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Manganese in PDB 4q42: Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine

Enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine, PDB code: 4q42 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) 49.49 / 2.05
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 178.447, 178.447, 178.447, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine (pdb code 4q42). 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 L- Ornithine, PDB code: 4q42:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4q42

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Manganese binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:18.5
occ:1.00
 OD1 A:ASP158 2.1 18.0 1.0
OD2 A:ASP262 2.2 17.8 1.0
OD2 A:ASP154 2.2 13.7 1.0
O A:HOH734 2.2 21.9 1.0
ND1 A:HIS131 2.3 15.7 1.0
O A:HOH696 2.6 31.6 1.0
CG A:ASP158 3.1 17.8 1.0
CG A:ASP154 3.1 16.1 1.0
CG A:HIS131 3.2 16.7 1.0
CG A:ASP262 3.2 17.9 1.0
CE1 A:HIS131 3.2 17.4 1.0
MN A:MN402 3.3 18.0 1.0
OD1 A:ASP154 3.4 13.7 1.0
OD2 A:ASP158 3.4 20.9 1.0
CB A:HIS131 3.5 17.6 1.0
CB A:ASP262 3.6 14.2 1.0
O A:HOH695 4.1 35.8 1.0
NE A:ORN403 4.3 34.5 1.0
OD1 A:ASP262 4.3 16.2 1.0
NE2 A:HIS131 4.3 20.9 1.0
CD2 A:HIS131 4.4 18.8 1.0
CB A:ASP158 4.4 15.8 1.0
NE1 A:TRP152 4.4 16.1 1.0
CB A:ASP154 4.5 12.3 1.0
CZ2 A:TRP152 4.6 15.5 1.0
CG A:GLU307 4.6 14.3 1.0
O A:HIS171 4.6 22.6 1.0
OE2 A:GLU307 4.8 18.7 1.0
CE2 A:TRP152 4.9 16.7 1.0
CA A:ASP262 4.9 13.9 1.0
OD1 A:ASP264 4.9 18.2 1.0
CA A:HIS131 5.0 17.7 1.0

Manganese binding site 2 out of 8 in 4q42

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Manganese binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:18.0
occ:1.00
 OD1 A:ASP154 2.2 13.7 1.0
O A:HOH734 2.2 21.9 1.0
OD1 A:ASP264 2.2 18.2 1.0
ND1 A:HIS156 2.3 15.8 1.0
OD2 A:ASP262 2.3 17.8 1.0
OD2 A:ASP264 2.4 14.9 1.0
CG A:ASP264 2.7 16.8 1.0
O A:HOH695 3.1 35.8 1.0
CG A:ASP262 3.1 17.9 1.0
CE1 A:HIS156 3.1 20.2 1.0
CG A:ASP154 3.2 16.1 1.0
MN A:MN401 3.3 18.5 1.0
CG A:HIS156 3.4 17.6 1.0
OD2 A:ASP154 3.6 13.7 1.0
CB A:HIS156 3.7 12.9 1.0
OD1 A:ASP262 3.7 16.2 1.0
N A:HIS156 4.0 13.2 1.0
CB A:ASP262 4.1 14.2 1.0
CB A:ASP264 4.2 13.5 1.0
OG1 A:THR276 4.2 25.6 1.0
N A:ALA155 4.2 14.6 1.0
NE2 A:HIS156 4.3 18.8 1.0
O A:HOH696 4.3 31.6 1.0
NE A:ORN403 4.3 34.5 1.0
CD2 A:HIS156 4.4 22.3 1.0
CA A:HIS156 4.5 13.1 1.0
CB A:ASP154 4.6 12.3 1.0
OD2 A:ASP158 4.6 20.9 1.0
CD A:ORN403 4.7 34.1 1.0
CB A:ALA155 4.7 13.4 1.0
OD1 A:ASP158 4.8 18.0 1.0
C A:ALA155 4.8 16.9 1.0
CA A:ALA155 4.8 16.6 1.0
O A:HOH538 4.9 17.1 1.0
CA A:ASP154 4.9 13.8 1.0
C A:ASP154 5.0 13.9 1.0

Manganese binding site 3 out of 8 in 4q42

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Manganese binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:17.8
occ:1.00
 OD1 B:ASP158 2.1 17.2 1.0
OD2 B:ASP262 2.2 15.1 1.0
ND1 B:HIS131 2.2 14.6 1.0
OD2 B:ASP154 2.2 15.4 1.0
O B:HOH720 2.2 22.7 1.0
O B:HOH696 2.6 27.2 1.0
CG B:ASP158 3.1 18.0 1.0
CG B:HIS131 3.2 17.3 1.0
CE1 B:HIS131 3.2 17.1 1.0
CG B:ASP154 3.2 14.8 1.0
CG B:ASP262 3.2 16.0 1.0
MN B:MN402 3.2 17.5 1.0
OD2 B:ASP158 3.4 18.8 1.0
CB B:HIS131 3.4 17.5 1.0
OD1 B:ASP154 3.5 13.4 1.0
CB B:ASP262 3.6 14.1 1.0
O B:HOH697 3.9 33.0 1.0
NE B:ORN403 4.2 35.7 1.0
OD1 B:ASP262 4.3 17.4 1.0
NE2 B:HIS131 4.3 17.7 1.0
CD2 B:HIS131 4.3 15.2 1.0
CB B:ASP158 4.4 14.9 1.0
NE1 B:TRP152 4.4 17.7 1.0
CB B:ASP154 4.5 13.2 1.0
CZ2 B:TRP152 4.6 13.4 1.0
CG B:GLU307 4.6 12.5 1.0
O B:HIS171 4.7 19.4 1.0
OE2 B:GLU307 4.8 19.6 1.0
CE2 B:TRP152 4.9 14.6 1.0
OD1 B:ASP264 4.9 16.9 1.0
CA B:ASP262 4.9 13.1 1.0
CA B:HIS131 5.0 17.3 1.0

