:1.00
OD2 B:ASP113 2.1 25.1 1.0
OD2 B:ASP109 2.2 24.0 1.0
O B:HOH587 2.2 28.0 1.0
OD2 B:ASP198 2.2 26.9 1.0
O B:HOH523 2.4 24.1 1.0
SG B:CYS86 2.7 35.3 1.0
CG B:ASP113 3.1 25.8 1.0
CG B:ASP109 3.2 27.2 1.0
CG B:ASP198 3.3 26.5 1.0
OD1 B:ASP113 3.3 24.1 1.0
CB B:ASP198 3.6 20.1 1.0
OD1 B:ASP109 3.6 21.9 1.0
O B:HOH535 3.8 34.8 1.0
CB B:CYS86 3.8 30.9 1.0
MG B:MG401 3.9 35.1 1.0
OD2 B:ASP200 4.0 28.2 1.0
OH B:TYR107 4.0 22.8 1.0
O B:GLY126 4.3 26.7 1.0
OD1 B:ASP198 4.4 22.8 1.0
CB B:ASP113 4.5 23.5 1.0
CE1 B:TYR107 4.5 21.7 1.0
CB B:ASP109 4.5 22.8 1.0
OE2 B:GLU241 4.5 32.7 1.0
CZ B:TYR107 4.7 25.8 1.0
CD B:GLU241 4.8 32.9 1.0
CG B:ASP200 4.8 25.6 1.0
OD1 B:ASP200 4.8 23.8 1.0
NE2 B:HIS196 4.8 29.6 1.0
OE1 B:GLU241 4.9 34.7 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: Fri Oct 4 11:01:25 2024

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