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Manganese in PDB 7eun: Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh

Enzymatic activity of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh

All present enzymatic activity of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh:
3.5.3.25;

Protein crystallography data

The structure of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh, PDB code: 7eun 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) 44.26 / 1.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.577, 47.208, 59.641, 83.54, 84.44, 70.2
R / Rfree (%) 11.5 / 13.8

Other elements in 7eun:

The structure of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh (pdb code 7eun). 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 N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh, PDB code: 7eun:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7eun

Go back to Manganese Binding Sites List in 7eun
Manganese binding site 1 out of 4 in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh


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 N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:6.2
occ:1.00
OD2 A:ASP109 2.1 6.1 1.0
O A:HOH643 2.2 9.7 1.0
OD2 A:ASP113 2.2 6.4 1.0
OD2 A:ASP198 2.3 5.6 1.0
O A:HOH513 2.3 7.2 1.0
SG A:CYS86 2.5 7.0 1.0
HB2 A:ASP198 3.0 6.8 1.0
CG A:ASP109 3.2 5.5 1.0
CG A:ASP113 3.2 6.8 1.0
CG A:ASP198 3.2 5.6 1.0
HB2 A:CYS86 3.2 8.9 1.0
HH A:TYR107 3.3 8.3 1.0
MN A:MN402 3.4 8.0 1.0
OD1 A:ASP113 3.4 7.2 1.0
CB A:CYS86 3.4 7.4 1.0
OD1 A:ASP109 3.5 6.0 1.0
CB A:ASP198 3.5 5.6 1.0
HB3 A:CYS86 3.7 8.9 1.0
HE1 A:TYR107 3.8 7.5 1.0
HB3 A:ASP198 3.8 6.8 1.0
OH A:TYR107 4.0 6.9 1.0
HE2 A:HIS196 4.1 11.0 1.0
OE2 A:GLU241 4.3 10.2 1.0
OD1 A:ASP198 4.3 6.2 1.0
O A:GLY126 4.3 13.2 1.0
HB2 A:HIS111 4.4 7.2 1.0
CE1 A:TYR107 4.5 6.2 1.0
HB2 A:ASP109 4.5 6.8 1.0
CB A:ASP109 4.5 5.7 1.0
HG3 A:GLU241 4.5 12.0 1.0
CD A:GLU241 4.5 9.6 1.0
CB A:ASP113 4.5 7.0 1.0
O B:HOH715 4.6 32.8 1.0
H A:CYS86 4.7 7.9 1.0
HB2 A:ASP113 4.7 8.4 1.0
CZ A:TYR107 4.7 6.0 1.0
OE1 A:GLU241 4.8 10.8 1.0
HB3 A:ASP113 4.8 8.4 1.0
CA A:CYS86 4.8 6.9 1.0
OD2 A:ASP200 4.9 7.0 1.0
NE2 A:HIS196 4.9 9.1 1.0
CA A:ASP198 5.0 5.9 1.0
HB3 A:ASP109 5.0 6.8 1.0

Manganese binding site 2 out of 4 in 7eun

Go back to Manganese Binding Sites List in 7eun
Manganese binding site 2 out of 4 in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh


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 N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:8.0
occ:1.00
OD1 A:ASP109 2.1 6.0 1.0
OD2 A:ASP200 2.1 7.0 1.0
O A:HOH513 2.2 7.2 1.0
OD2 A:ASP198 2.2 5.6 1.0
ND1 A:HIS111 2.2 6.0 1.0
OD1 A:ASP200 2.4 6.6 1.0
CG A:ASP200 2.6 6.7 1.0
CG A:ASP109 3.0 5.5 1.0
CG A:ASP198 3.1 5.6 1.0
HB2 A:HIS111 3.1 7.2 1.0
CE1 A:HIS111 3.1 6.4 1.0
H A:HIS111 3.2 6.8 1.0
HE1 A:HIS111 3.2 7.7 1.0
CG A:HIS111 3.3 6.0 1.0
MN A:MN401 3.4 6.2 1.0
OD2 A:ASP109 3.4 6.1 1.0
OD1 A:ASP198 3.6 6.2 1.0
CB A:HIS111 3.7 6.0 1.0
H A:GLY110 3.7 6.4 1.0
N A:HIS111 3.9 5.6 1.0
HB3 A:ASP198 3.9 6.8 1.0
CB A:ASP198 4.1 5.6 1.0
CB A:ASP200 4.1 6.8 1.0
O B:HOH715 4.1 32.8 1.0
N A:GLY110 4.1 5.4 1.0
NE2 A:HIS111 4.3 6.7 1.0
OD1 A:ASP113 4.3 7.2 1.0
CD2 A:HIS111 4.4 6.9 1.0
HA A:ASP109 4.4 6.5 1.0
CB A:ASP109 4.4 5.7 1.0
O A:HOH616 4.4 16.9 1.0
CA A:HIS111 4.4 5.9 1.0
HB2 A:ASP198 4.4 6.8 1.0
O A:HOH531 4.4 19.1 1.0
O A:HOH643 4.4 9.7 1.0
HB3 A:ASP200 4.4 8.2 1.0
HB3 A:HIS111 4.5 7.2 1.0
HB2 A:ASP200 4.5 8.2 1.0
HA3 A:GLY110 4.6 7.4 1.0
C A:GLY110 4.7 5.9 1.0
H A:ASP200 4.7 6.9 1.0
CA A:GLY110 4.7 6.2 1.0
CA A:ASP109 4.7 5.5 1.0
C A:ASP109 4.8 5.5 1.0
HB3 A:ASP109 4.8 6.8 1.0
OD2 A:ASP113 4.8 6.4 1.0
HB2 B:LYS36 4.9 10.3 1.0
CG A:ASP113 5.0 6.8 1.0

Manganese binding site 3 out of 4 in 7eun

Go back to Manganese Binding Sites List in 7eun
Manganese binding site 3 out of 4 in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh


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 N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:7.8
occ:1.00
OD2 B:ASP109 2.1 7.2 1.0
O2 B:ABH405 2.2 11.7 1.0
OD2 B:ASP113 2.2 7.4 1.0
O1 B:ABH405 2.3 8.2 1.0
OD2 B:ASP198 2.3 7.4 1.0
HO1 B:ABH405 2.4 9.8 1.0
SG B:CYS86 2.5 8.2 1.0
B B:ABH405 2.8 10.3 1.0
HO2 B:ABH405 2.9 14.0 1.0
HB2 B:ASP198 3.1 7.4 1.0
CG B:ASP113 3.1 7.4 1.0
CG B:ASP109 3.2 6.7 1.0
HB2 B:CYS86 3.2 9.8 1.0
HH B:TYR107 3.3 9.2 1.0
CG B:ASP198 3.3 6.5 1.0
CB B:CYS86 3.4 8.2 1.0
OD1 B:ASP113 3.4 8.4 1.0
MN B:MN402 3.4 8.8 1.0
OD1 B:ASP109 3.5 6.6 1.0
HB3 B:CYS86 3.5 9.8 1.0
O3 B:ABH405 3.6 9.9 1.0
CB B:ASP198 3.6 6.1 1.0
HE1 B:TYR107 3.7 8.2 1.0
HB3 B:ASP198 3.8 7.4 1.0
HE2 B:HIS196 3.9 11.5 1.0
OH B:TYR107 4.0 7.7 1.0
MG B:MG403 4.1 10.1 1.0
CE B:ABH405 4.2 10.9 1.0
OE1 B:GLU241 4.2 12.7 1.0
HCE2 B:ABH405 4.2 13.1 1.0
O B:GLY126 4.4 11.5 1.0
HO3 B:ABH405 4.4 11.9 1.0
CE1 B:TYR107 4.4 6.8 1.0
OD1 B:ASP198 4.4 7.8 1.0
HB2 B:HIS111 4.5 9.8 1.0
CB B:ASP109 4.5 6.9 1.0
HB2 B:ASP109 4.5 8.3 1.0
CB B:ASP113 4.5 7.9 1.0
CD B:GLU241 4.5 11.6 1.0
CZ B:TYR107 4.7 6.7 1.0
OE2 B:GLU241 4.7 11.1 1.0
HB2 B:ASP113 4.7 9.5 1.0
H B:CYS86 4.8 8.6 1.0
NE2 B:HIS196 4.8 9.6 1.0
HCE1 B:ABH405 4.8 13.1 1.0
HB3 B:ASP113 4.8 9.5 1.0
CA B:CYS86 4.8 7.7 1.0
HCD2 B:ABH405 4.9 14.9 1.0
HG3 B:GLU241 4.9 14.0 1.0
OD2 B:ASP200 4.9 8.2 1.0
O B:HOH509 5.0 27.4 1.0
HB3 B:ASP109 5.0 8.3 1.0

Manganese binding site 4 out of 4 in 7eun

Go back to Manganese Binding Sites List in 7eun
Manganese binding site 4 out of 4 in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh


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 N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:8.8
occ:1.00
O1 B:ABH405 2.1 8.2 1.0
OD1 B:ASP109 2.1 6.6 1.0
ND1 B:HIS111 2.2 8.4 1.0
OD2 B:ASP200 2.2 8.2 1.0
OD2 B:ASP198 2.4 7.4 1.0
OD1 B:ASP200 2.5 8.0 1.0
HO1 B:ABH405 2.7 9.8 1.0
CG B:ASP200 2.7 7.7 1.0
O3 B:ABH405 2.9 9.9 1.0
HB2 B:HIS111 3.1 9.8 1.0
CG B:ASP109 3.1 6.7 1.0
CE1 B:HIS111 3.1 9.1 1.0
B B:ABH405 3.1 10.3 1.0
MG B:MG403 3.2 10.1 1.0
HE1 B:HIS111 3.2 10.9 1.0
CG B:ASP198 3.2 6.5 1.0
CG B:HIS111 3.3 8.3 1.0
H B:HIS111 3.3 9.3 1.0
OD2 B:ASP109 3.4 7.2 1.0
MN B:MN401 3.4 7.8 1.0
HCD2 B:ABH405 3.5 14.9 1.0
CB B:HIS111 3.6 8.2 1.0
H B:GLY110 3.7 8.3 1.0
HO3 B:ABH405 3.8 11.9 1.0
OD1 B:ASP198 3.8 7.8 1.0
N B:HIS111 3.9 7.8 1.0
HB3 B:ASP198 4.0 7.4 1.0
O2 B:ABH405 4.0 11.7 1.0
N B:GLY110 4.2 6.9 1.0
CB B:ASP200 4.2 7.5 1.0
CB B:ASP198 4.2 6.1 1.0
CD B:ABH405 4.2 12.4 1.0
CE B:ABH405 4.2 10.9 1.0
NE2 B:HIS111 4.3 10.2 1.0
OD1 B:ASP113 4.3 8.4 1.0
CD2 B:HIS111 4.3 9.6 1.0
CA B:HIS111 4.4 7.6 1.0
HB3 B:HIS111 4.4 9.8 1.0
CB B:ASP109 4.4 6.9 1.0
HCD1 B:ABH405 4.4 14.9 1.0
HA B:ASP109 4.5 7.9 1.0
HB2 B:ASP198 4.5 7.4 1.0
HB3 B:ASP200 4.5 9.0 1.0
HB2 B:ASP200 4.5 9.0 1.0
HA3 B:GLY110 4.6 9.0 1.0
C B:GLY110 4.7 7.2 1.0
HO2 B:ABH405 4.7 14.0 1.0
HD2 B:TYR211 4.7 26.4 1.0
CA B:GLY110 4.7 7.5 1.0
OE1 B:GLU241 4.7 12.7 1.0
HB3 B:ASP109 4.8 8.3 1.0
OD1 B:ASP210 4.8 16.2 1.0
CA B:ASP109 4.8 6.6 1.0
OD2 B:ASP113 4.8 7.4 1.0
HCE2 B:ABH405 4.8 13.1 1.0
C B:ASP109 4.9 6.6 1.0
H B:ASP200 4.9 8.0 1.0
HB2 B:TYR211 4.9 23.0 1.0
HCE1 B:ABH405 5.0 13.1 1.0
CG B:ASP113 5.0 7.4 1.0

Reference:

K.Oda, T.Sakaguchi, Y.Matoba. Catalytic Mechanism of Dcsb: Arginase Framework Used For Hydrolyzing Its Inhibitor. Protein Sci. V. 31 E4338 2022.
ISSN: ESSN 1469-896X
PubMed: 35634777
DOI: 10.1002/PRO.4338
Page generated: Sun Oct 6 08:34:29 2024

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