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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

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