Atomistry » Manganese » PDB 7d7z-7eww » 7euk
Atomistry »
  Manganese »
    PDB 7d7z-7eww »
      7euk »

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

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

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

Protein crystallography data

The structure of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with L-Orn, PDB code: 7euk 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) 44.00 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.392, 46.963, 59.317, 83.53, 84.71, 70.14
R / Rfree (%) 15.8 / 17.9

Other elements in 7euk:

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

Magnesium (Mg) 1 atom

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 7euk

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


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 L-Orn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:7.1
occ:1.00
 OD2 A:ASP109 2.1 5.9 1.0
O A:HOH621 2.2 9.3 1.0
OD2 A:ASP113 2.2 7.1 1.0
OD2 A:ASP198 2.3 6.0 1.0
O A:HOH522 2.4 7.9 1.0
SG A:CYS86 2.5 8.0 1.0
CG A:ASP113 3.2 8.2 1.0
CG A:ASP109 3.2 5.7 1.0
CG A:ASP198 3.2 6.6 1.0
MN A:MN402 3.4 7.0 1.0
CB A:CYS86 3.4 7.2 1.0
OD1 A:ASP113 3.4 7.7 1.0
CB A:ASP198 3.5 6.0 1.0
OD1 A:ASP109 3.5 6.4 1.0
OH A:TYR107 4.0 7.6 1.0
OE2 A:GLU241 4.2 10.4 1.0
O A:GLY126 4.3 14.8 1.0
OD1 A:ASP198 4.3 6.8 1.0
CD A:GLU241 4.4 10.6 1.0
CE1 A:TYR107 4.5 6.8 1.0
CB A:ASP109 4.5 6.3 1.0
CB A:ASP113 4.5 8.9 1.0
OE1 A:GLU241 4.6 10.8 1.0
CZ A:TYR107 4.7 6.7 1.0
CA A:CYS86 4.8 7.6 1.0
NE2 A:HIS196 4.9 8.8 1.0
OD2 A:ASP200 4.9 8.0 1.0
O A:HOH507 4.9 11.7 1.0
CA A:ASP198 4.9 6.1 1.0

Manganese binding site 2 out of 4 in 7euk

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


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 L-Orn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:7.0
occ:1.00
 OD1 A:ASP109 2.1 6.4 1.0
OD2 A:ASP200 2.2 8.0 1.0
OD2 A:ASP198 2.2 6.0 1.0
O A:HOH522 2.2 7.9 1.0
ND1 A:HIS111 2.3 7.6 1.0
OD1 A:ASP200 2.4 7.5 1.0
CG A:ASP200 2.6 7.0 1.0
CG A:ASP198 3.1 6.6 1.0
CG A:ASP109 3.1 5.7 1.0
CE1 A:HIS111 3.1 7.8 1.0
CG A:HIS111 3.3 6.5 1.0
MN A:MN401 3.4 7.1 1.0
OD2 A:ASP109 3.4 5.9 1.0
OD1 A:ASP198 3.6 6.8 1.0
CB A:HIS111 3.6 6.4 1.0
N A:HIS111 3.8 6.8 1.0
O A:HOH507 3.8 11.7 1.0
CB A:ASP198 4.1 6.0 1.0
N A:GLY110 4.1 6.5 1.0
CB A:ASP200 4.1 7.0 1.0
NE2 A:HIS111 4.3 7.7 1.0
OD1 A:ASP113 4.4 7.7 1.0
CA A:HIS111 4.4 7.3 1.0
O A:HOH615 4.4 17.4 1.0
CD2 A:HIS111 4.4 7.7 1.0
O A:HOH621 4.4 9.3 1.0
CB A:ASP109 4.4 6.3 1.0
C A:GLY110 4.6 6.4 1.0
O A:HOH788 4.7 25.7 1.0
CA A:GLY110 4.7 7.7 1.0
CA A:ASP109 4.8 6.8 1.0
C A:ASP109 4.8 7.7 1.0
OD2 A:ASP113 4.8 7.1 1.0
CG A:ASP113 5.0 8.2 1.0

Manganese binding site 3 out of 4 in 7euk

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


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 L-Orn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:8.5
occ:1.00
 OD2 B:ASP109 2.2 8.0 1.0
O B:HOH627 2.2 12.4 1.0
OD2 B:ASP113 2.2 7.8 1.0
OD2 B:ASP198 2.3 8.5 1.0
O B:HOH501 2.3 10.2 1.0
SG B:CYS86 2.5 8.8 1.0
CG B:ASP113 3.1 8.2 1.0
CG B:ASP109 3.2 7.8 1.0
CG B:ASP198 3.2 8.2 1.0
MN B:MN402 3.3 9.9 1.0
OD1 B:ASP113 3.4 9.3 1.0
CB B:CYS86 3.4 9.3 1.0
OD1 B:ASP109 3.5 8.1 1.0
CB B:ASP198 3.5 8.0 1.0
NE B:ORN403 3.9 21.7 1.0
OH B:TYR107 4.1 8.3 1.0
OE2 B:GLU241 4.3 11.1 1.0
OD1 B:ASP198 4.3 8.8 1.0
O B:GLY126 4.4 16.0 1.0
CE1 B:TYR107 4.5 8.0 1.0
CD B:GLU241 4.5 10.2 1.0
CB B:ASP109 4.5 8.5 1.0
CB B:ASP113 4.5 8.5 1.0
CZ B:TYR107 4.7 8.5 1.0
OE1 B:GLU241 4.8 11.8 1.0
CA B:CYS86 4.8 8.8 1.0
NE2 B:HIS196 4.9 9.7 1.0
OD2 B:ASP200 4.9 9.6 1.0
CA B:ASP198 5.0 8.0 1.0

Manganese binding site 4 out of 4 in 7euk

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


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 L-Orn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:9.9
occ:1.00
 OD1 B:ASP109 2.1 8.1 1.0
OD2 B:ASP200 2.1 9.6 1.0
O B:HOH501 2.2 10.2 1.0
ND1 B:HIS111 2.2 9.3 1.0
OD2 B:ASP198 2.3 8.5 1.0
OD1 B:ASP200 2.4 9.2 1.0
CG B:ASP200 2.6 10.2 1.0
CG B:ASP109 3.1 7.8 1.0
CE1 B:HIS111 3.1 9.7 1.0
CG B:ASP198 3.1 8.2 1.0
CG B:HIS111 3.3 9.5 1.0
MN B:MN401 3.3 8.5 1.0
OD2 B:ASP109 3.4 8.0 1.0
OD1 B:ASP198 3.6 8.8 1.0
NE B:ORN403 3.7 21.7 1.0
CB B:HIS111 3.7 9.2 1.0
N B:HIS111 3.9 9.2 1.0
N B:GLY110 4.1 8.6 1.0
CB B:ASP200 4.1 9.6 1.0
CB B:ASP198 4.1 8.0 1.0
O B:HOH627 4.2 12.4 1.0
NE2 B:HIS111 4.3 12.7 1.0
OD1 B:ASP113 4.3 9.3 1.0
CD2 B:HIS111 4.4 11.5 1.0
CB B:ASP109 4.4 8.5 1.0
CA B:HIS111 4.5 9.5 1.0
O B:HOH584 4.5 10.4 1.0
C B:GLY110 4.6 9.2 1.0
CA B:GLY110 4.7 8.2 1.0
CD B:ORN403 4.7 23.8 1.0
CA B:ASP109 4.8 9.0 1.0
OD2 B:ASP113 4.8 7.8 1.0
C B:ASP109 4.8 8.1 1.0
CG B:ASP113 5.0 8.2 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 08:33:41 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy