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Manganese in PDB 4q3u: Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha

Enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha, PDB code: 4q3u was solved by Y.Hai, J.E.Edwards, M.C.Van Zandt, K.F.Hoffmann, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.46 / 2.50
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 178.318, 178.318, 178.318, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 22.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha (pdb code 4q3u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha, PDB code: 4q3u:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4q3u

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Manganese binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


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 Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:29.4
occ:1.00
 OH1 A:NNH405 2.0 34.1 1.0
OD2 A:ASP158 2.1 27.6 1.0
ND1 A:HIS131 2.2 25.0 1.0
OD2 A:ASP154 2.2 23.8 1.0
OD2 A:ASP262 2.2 26.1 1.0
CG A:HIS131 3.1 28.3 1.0
CE1 A:HIS131 3.1 26.7 1.0
CG A:ASP158 3.1 28.4 1.0
NH1 A:NNH405 3.2 30.8 1.0
CG A:ASP154 3.2 27.1 1.0
MN A:MN402 3.2 27.1 1.0
CG A:ASP262 3.3 24.7 1.0
CB A:HIS131 3.4 24.5 1.0
OD1 A:ASP154 3.5 28.1 1.0
OD1 A:ASP158 3.5 30.1 1.0
CB A:ASP262 3.7 22.7 1.0
NE2 A:HIS131 4.2 26.4 1.0
CE A:NNH405 4.2 29.7 1.0
CD2 A:HIS131 4.2 27.5 1.0
OD1 A:ASP262 4.3 24.6 1.0
NH2 A:NNH405 4.5 30.4 1.0
CB A:ASP158 4.5 25.1 1.0
CG A:GLU307 4.5 29.4 1.0
NE1 A:TRP152 4.5 25.2 1.0
CB A:ASP154 4.5 25.6 1.0
O A:HIS171 4.6 33.1 1.0
CZ2 A:TRP152 4.6 24.2 1.0
OE2 A:GLU307 4.8 30.3 1.0
CB A:HIS156 4.8 26.4 1.0
ND1 A:HIS156 4.9 28.2 1.0
OD2 A:ASP264 4.9 23.3 1.0
CE2 A:TRP152 4.9 24.7 1.0
CA A:HIS131 4.9 29.6 1.0
CA A:ASP262 5.0 25.4 1.0

Manganese binding site 2 out of 8 in 4q3u

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Manganese binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


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 Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:27.1
occ:1.00
 OH1 A:NNH405 2.1 34.1 1.0
ND1 A:HIS156 2.2 28.2 1.0
OD1 A:ASP154 2.2 28.1 1.0
OD2 A:ASP262 2.3 26.1 1.0
OD2 A:ASP264 2.3 23.3 1.0
OD1 A:ASP264 2.3 24.2 1.0
CG A:ASP264 2.6 26.4 1.0
NH1 A:NNH405 3.0 30.8 1.0
CG A:ASP262 3.1 24.7 1.0
CE1 A:HIS156 3.1 27.5 1.0
CG A:ASP154 3.2 27.1 1.0
MN A:MN401 3.2 29.4 1.0
CG A:HIS156 3.3 29.4 1.0
OD2 A:ASP154 3.4 23.8 1.0
NH2 A:NNH405 3.4 30.4 1.0
CE A:NNH405 3.5 29.7 1.0
CB A:HIS156 3.6 26.4 1.0
OD1 A:ASP262 3.7 24.6 1.0
N A:HIS156 3.9 28.2 1.0
CB A:ASP262 4.0 22.7 1.0
CB A:ASP264 4.2 24.9 1.0
NE2 A:HIS156 4.3 28.6 1.0
N A:ALA155 4.3 22.4 1.0
CD2 A:HIS156 4.4 27.8 1.0
CA A:HIS156 4.4 30.6 1.0
OG1 A:THR276 4.5 39.0 1.0
CB A:ASP154 4.5 25.6 1.0
C A:ALA155 4.7 27.6 1.0
CB A:ALA155 4.7 24.9 1.0
OD2 A:ASP158 4.8 27.6 1.0
O A:HOH505 4.8 26.7 1.0
CA A:ALA155 4.8 28.3 1.0
ND A:NNH405 4.8 29.2 1.0
CA A:ASP154 4.9 24.4 1.0
OD1 A:ASP158 5.0 30.1 1.0

