Atomistry » Manganese » PDB 5z2k-6a9u » 5zeh
Atomistry »
  Manganese »
    PDB 5z2k-6a9u »
      5zeh »

Manganese in PDB 5zeh: Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A

Enzymatic activity of Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A

All present enzymatic activity of Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A, PDB code: 5zeh was solved by A.Malik, V.Dalal, S.Ankri, S.Tomar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.68 / 2.36
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.605, 97.494, 133.255, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 26.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A (pdb code 5zeh). 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 Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A, PDB code: 5zeh:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5zeh

Go back to Manganese Binding Sites List in 5zeh
Manganese binding site 1 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A


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 Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:77.3
occ:1.00
 OD2 A:ASP124 2.0 62.1 1.0
OD2 A:ASP225 2.2 64.9 1.0
ND1 A:HIS98 2.3 58.9 1.0
OD2 A:ASP128 2.3 66.7 1.0
O A:HOH401 2.3 51.5 1.0
O A:HOH406 2.7 68.4 1.0
CG A:ASP124 3.0 63.8 1.0
CG A:HIS98 3.0 58.4 1.0
CB A:HIS98 3.2 58.5 1.0
CG A:ASP128 3.2 67.0 1.0
CG A:ASP225 3.3 64.8 1.0
CE1 A:HIS98 3.3 59.1 1.0
OD1 A:ASP124 3.4 64.0 1.0
MN A:MN303 3.4 76.7 1.0
OD1 A:ASP128 3.4 67.3 1.0
NE A:ORN301 3.8 84.0 1.0
CB A:ASP225 4.1 65.0 1.0
CD2 A:HIS98 4.2 58.1 1.0
OD1 A:ASP225 4.3 65.6 1.0
NE2 A:HIS98 4.3 58.5 1.0
CB A:ASP124 4.3 64.9 1.0
NE1 A:TRP122 4.4 63.1 1.0
O A:HIS141 4.4 63.3 1.0
CZ2 A:TRP122 4.5 61.3 1.0
CB A:ASP128 4.6 67.3 1.0
O A:HOH403 4.6 55.3 1.0
ND1 A:HIS126 4.6 66.9 1.0
CA A:HIS98 4.7 58.1 1.0
O A:HIS126 4.7 67.8 1.0
CB A:HIS126 4.7 67.3 1.0
OE2 A:GLU270 4.8 62.8 1.0
CE2 A:TRP122 4.8 62.3 1.0
CG A:GLU270 4.8 62.6 1.0

Manganese binding site 2 out of 4 in 5zeh

Go back to Manganese Binding Sites List in 5zeh
Manganese binding site 2 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A


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 Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:76.7
occ:1.00
 OD1 A:ASP124 2.0 64.0 1.0
O A:HOH401 2.0 51.5 1.0
OD2 A:ASP225 2.3 64.9 1.0
ND1 A:HIS126 2.3 66.9 1.0
OD2 A:ASP227 2.5 66.7 1.0
OD1 A:ASP227 2.6 68.4 1.0
CG A:ASP227 2.9 67.2 1.0
CG A:ASP225 2.9 64.8 1.0
CG A:ASP124 3.0 63.8 1.0
CE1 A:HIS126 3.1 67.4 1.0
OD1 A:ASP225 3.3 65.6 1.0
OD2 A:ASP124 3.3 62.1 1.0
MN A:MN302 3.4 77.3 1.0
CG A:HIS126 3.5 67.4 1.0
N A:ALA125 3.8 67.2 1.0
O A:HOH403 3.8 55.3 1.0
N A:HIS126 3.9 68.1 1.0
CB A:ASP225 4.0 65.0 1.0
CB A:HIS126 4.0 67.3 1.0
NE A:ORN301 4.3 84.0 1.0
CB A:ASP124 4.3 64.9 1.0
CB A:ALA125 4.3 68.3 1.0
NE2 A:HIS126 4.3 68.3 1.0
CB A:ASP227 4.3 67.2 1.0
CA A:ALA125 4.4 68.5 1.0
OG1 A:THR239 4.5 65.9 1.0
CD2 A:HIS126 4.5 68.2 1.0
CA A:ASP124 4.6 66.1 1.0
O A:HOH406 4.6 68.4 1.0
CA A:HIS126 4.6 68.3 1.0
C A:ASP124 4.6 67.3 1.0
C A:ALA125 4.6 68.8 1.0
CD A:ORN301 4.9 84.0 1.0
C A:ASP227 4.9 67.8 1.0
CA A:ASP227 5.0 67.5 1.0
N A:GLY228 5.0 67.2 1.0

