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Manganese in PDB 9ixc: Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86

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

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

Protein crystallography data

The structure of Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86, PDB code: 9ixc 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) 35.22 / 1.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.94, 46.743, 58.338, 85.33, 86.91, 70.59
R / Rfree (%) 16.5 / 18.6

Other elements in 9ixc:

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

Magnesium (Mg) 1 atom

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 9ixc

Go back to Manganese Binding Sites List in 9ixc
Manganese binding site 1 out of 4 in the Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:3.6
occ:0.72
 OD2 A:ASP109 2.2 5.9 1.0
O A:HOH598 2.2 9.6 1.0
OD2 A:ASP113 2.2 7.2 1.0
OD2 A:ASP198 2.3 7.1 1.0
O A:HOH518 2.3 7.1 1.0
SG A:CYS86 2.5 7.7 1.0
CG A:ASP113 3.2 7.9 1.0
CG A:ASP109 3.2 5.1 1.0
CG A:ASP198 3.3 7.0 1.0
MN A:MN402 3.4 2.9 0.7
OD1 A:ASP113 3.4 8.3 1.0
CB A:CYS86 3.4 6.2 1.0
OD1 A:ASP109 3.5 6.4 1.0
CB A:ASP198 3.5 7.1 1.0
OH A:TYR107 4.0 7.4 1.0
OE2 A:GLU241 4.3 10.9 1.0
OD1 A:ASP198 4.4 7.1 1.0
O A:GLY126 4.4 16.2 1.0
CD A:GLU241 4.5 11.8 1.0
CE1 A:TYR107 4.5 7.3 1.0
CB A:ASP109 4.5 7.0 1.0
CB A:ASP113 4.5 8.1 1.0
CZ A:TYR107 4.7 5.8 1.0
OE1 A:GLU241 4.7 13.7 1.0
O B:HOH519 4.7 23.3 1.0
CA A:CYS86 4.8 7.1 1.0
NE2 A:HIS196 4.9 9.1 1.0
CA A:ASP198 5.0 7.4 1.0
OD2 A:ASP200 5.0 7.3 1.0

Manganese binding site 2 out of 4 in 9ixc

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Manganese binding site 2 out of 4 in the Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:2.9
occ:0.68
 OD1 A:ASP109 2.1 6.4 1.0
OD2 A:ASP200 2.2 7.3 1.0
O A:HOH518 2.2 7.1 1.0
ND1 A:HIS111 2.3 6.7 1.0
OD2 A:ASP198 2.3 7.1 1.0
OD1 A:ASP200 2.4 6.7 1.0
CG A:ASP200 2.6 6.6 1.0
CG A:ASP109 3.1 5.1 1.0
CG A:ASP198 3.1 7.0 1.0
CE1 A:HIS111 3.2 7.0 1.0
CG A:HIS111 3.3 7.5 1.0
MN A:MN401 3.4 3.6 0.7
OD2 A:ASP109 3.4 5.9 1.0
OD1 A:ASP198 3.6 7.1 1.0
CB A:HIS111 3.6 7.3 1.0
N A:HIS111 3.8 6.7 1.0
O A:HOH519 4.0 17.5 1.0
CB A:ASP198 4.1 7.1 1.0
CB A:ASP200 4.1 7.2 1.0
N A:GLY110 4.1 7.0 1.0
O B:HOH519 4.3 23.3 1.0
NE2 A:HIS111 4.3 7.8 1.0
CA A:HIS111 4.4 7.6 1.0
OD1 A:ASP113 4.4 8.3 1.0
O A:HOH598 4.4 9.6 1.0
O A:HOH603 4.4 17.4 1.0
CD2 A:HIS111 4.4 8.5 1.0
CB A:ASP109 4.4 7.0 1.0
C A:GLY110 4.6 7.2 1.0
CA A:GLY110 4.7 9.2 1.0
CA A:ASP109 4.8 6.9 1.0
C A:ASP109 4.8 6.6 1.0
OD2 A:ASP113 4.8 7.2 1.0

Manganese binding site 3 out of 4 in 9ixc

Go back to Manganese Binding Sites List in 9ixc
Manganese binding site 3 out of 4 in the Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:6.2
occ:0.70
 OD B:CSO86 1.9 12.5 0.4
OD2 B:ASP113 2.2 9.3 1.0
OD2 B:ASP109 2.2 8.6 1.0
O B:HOH649 2.2 15.2 1.0
OD2 B:ASP198 2.3 10.4 1.0
O B:HOH521 2.3 11.4 1.0
SG B:CSO86 2.5 8.9 0.6
SG B:CSO86 2.9 8.9 0.4
CG B:ASP113 3.1 8.5 1.0
CG B:ASP109 3.2 8.8 1.0
CG B:ASP198 3.2 8.0 1.0
MN B:MN402 3.3 6.7 0.7
OD1 B:ASP113 3.4 9.5 1.0
CB B:CSO86 3.4 9.2 0.6
OD1 B:ASP109 3.5 9.0 1.0
CB B:ASP198 3.5 8.8 1.0
CB B:CSO86 3.7 8.7 0.4
OH B:TYR107 4.0 9.2 1.0
OD1 B:ASP198 4.3 8.9 1.0
OE2 B:GLU241 4.4 13.0 1.0
O B:GLY126 4.4 12.7 1.0
CE1 B:TYR107 4.5 8.7 1.0
CB B:ASP109 4.5 8.7 1.0
CB B:ASP113 4.5 10.8 1.0
CD B:GLU241 4.6 11.6 1.0
CZ B:TYR107 4.7 8.7 1.0
O B:HOH684 4.8 24.9 1.0
NE2 B:HIS196 4.8 12.9 1.0
CA B:CSO86 4.9 9.4 0.6
OD2 B:ASP200 4.9 11.0 1.0
CA B:ASP198 5.0 7.8 1.0
OE1 B:GLU241 5.0 15.0 1.0

Manganese binding site 4 out of 4 in 9ixc

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Manganese binding site 4 out of 4 in the Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Manganese-Rebound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:6.7
occ:0.71
 OD1 B:ASP109 2.2 9.0 1.0
OD2 B:ASP200 2.2 11.0 1.0
O B:HOH521 2.2 11.4 1.0
ND1 B:HIS111 2.2 12.3 1.0
OD2 B:ASP198 2.3 10.4 1.0
OD1 B:ASP200 2.4 9.8 1.0
CG B:ASP200 2.6 9.8 1.0
CE1 B:HIS111 3.1 13.3 1.0
CG B:ASP109 3.1 8.8 1.0
CG B:ASP198 3.1 8.0 1.0
MN B:MN401 3.3 6.2 0.7
CG B:HIS111 3.3 10.6 1.0
OD2 B:ASP109 3.4 8.6 1.0
OD1 B:ASP198 3.7 8.9 1.0
CB B:HIS111 3.8 11.4 1.0
N B:HIS111 3.9 9.3 1.0
N B:GLY110 4.1 9.0 1.0
CB B:ASP200 4.1 10.5 1.0
CB B:ASP198 4.1 8.8 1.0
O B:HOH649 4.2 15.2 1.0
NE2 B:HIS111 4.3 14.1 1.0
OD1 B:ASP113 4.3 9.5 1.0
CD2 B:HIS111 4.4 13.0 1.0
CB B:ASP109 4.5 8.7 1.0
CA B:HIS111 4.5 10.0 1.0
O B:HOH684 4.5 24.9 1.0
O B:HOH550 4.6 14.6 1.0
C B:GLY110 4.6 10.5 1.0
CA B:GLY110 4.7 10.0 1.0
OD2 B:ASP113 4.8 9.3 1.0
CA B:ASP109 4.8 8.3 1.0
C B:ASP109 4.8 8.2 1.0
OD B:CSO86 4.8 12.5 0.4
CG B:ASP113 5.0 8.5 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 20:28:12 2024

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