Manganese binding site 3 out of 8 in 4q3u

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Manganese binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


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 Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:29.0
occ:1.00
 OH1 B:NNH405 1.8 34.1 1.0
OD2 B:ASP158 2.0 30.4 1.0
ND1 B:HIS131 2.2 30.1 1.0
OD2 B:ASP154 2.2 24.1 1.0
OD2 B:ASP262 2.3 25.5 1.0
NH1 B:NNH405 2.9 32.2 1.0
CG B:ASP158 3.1 27.3 1.0
CE1 B:HIS131 3.1 32.0 1.0
CG B:HIS131 3.2 32.0 1.0
CG B:ASP154 3.2 28.4 1.0
MN B:MN402 3.2 26.8 1.0
CG B:ASP262 3.3 25.9 1.0
CB B:HIS131 3.5 30.1 1.0
OD1 B:ASP154 3.5 25.4 1.0
OD1 B:ASP158 3.5 25.2 1.0
CB B:ASP262 3.7 26.2 1.0
CE B:NNH405 4.1 28.6 1.0
NE2 B:HIS131 4.2 29.7 1.0
CD2 B:HIS131 4.3 27.4 1.0
CB B:ASP158 4.4 23.7 1.0
OD1 B:ASP262 4.4 28.2 1.0
NH2 B:NNH405 4.4 27.9 1.0
NE1 B:TRP152 4.4 27.6 1.0
CB B:ASP154 4.5 26.5 1.0
O B:HIS171 4.6 28.6 1.0
CG B:GLU307 4.6 26.2 1.0
CZ2 B:TRP152 4.6 31.3 1.0
OE2 B:GLU307 4.8 28.3 1.0
ND1 B:HIS156 4.8 32.6 1.0
OD2 B:ASP264 4.8 27.7 1.0
CE2 B:TRP152 4.9 26.2 1.0
CA B:ASP262 5.0 25.0 1.0
OD1 B:ASP264 5.0 26.9 1.0
CA B:HIS131 5.0 30.6 1.0

Manganese binding site 4 out of 8 in 4q3u

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Manganese binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


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 Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:26.8
occ:1.00
 OH1 B:NNH405 2.1 34.1 1.0
ND1 B:HIS156 2.2 32.6 1.0
OD2 B:ASP262 2.2 25.5 1.0
OD1 B:ASP154 2.2 25.4 1.0
OD2 B:ASP264 2.2 27.7 1.0
OD1 B:ASP264 2.3 26.9 1.0
CG B:ASP264 2.6 27.9 1.0
NH1 B:NNH405 2.9 32.2 1.0
CE1 B:HIS156 2.9 29.2 1.0
CG B:ASP262 3.1 25.9 1.0
CG B:ASP154 3.2 28.4 1.0
MN B:MN401 3.2 29.0 1.0
CG B:HIS156 3.3 32.5 1.0
OD2 B:ASP154 3.4 24.1 1.0
NH2 B:NNH405 3.4 27.9 1.0
CE B:NNH405 3.5 28.6 1.0
OD1 B:ASP262 3.7 28.2 1.0
CB B:HIS156 3.8 30.3 1.0
CB B:ASP262 3.9 26.2 1.0
N B:HIS156 4.0 30.5 1.0
NE2 B:HIS156 4.1 29.9 1.0
CB B:ASP264 4.1 28.0 1.0
N B:ALA155 4.2 27.4 1.0
CD2 B:HIS156 4.3 31.2 1.0
CB B:ALA155 4.5 28.3 1.0
OG1 B:THR276 4.5 38.3 1.0
CB B:ASP154 4.5 26.5 1.0
CA B:HIS156 4.6 30.3 1.0
OD2 B:ASP158 4.7 30.4 1.0
CA B:ALA155 4.7 28.6 1.0
ND B:NNH405 4.7 31.4 1.0
O B:HOH502 4.7 28.1 1.0
C B:ALA155 4.8 29.7 1.0
CA B:ASP154 4.9 23.9 1.0
OD1 B:ASP158 4.9 25.2 1.0

