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Manganese in PDB 5zee: Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A

Enzymatic activity of Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A

All present enzymatic activity of Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A, PDB code: 5zee 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) 45.14 / 1.74
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.722, 97.538, 125.067, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A (pdb code 5zee). 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 N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A, PDB code: 5zee:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5zee

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Manganese binding site 1 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 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 N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:30.0
occ:1.00
 OH1 A:HAR301 1.9 27.3 1.0
OD2 A:ASP124 1.9 29.6 1.0
ND1 A:HIS98 2.0 25.2 1.0
OD2 A:ASP128 2.1 35.0 1.0
OD2 A:ASP225 2.3 35.0 1.0
NH1 A:HAR301 2.7 40.5 1.0
CG A:ASP124 2.9 28.8 1.0
CG A:HIS98 2.9 25.6 1.0
CE1 A:HIS98 3.0 28.5 1.0
CB A:HIS98 3.2 26.2 1.0
OD1 A:ASP124 3.2 27.6 1.0
CG A:ASP128 3.2 30.5 1.0
MN A:MN303 3.3 36.3 1.0
CG A:ASP225 3.3 27.3 1.0
CB A:ASP225 3.6 28.4 1.0
OD1 A:ASP128 3.7 30.3 1.0
NE1 A:TRP122 4.0 28.1 1.0
CD2 A:HIS98 4.1 25.8 1.0
CZ A:HAR301 4.1 49.9 1.0
NE2 A:HIS98 4.1 28.0 1.0
CB A:ASP124 4.2 28.0 1.0
CZ2 A:TRP122 4.3 24.6 1.0
CE2 A:TRP122 4.4 26.0 1.0
OD1 A:ASP225 4.5 28.4 1.0
CB A:ASP128 4.5 28.1 1.0
NH2 A:HAR301 4.6 26.2 1.0
O A:HIS126 4.7 29.9 1.0
O A:HIS141 4.7 30.1 1.0
CA A:HIS98 4.8 25.2 1.0
NE A:HAR301 4.9 65.7 1.0
CG2 A:VAL269 5.0 28.3 1.0

Manganese binding site 2 out of 4 in 5zee

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Manganese binding site 2 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 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 N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:36.3
occ:1.00
 OH1 A:HAR301 1.9 27.3 1.0
OD1 A:ASP124 2.3 27.6 1.0
OD2 A:ASP225 2.3 35.0 1.0
OD2 A:ASP227 2.4 29.3 1.0
ND1 A:HIS126 2.5 31.0 1.0
OD1 A:ASP227 2.5 30.9 1.0
NH2 A:HAR301 2.8 26.2 1.0
CG A:ASP227 2.8 31.5 1.0
NH1 A:HAR301 2.9 40.5 1.0
CG A:ASP225 3.1 27.3 1.0
CZ A:HAR301 3.2 49.9 1.0
CE1 A:HIS126 3.3 30.8 1.0
MN A:MN302 3.3 30.0 1.0
CG A:ASP124 3.3 28.8 1.0
OD1 A:ASP225 3.5 28.4 1.0
CG A:HIS126 3.6 29.3 1.0
OD2 A:ASP124 3.6 29.6 1.0
NE A:HAR301 3.7 65.7 1.0
CB A:HIS126 4.0 28.6 1.0
CB A:ASP225 4.2 28.4 1.0
OG1 A:THR239 4.2 39.7 1.0
N A:HIS126 4.2 29.2 1.0
CB A:ASP227 4.3 30.6 1.0
N A:ALA125 4.4 31.5 1.0
NE2 A:HIS126 4.5 30.7 1.0
O A:HOH463 4.6 36.5 1.0
CD2 A:HIS126 4.6 31.7 1.0
OD2 A:ASP128 4.7 35.0 1.0
CB A:ASP124 4.7 28.0 1.0
CD A:HAR301 4.7 66.5 1.0
CA A:HIS126 4.7 28.6 1.0
OD1 A:ASP128 4.8 30.3 1.0
CB A:ALA125 4.8 31.8 1.0
CA A:ALA125 5.0 32.2 1.0
CA A:ASP124 5.0 27.7 1.0

Manganese binding site 3 out of 4 in 5zee

Go back to Manganese Binding Sites List in 5zee
Manganese binding site 3 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 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 N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:34.2
occ:1.00
 OD2 B:ASP124 2.0 25.3 1.0
ND1 B:HIS98 2.1 25.6 1.0
OH1 B:HAR301 2.1 29.5 1.0
OD2 B:ASP128 2.1 32.8 1.0
OD2 B:ASP225 2.2 27.9 1.0
NH1 B:HAR301 2.5 39.4 1.0
CG B:ASP124 2.9 27.7 1.0
CG B:HIS98 3.0 25.7 1.0
CE1 B:HIS98 3.1 26.6 1.0
CG B:ASP128 3.2 33.1 1.0
OD1 B:ASP124 3.2 28.7 1.0
CB B:HIS98 3.3 27.6 1.0
CG B:ASP225 3.3 27.6 1.0
MN B:MN303 3.3 35.8 1.0
OD1 B:ASP128 3.6 33.5 1.0
CB B:ASP225 3.6 28.2 1.0
CZ B:HAR301 4.0 45.3 1.0
NE1 B:TRP122 4.1 27.7 1.0
CD2 B:HIS98 4.2 26.7 1.0
NE2 B:HIS98 4.2 26.8 1.0
CB B:ASP124 4.3 26.2 1.0
OD1 B:ASP225 4.4 29.7 1.0
CZ2 B:TRP122 4.4 29.0 1.0
CB B:ASP128 4.5 31.1 1.0
NH2 B:HAR301 4.5 25.1 1.0
CE2 B:TRP122 4.5 29.7 1.0
O B:HIS141 4.7 32.6 1.0
O B:HIS126 4.7 26.9 1.0
NE B:HAR301 4.7 55.6 1.0
CA B:HIS98 4.8 26.5 1.0
CG B:GLU270 5.0 31.0 1.0
CG2 B:VAL269 5.0 28.9 1.0

Manganese binding site 4 out of 4 in 5zee

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Manganese binding site 4 out of 4 in the Crystal Structure of Entamoeba Histolytica Arginase in Complex with N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 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 N(Omega)-Hydroxy-L-Arginine (Noha) at 1.74 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:35.8
occ:1.00
 OH1 B:HAR301 2.1 29.5 1.0
OD1 B:ASP124 2.3 28.7 1.0
OD2 B:ASP227 2.4 34.3 1.0
OD2 B:ASP225 2.4 27.9 1.0
OD1 B:ASP227 2.5 30.8 1.0
ND1 B:HIS126 2.5 29.4 1.0
CG B:ASP227 2.7 32.0 1.0
NH2 B:HAR301 2.7 25.1 1.0
NH1 B:HAR301 3.0 39.4 1.0
CG B:ASP225 3.1 27.6 1.0
CE1 B:HIS126 3.3 35.7 1.0
MN B:MN302 3.3 34.2 1.0
CZ B:HAR301 3.3 45.3 1.0
CG B:ASP124 3.3 27.7 1.0
OD1 B:ASP225 3.5 29.7 1.0
CG B:HIS126 3.6 33.7 1.0
OD2 B:ASP124 3.7 25.3 1.0
CB B:HIS126 4.0 30.2 1.0
NE B:HAR301 4.2 55.6 1.0
CB B:ASP225 4.2 28.2 1.0
N B:HIS126 4.2 27.4 1.0
OG1 B:THR239 4.2 38.5 1.0
CB B:ASP227 4.2 31.1 1.0
N B:ALA125 4.4 28.7 1.0
CD B:HAR301 4.5 64.2 1.0
NE2 B:HIS126 4.5 32.6 1.0
O B:HOH449 4.6 34.4 1.0
CD2 B:HIS126 4.6 33.5 1.0
CB B:ASP124 4.7 26.2 1.0
CA B:HIS126 4.7 28.3 1.0
OD1 B:ASP128 4.8 33.5 1.0
OD2 B:ASP128 4.8 32.8 1.0
CB B:ALA125 4.8 30.3 1.0
CA B:ALA125 4.9 29.4 1.0
CA B:ASP124 5.0 26.0 1.0
C B:ALA125 5.0 28.6 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 03:40:01 2024

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