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Manganese in PDB 5zef: Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 A

Enzymatic activity of Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 A

All present enzymatic activity of Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 A:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 A, PDB code: 5zef 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) 41.00 / 2.01
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.947, 98.358, 135.329, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 A (pdb code 5zef). 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- Norvaline at 2.01 A, PDB code: 5zef:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5zef

Go back to Manganese Binding Sites List in 5zef
Manganese binding site 1 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 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- Norvaline at 2.01 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:44.5
occ:1.00
 OD2 A:ASP124 1.8 30.5 1.0
ND1 A:HIS98 2.2 33.1 1.0
OD2 A:ASP128 2.2 42.2 1.0
OD2 A:ASP225 2.2 32.3 1.0
O A:HOH426 2.3 39.4 1.0
CG A:ASP124 2.8 37.3 1.0
CG A:HIS98 3.1 35.3 1.0
CG A:ASP128 3.1 42.1 1.0
CB A:HIS98 3.2 36.9 1.0
CE1 A:HIS98 3.3 34.4 1.0
CG A:ASP225 3.3 38.8 1.0
OD1 A:ASP124 3.3 40.0 1.0
MN A:MN303 3.4 47.5 1.0
OD1 A:ASP128 3.4 42.0 1.0
CB A:ASP225 3.6 41.0 1.0
NE1 A:TRP122 4.1 40.0 1.0
CB A:ASP124 4.2 38.4 1.0
CD2 A:HIS98 4.2 34.3 1.0
NE2 A:HIS98 4.3 34.3 1.0
OD1 A:ASP225 4.4 42.6 1.0
O A:HOH463 4.4 42.4 1.0
CZ2 A:TRP122 4.5 36.2 1.0
CB A:ASP128 4.5 40.0 1.0
O A:HIS141 4.5 39.6 1.0
CE2 A:TRP122 4.6 37.5 1.0
O A:HIS126 4.7 41.7 1.0
CA A:HIS98 4.8 36.6 1.0
OE2 A:GLU270 5.0 39.5 1.0

Manganese binding site 2 out of 4 in 5zef

Go back to Manganese Binding Sites List in 5zef
Manganese binding site 2 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 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- Norvaline at 2.01 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:47.5
occ:1.00
 OD2 A:ASP227 2.4 40.1 1.0
OD1 A:ASP124 2.4 40.0 1.0
OD2 A:ASP225 2.4 32.3 1.0
ND1 A:HIS126 2.5 34.3 1.0
OD1 A:ASP227 2.6 39.7 1.0
O A:HOH426 2.8 39.4 1.0
CG A:ASP227 2.8 41.7 1.0
O A:HOH463 3.0 42.4 1.0
CG A:ASP225 3.1 38.8 1.0
CE1 A:HIS126 3.3 38.2 1.0
CG A:ASP124 3.3 37.3 1.0
MN A:MN302 3.4 44.5 1.0
OD1 A:ASP225 3.4 42.6 1.0
CG A:HIS126 3.6 38.1 1.0
OD2 A:ASP124 3.6 30.5 1.0
CB A:HIS126 4.0 37.8 1.0
OG1 A:THR239 4.0 40.6 1.0
CB A:ASP225 4.2 41.0 1.0
N A:HIS126 4.3 38.2 1.0
CB A:ASP227 4.3 40.4 1.0
N A:ALA125 4.4 38.7 1.0
NE2 A:HIS126 4.5 38.2 1.0
O A:HOH428 4.5 43.4 1.0
CD A:NVA301 4.5 57.1 1.0
OD1 A:ASP128 4.6 42.0 1.0
CD2 A:HIS126 4.7 37.3 1.0
CB A:ASP124 4.7 38.4 1.0
CA A:HIS126 4.8 40.4 1.0
CB A:ALA125 4.8 40.1 1.0
CA A:ALA125 5.0 41.0 1.0
CG A:GLU270 5.0 39.9 1.0
OD2 A:ASP128 5.0 42.2 1.0

Manganese binding site 3 out of 4 in 5zef

Go back to Manganese Binding Sites List in 5zef
Manganese binding site 3 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 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- Norvaline at 2.01 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:40.4
occ:1.00
 OD2 B:ASP124 1.8 29.4 1.0
ND1 B:HIS98 2.1 37.9 1.0
OD2 B:ASP225 2.3 34.4 1.0
OD2 B:ASP128 2.3 35.1 1.0
O B:HOH431 2.3 36.7 1.0
CG B:ASP124 2.9 39.2 1.0
CG B:HIS98 3.0 36.3 1.0
CB B:HIS98 3.2 39.3 1.0
CG B:ASP128 3.2 37.2 1.0
CE1 B:HIS98 3.2 40.4 1.0
CG B:ASP225 3.3 37.9 1.0
OD1 B:ASP124 3.4 44.9 1.0
MN B:MN303 3.4 48.0 1.0
OD1 B:ASP128 3.5 39.7 1.0
CB B:ASP225 3.6 41.2 1.0
O B:HOH437 4.0 29.2 1.0
CD2 B:HIS98 4.2 39.7 1.0
NE1 B:TRP122 4.2 42.4 1.0
CB B:ASP124 4.2 41.2 1.0
NE2 B:HIS98 4.3 40.3 1.0
OD1 B:ASP225 4.4 42.5 1.0
CZ2 B:TRP122 4.5 39.9 1.0
CB B:ASP128 4.5 39.4 1.0
O B:HIS141 4.5 44.1 1.0
CE2 B:TRP122 4.6 39.5 1.0
CA B:HIS98 4.7 38.6 1.0
O B:HIS126 4.8 42.0 1.0
CG B:GLU270 4.9 43.7 1.0
OE2 B:GLU270 4.9 45.1 1.0
CG2 B:VAL269 5.0 41.6 1.0
CA B:ASP225 5.0 38.8 1.0

Manganese binding site 4 out of 4 in 5zef

Go back to Manganese Binding Sites List in 5zef
Manganese binding site 4 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with L- Norvaline at 2.01 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- Norvaline at 2.01 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:48.0
occ:1.00
 O B:HOH437 2.1 29.2 1.0
OD1 B:ASP124 2.3 44.9 1.0
OD2 B:ASP227 2.4 43.9 1.0
OD2 B:ASP225 2.5 34.4 1.0
ND1 B:HIS126 2.5 42.3 1.0
OD1 B:ASP227 2.5 42.6 1.0
O B:HOH431 2.6 36.7 1.0
CG B:ASP227 2.8 44.7 1.0
CG B:ASP225 3.1 37.9 1.0
CG B:ASP124 3.2 39.2 1.0
CE1 B:HIS126 3.3 46.8 1.0
OD1 B:ASP225 3.4 42.5 1.0
MN B:MN302 3.4 40.4 1.0
CG B:HIS126 3.5 45.2 1.0
OD2 B:ASP124 3.6 29.4 1.0
CB B:HIS126 3.9 43.9 1.0
OG1 B:THR239 4.1 48.7 1.0
N B:HIS126 4.2 42.6 1.0
CB B:ASP225 4.2 41.2 1.0
N B:ALA125 4.3 42.3 1.0
CB B:ASP227 4.3 45.0 1.0
CD B:NVA301 4.4 83.0 1.0
NE2 B:HIS126 4.4 50.2 1.0
CB B:ASP124 4.6 41.2 1.0
CD2 B:HIS126 4.6 48.7 1.0
OD1 B:ASP128 4.7 39.7 1.0
CB B:ALA125 4.7 45.5 1.0
CA B:HIS126 4.7 43.3 1.0
O B:HOH436 4.8 44.8 1.0
CA B:ALA125 4.9 44.2 1.0
CA B:ASP124 4.9 40.7 1.0
C B:ALA125 5.0 44.1 1.0
OD2 B:ASP128 5.0 35.1 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 03:40:10 2024

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