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Magnesium in PDB 9ixf: Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86.

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

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

Protein crystallography data

The structure of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86., PDB code: 9ixf 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) 43.92 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.876, 46.683, 58.222, 85.39, 86.78, 70.54
R / Rfree (%) 15.8 / 20.1

Other elements in 9ixf:

The structure of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized 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 Oxidized CYS86. (pdb code 9ixf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86., PDB code: 9ixf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9ixf

Go back to Magnesium Binding Sites List in 9ixf
Magnesium binding site 1 out of 4 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized 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 Oxidized CYS86. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:6.0
occ:0.92
 OD1 A:ASP109 2.0 8.5 1.0
OD2 A:ASP200 2.1 12.3 1.0
O A:HOH551 2.1 11.1 1.0
OD2 A:ASP198 2.2 12.7 1.0
OD1 A:ASP200 2.3 10.1 1.0
ND1 A:HIS111 2.3 10.2 1.0
CG A:ASP200 2.5 14.3 1.0
CG A:ASP109 3.0 9.5 1.0
CG A:ASP198 3.1 10.2 1.0
CE1 A:HIS111 3.2 12.4 1.0
CG A:HIS111 3.3 9.9 1.0
MN A:MN401 3.3 8.1 0.8
OD2 A:ASP109 3.4 8.5 1.0
OD1 A:ASP198 3.6 9.7 1.0
CB A:HIS111 3.7 10.7 1.0
N A:HIS111 3.8 10.1 1.0
O A:HOH505 4.0 19.1 1.0
N A:GLY110 4.0 9.0 1.0
CB A:ASP200 4.0 12.6 1.0
CB A:ASP198 4.0 10.7 1.0
O A:HOH608 4.3 13.8 1.0
NE2 A:HIS111 4.3 12.6 1.0
O A:HOH693 4.3 27.1 1.0
CB A:ASP109 4.4 7.8 1.0
CA A:HIS111 4.4 10.2 1.0
OD1 A:ASP113 4.4 10.3 1.0
CD2 A:HIS111 4.4 13.6 1.0
O A:HOH604 4.4 22.9 1.0
CA A:GLY110 4.6 9.2 1.0
C A:GLY110 4.6 11.8 1.0
CA A:ASP109 4.7 9.0 1.0
C A:ASP109 4.7 10.7 1.0
OD2 A:ASP113 4.8 11.5 1.0
CA A:ASP200 5.0 8.9 1.0
CG A:ASP113 5.0 12.3 1.0

Magnesium binding site 2 out of 4 in 9ixf

Go back to Magnesium Binding Sites List in 9ixf
Magnesium binding site 2 out of 4 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized 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 Oxidized CYS86. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:7.4
occ:0.83
 OD B:CSO86 1.8 17.6 0.5
O B:HOH630 2.1 18.5 1.0
OD2 B:ASP109 2.1 14.2 1.0
OD2 B:ASP113 2.1 15.4 1.0
O B:HOH560 2.1 18.4 1.0
OD2 B:ASP198 2.1 16.9 1.0
SG B:CSO86 2.6 17.1 0.5
SG B:CSO86 3.1 17.1 0.5
CG B:ASP113 3.1 14.8 1.0
CG B:ASP109 3.1 16.9 1.0
CG B:ASP198 3.2 15.5 1.0
OD1 B:ASP113 3.4 15.8 1.0
OD1 B:ASP109 3.4 20.4 1.0
CB B:ASP198 3.5 14.1 1.0
CB B:CSO86 3.7 15.9 0.5
CB B:CSO86 3.8 15.9 0.5
MG B:MG402 3.9 12.8 0.7
O B:HOH582 3.9 22.6 1.0
OH B:TYR107 4.0 15.1 1.0
OD2 B:ASP200 4.2 18.6 1.0
O B:GLY126 4.2 20.0 1.0
OD1 B:ASP198 4.3 14.6 1.0
CB B:ASP113 4.4 12.2 1.0
CB B:ASP109 4.4 14.9 1.0
CE1 B:TYR107 4.5 12.5 1.0
OE2 B:GLU241 4.5 20.4 1.0
CZ B:TYR107 4.7 15.6 1.0
CD B:GLU241 4.7 20.6 1.0
OE1 B:GLU241 4.8 19.8 1.0
OD1 B:ASP200 4.8 15.2 1.0
CG B:ASP200 4.9 18.1 1.0
NE2 B:HIS196 5.0 19.8 1.0

Magnesium binding site 3 out of 4 in 9ixf

Go back to Magnesium Binding Sites List in 9ixf
Magnesium binding site 3 out of 4 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized 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 Oxidized CYS86. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:12.8
occ:0.73
 O B:HOH582 2.0 22.6 1.0
OE2 B:GLU241 2.0 20.4 1.0
O B:HOH504 2.1 18.4 1.0
OD2 B:ASP200 2.1 18.6 1.0
OD2 B:ASP198 2.2 16.9 1.0
OD1 B:ASP198 2.3 14.6 1.0
CG B:ASP198 2.6 15.5 1.0
CG B:ASP200 3.0 18.1 1.0
CD B:GLU241 3.2 20.6 1.0
O B:HOH560 3.5 18.4 1.0
CB B:ASP200 3.7 18.3 1.0
O B:HOH630 3.8 18.5 1.0
O B:HOH585 3.8 29.8 1.0
MG B:MG401 3.9 7.4 0.8
OD1 B:ASP200 3.9 15.2 1.0
CG B:GLU241 4.0 16.5 1.0
OE1 B:GLU241 4.0 19.8 1.0
CB B:GLU241 4.0 15.8 1.0
CB B:ASP198 4.1 14.1 1.0
O B:ASP210 4.1 30.5 1.0
OD1 B:ASP210 4.3 41.2 1.0
N B:ASP200 4.5 12.7 1.0
CA B:ASP200 4.8 15.4 1.0
SG B:CSO86 4.8 17.1 0.5
OD B:CSO86 4.8 17.6 0.5
SG B:CSO86 4.9 17.1 0.5
O B:HOH704 4.9 33.1 1.0
OD2 B:ASP109 4.9 14.2 1.0

Magnesium binding site 4 out of 4 in 9ixf

Go back to Magnesium Binding Sites List in 9ixf
Magnesium binding site 4 out of 4 in the Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Manganese-Free N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:21.7
occ:0.67
 O B:HOH615 1.9 24.7 1.0
O B:HOH671 2.1 23.8 1.0
O B:HOH549 2.1 28.4 1.0
OE2 B:GLU162 2.1 24.2 1.0
O B:HOH547 2.2 30.6 1.0
O B:HOH670 2.2 30.1 1.0
CD B:GLU162 3.2 22.8 1.0
OE1 B:GLU162 3.5 24.2 1.0
OD1 B:ASP159 3.8 43.5 1.0
ND2 B:ASN115 4.1 21.1 1.0
O B:HIS111 4.1 24.5 1.0
O B:HOH520 4.3 27.0 1.0
ND1 B:HIS111 4.4 25.2 1.0
CB B:HIS111 4.4 16.4 1.0
CG B:GLU162 4.5 22.3 1.0
N B:ASP159 4.6 25.9 1.0
O B:HOH521 4.7 31.4 1.0
C B:HIS111 4.8 22.9 1.0
CB B:GLU162 4.8 24.9 1.0
CG B:ASP159 4.9 40.6 1.0
CG B:HIS111 4.9 20.2 1.0
O B:HOH673 4.9 23.3 1.0
CG2 B:ILE158 4.9 25.0 1.0
CA B:HIS111 4.9 14.9 1.0
CA B:ILE158 5.0 22.6 1.0

Reference:

K.Oda, Y.Matoba. Copper Inactivates Dcsb By Oxidizing the Metal Ligand CYS86 to Sulfinic Acid. Febs J. 2024.
ISSN: ISSN 1742-464X
DOI: 10.1111/FEBS.17325
Page generated: Wed Nov 27 19:10:15 2024

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