Manganese binding site 3 out of 4 in 5zeh

Go back to Manganese Binding Sites List in 5zeh
Manganese binding site 3 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A


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 Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:73.8
occ:1.00
 OD2 B:ASP124 2.0 55.0 1.0
O B:HOH402 2.1 46.3 1.0
OD2 B:ASP128 2.3 64.2 1.0
ND1 B:HIS98 2.3 57.6 1.0
OD2 B:ASP225 2.5 58.2 1.0
CG B:ASP124 3.0 56.4 1.0
CG B:HIS98 3.1 57.3 1.0
CB B:HIS98 3.2 58.3 1.0
CG B:ASP128 3.2 65.3 1.0
MN B:MN303 3.3 72.5 1.0
CE1 B:HIS98 3.3 56.8 1.0
OD1 B:ASP124 3.4 57.0 1.0
OD1 B:ASP128 3.4 66.9 1.0
CG B:ASP225 3.5 57.8 1.0
CB B:ASP225 4.0 57.3 1.0
NE B:ORN301 4.1 85.2 1.0
CD2 B:HIS98 4.2 56.8 1.0
CB B:ASP124 4.3 56.5 1.0
NE1 B:TRP122 4.3 58.1 1.0
NE2 B:HIS98 4.3 56.5 1.0
O B:HIS141 4.4 63.6 1.0
OD1 B:ASP225 4.5 57.9 1.0
CZ2 B:TRP122 4.5 56.8 1.0
CB B:ASP128 4.6 65.6 1.0
O B:HOH412 4.6 61.5 1.0
O B:HIS126 4.6 63.7 1.0
CA B:HIS98 4.7 58.2 1.0
CE2 B:TRP122 4.7 57.0 1.0
CB B:HIS126 4.8 64.3 1.0
OE2 B:GLU270 4.8 64.0 1.0
CG B:GLU270 4.9 62.8 1.0
ND1 B:HIS126 5.0 64.9 1.0

Manganese binding site 4 out of 4 in 5zeh

Go back to Manganese Binding Sites List in 5zeh
Manganese binding site 4 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A


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 Entamoeba Histolytica Arginase in Complex with L- Ornithine at 2.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:72.5
occ:1.00
 O B:HOH402 2.1 46.3 1.0
OD1 B:ASP124 2.2 57.0 1.0
OD1 B:ASP227 2.4 62.9 1.0
OD2 B:ASP225 2.4 58.2 1.0
ND1 B:HIS126 2.6 64.9 1.0
OD2 B:ASP227 2.8 64.1 1.0
CG B:ASP227 2.9 63.3 1.0
CG B:ASP124 3.1 56.4 1.0
CG B:ASP225 3.3 57.8 1.0
MN B:MN302 3.3 73.8 1.0
CE1 B:HIS126 3.4 66.0 1.0
OD2 B:ASP124 3.4 55.0 1.0
O B:HOH412 3.5 61.5 1.0
CG B:HIS126 3.6 65.5 1.0
OD1 B:ASP225 3.9 57.9 1.0
CB B:HIS126 4.0 64.3 1.0
CB B:ASP225 4.1 57.3 1.0
N B:HIS126 4.1 63.4 1.0
N B:ALA125 4.1 60.4 1.0
NE B:ORN301 4.2 85.2 1.0
OG1 B:THR239 4.3 63.8 1.0
CB B:ASP227 4.4 63.5 1.0
CB B:ASP124 4.5 56.5 1.0
NE2 B:HIS126 4.5 67.8 1.0
CB B:ALA125 4.5 63.5 1.0
CD B:ORN301 4.6 85.4 1.0
CA B:HIS126 4.7 64.5 1.0
CD2 B:HIS126 4.7 67.3 1.0
CA B:ALA125 4.7 62.7 1.0
CA B:ASP124 4.8 57.4 1.0
C B:ALA125 4.9 63.7 1.0
C B:ASP124 4.9 59.3 1.0
CG B:GLU270 5.0 62.8 1.0

Reference:

A.Malik, V.Dalal, S.Ankri, S.Tomar. Structural Insights Into Entamoeba Histolytica Arginase and Structure-Based Identification of Novel Non-Amino Acid Based Inhibitors As Potential Antiamoebic Molecules. Febs J. V. 286 4135 2019.
ISSN: ISSN 1742-464X
PubMed: 31199070
DOI: 10.1111/FEBS.14960
Page generated: Sun Oct 6 03:41:02 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy