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

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

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