Manganese binding site 5 out of 8 in 4q3u

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Manganese binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:36.0
occ:1.00
 OH1 C:NNH405 1.8 40.5 1.0
OD2 C:ASP158 2.1 33.3 1.0
OD2 C:ASP262 2.2 32.7 1.0
ND1 C:HIS131 2.2 35.6 1.0
OD2 C:ASP154 2.2 33.7 1.0
NH1 C:NNH405 3.0 41.1 1.0
CG C:HIS131 3.1 38.0 1.0
CG C:ASP158 3.2 34.1 1.0
CE1 C:HIS131 3.2 38.2 1.0
MN C:MN402 3.2 37.8 1.0
CG C:ASP262 3.2 35.0 1.0
CG C:ASP154 3.2 35.3 1.0
CB C:HIS131 3.4 36.4 1.0
OD1 C:ASP154 3.5 36.9 1.0
OD1 C:ASP158 3.6 38.8 1.0
CB C:ASP262 3.6 34.3 1.0
CE C:NNH405 4.2 35.1 1.0
NE2 C:HIS131 4.3 34.5 1.0
CD2 C:HIS131 4.3 36.7 1.0
OD1 C:ASP262 4.3 39.4 1.0
NH2 C:NNH405 4.4 36.3 1.0
NE1 C:TRP152 4.4 37.1 1.0
CB C:ASP158 4.5 33.0 1.0
O C:HIS171 4.5 36.9 1.0
CG C:GLU307 4.5 37.1 1.0
CB C:ASP154 4.5 35.5 1.0
CZ2 C:TRP152 4.6 34.3 1.0
OE2 C:GLU307 4.8 38.3 1.0
OD2 C:ASP264 4.8 34.0 1.0
CE2 C:TRP152 4.8 36.9 1.0
ND1 C:HIS156 4.9 36.0 1.0
CA C:ASP262 4.9 36.8 1.0
CA C:HIS131 4.9 37.9 1.0
CB C:HIS156 5.0 34.5 1.0

Manganese binding site 6 out of 8 in 4q3u

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Manganese binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:37.8
occ:1.00
 ND1 C:HIS156 2.2 36.0 1.0
OH1 C:NNH405 2.2 40.5 1.0
OD2 C:ASP264 2.2 34.0 1.0
OD1 C:ASP154 2.2 36.9 1.0
OD2 C:ASP262 2.3 32.7 1.0
OD1 C:ASP264 2.4 38.1 1.0
CG C:ASP264 2.7 36.7 1.0
NH1 C:NNH405 3.0 41.1 1.0
CE1 C:HIS156 3.0 35.8 1.0
CG C:ASP262 3.1 35.0 1.0
CG C:ASP154 3.1 35.3 1.0
MN C:MN401 3.2 36.0 1.0
CG C:HIS156 3.3 33.0 1.0
NH2 C:NNH405 3.4 36.3 1.0
OD2 C:ASP154 3.4 33.7 1.0
CE C:NNH405 3.5 35.1 1.0
OD1 C:ASP262 3.7 39.4 1.0
CB C:HIS156 3.7 34.5 1.0
CB C:ASP262 4.0 34.3 1.0
N C:HIS156 4.0 34.4 1.0
CB C:ASP264 4.2 32.5 1.0
NE2 C:HIS156 4.2 38.6 1.0
N C:ALA155 4.3 35.9 1.0
CD2 C:HIS156 4.3 33.9 1.0
OG1 C:THR276 4.5 43.4 1.0
CA C:HIS156 4.5 35.1 1.0
CB C:ASP154 4.5 35.5 1.0
OD2 C:ASP158 4.7 33.3 1.0
ND C:NNH405 4.7 35.0 1.0
O C:HOH507 4.7 36.5 1.0
CB C:ALA155 4.8 37.0 1.0
C C:ALA155 4.8 37.0 1.0
CA C:ASP154 4.9 32.5 1.0
CA C:ALA155 4.9 33.6 1.0
OD1 C:ASP158 4.9 38.8 1.0

Manganese binding site 7 out of 8 in 4q3u

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Manganese binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:51.8
occ:1.00
 OH1 D:NNH403 2.0 53.6 1.0
OD2 D:ASP158 2.3 54.4 1.0
OD2 D:ASP154 2.4 54.3 1.0
ND1 D:HIS131 2.4 55.1 1.0
OD2 D:ASP262 2.5 49.8 1.0
NH1 D:NNH403 3.2 60.8 1.0
CG D:ASP158 3.2 60.4 1.0
CG D:HIS131 3.3 60.3 1.0
CG D:ASP154 3.4 56.2 1.0
MN D:MN402 3.4 60.0 1.0
CB D:HIS131 3.4 60.5 1.0
CG D:ASP262 3.4 55.4 1.0
CE1 D:HIS131 3.5 60.2 1.0
OD1 D:ASP158 3.5 60.7 1.0
OD1 D:ASP154 3.6 57.0 1.0
CB D:ASP262 3.6 55.2 1.0
CE D:NNH403 4.3 56.4 1.0
NE1 D:TRP152 4.4 60.5 1.0
CZ2 D:TRP152 4.4 59.8 1.0
CD2 D:HIS131 4.5 63.6 1.0
CB D:ASP158 4.5 58.6 1.0
NE2 D:HIS131 4.5 64.7 1.0
OD1 D:ASP262 4.5 56.4 1.0
O D:HIS171 4.6 63.4 1.0
CG D:GLU307 4.6 57.6 1.0
NH2 D:NNH403 4.6 55.8 1.0
CB D:ASP154 4.7 61.4 1.0
CE2 D:TRP152 4.8 58.9 1.0
CA D:HIS131 4.9 64.9 1.0
CA D:ASP262 4.9 55.3 1.0
OE2 D:GLU307 4.9 51.2 1.0
OD2 D:ASP264 5.0 51.9 1.0

Manganese binding site 8 out of 8 in 4q3u

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Manganese binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Nor-Noha within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:60.0
occ:1.00
 OD1 D:ASP264 2.3 56.5 1.0
OH1 D:NNH403 2.3 53.6 1.0
OD2 D:ASP262 2.3 49.8 1.0
ND1 D:HIS156 2.4 54.7 1.0
OD1 D:ASP154 2.4 57.0 1.0
OD2 D:ASP264 2.4 51.9 1.0
CG D:ASP264 2.7 53.8 1.0
NH1 D:NNH403 3.0 60.8 1.0
CG D:ASP262 3.1 55.4 1.0
CE1 D:HIS156 3.2 55.9 1.0
CG D:ASP154 3.3 56.2 1.0
MN D:MN401 3.4 51.8 1.0
CG D:HIS156 3.5 61.2 1.0
NH2 D:NNH403 3.5 55.8 1.0
CE D:NNH403 3.6 56.4 1.0
OD2 D:ASP154 3.6 54.3 1.0
OD1 D:ASP262 3.8 56.4 1.0
CB D:HIS156 3.9 59.1 1.0
N D:HIS156 3.9 57.1 1.0
CB D:ASP262 4.0 55.2 1.0
CB D:ASP264 4.2 54.0 1.0
N D:ALA155 4.3 57.0 1.0
NE2 D:HIS156 4.4 66.4 1.0
CA D:HIS156 4.5 60.9 1.0
CB D:ALA155 4.5 55.1 1.0
CD2 D:HIS156 4.6 62.0 1.0
CB D:ASP154 4.7 61.4 1.0
CA D:ALA155 4.7 56.6 1.0
C D:ALA155 4.7 58.0 1.0
ND D:NNH403 4.8 59.6 1.0
OD1 D:ASP158 4.9 60.7 1.0

Reference:

Y.Hai, J.E.Edwards, M.C.Van Zandt, K.F.Hoffmann, D.W.Christianson. Crystal Structure of Schistosoma Mansoni Arginase, A Potential Drug Target For the Treatment of Schistosomiasis. Biochemistry V. 53 4671 2014.
ISSN: ISSN 0006-2960
PubMed: 25007099
DOI: 10.1021/BI5004519
Page generated: Sat Oct 5 20:53:51 2024

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