Manganese binding site 4 out of 8 in 4q42

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Manganese binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:17.5
occ:1.00
 O B:HOH720 2.2 22.7 1.0
OD1 B:ASP154 2.2 13.4 1.0
OD1 B:ASP264 2.2 16.9 1.0
OD2 B:ASP262 2.3 15.1 1.0
ND1 B:HIS156 2.3 17.8 1.0
OD2 B:ASP264 2.5 15.3 1.0
CG B:ASP264 2.7 16.8 1.0
O B:HOH697 3.1 33.0 1.0
CE1 B:HIS156 3.1 17.7 1.0
CG B:ASP262 3.1 16.0 1.0
CG B:ASP154 3.2 14.8 1.0
MN B:MN401 3.2 17.8 1.0
CG B:HIS156 3.4 17.3 1.0
OD2 B:ASP154 3.5 15.4 1.0
OD1 B:ASP262 3.7 17.4 1.0
CB B:HIS156 3.8 16.1 1.0
N B:HIS156 4.0 13.7 1.0
CB B:ASP262 4.0 14.1 1.0
O B:HOH696 4.1 27.2 1.0
NE B:ORN403 4.2 35.7 1.0
CB B:ASP264 4.2 12.7 1.0
OG1 B:THR276 4.2 26.6 1.0
N B:ALA155 4.3 14.8 1.0
NE2 B:HIS156 4.3 20.1 1.0
CD2 B:HIS156 4.4 16.9 1.0
CD B:ORN403 4.5 30.4 1.0
CA B:HIS156 4.5 14.6 1.0
CB B:ASP154 4.5 13.2 1.0
OD2 B:ASP158 4.6 18.8 1.0
CB B:ALA155 4.7 15.3 1.0
OD1 B:ASP158 4.7 17.2 1.0
O B:HOH553 4.8 19.6 1.0
C B:ALA155 4.9 18.6 1.0
CA B:ALA155 4.9 15.6 1.0
CA B:ASP154 4.9 12.4 1.0

Manganese binding site 5 out of 8 in 4q42

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Manganese binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:27.2
occ:1.00
 OD1 C:ASP158 2.2 25.3 1.0
OD2 C:ASP154 2.2 23.1 1.0
OD2 C:ASP262 2.2 24.4 1.0
O C:HOH598 2.3 29.4 1.0
ND1 C:HIS131 2.3 26.5 1.0
O C:HOH634 2.6 36.0 1.0
CG C:ASP158 3.1 28.1 1.0
CG C:ASP154 3.2 26.8 1.0
CG C:HIS131 3.2 28.8 1.0
MN C:MN402 3.2 28.6 1.0
CG C:ASP262 3.3 27.4 1.0
CE1 C:HIS131 3.3 26.7 1.0
OD2 C:ASP158 3.3 29.4 1.0
CB C:HIS131 3.5 26.4 1.0
OD1 C:ASP154 3.5 26.7 1.0
CB C:ASP262 3.7 26.3 1.0
NE C:ORN403 4.3 39.0 1.0
OD1 C:ASP262 4.3 26.7 1.0
NE2 C:HIS131 4.3 28.6 1.0
CD2 C:HIS131 4.3 29.1 1.0
NE1 C:TRP152 4.4 27.4 1.0
CB C:ASP158 4.4 22.9 1.0
CB C:ASP154 4.5 20.5 1.0
CZ2 C:TRP152 4.5 22.8 1.0
O C:HIS171 4.6 28.3 1.0
CG C:GLU307 4.7 26.1 1.0
CE2 C:TRP152 4.8 27.8 1.0
OE2 C:GLU307 4.9 28.6 1.0
CA C:HIS131 5.0 30.0 1.0
CA C:ASP262 5.0 27.4 1.0

Manganese binding site 6 out of 8 in 4q42

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Manganese binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:28.6
occ:1.00
 O C:HOH598 2.2 29.4 1.0
OD1 C:ASP154 2.3 26.7 1.0
OD1 C:ASP264 2.3 27.2 1.0
ND1 C:HIS156 2.3 24.4 1.0
OD2 C:ASP262 2.4 24.4 1.0
OD2 C:ASP264 2.5 29.2 1.0
CG C:ASP264 2.7 28.0 1.0
CE1 C:HIS156 3.1 24.7 1.0
CG C:ASP262 3.2 27.4 1.0
CG C:ASP154 3.2 26.8 1.0
MN C:MN401 3.2 27.2 1.0
CG C:HIS156 3.4 23.0 1.0
OD2 C:ASP154 3.4 23.1 1.0
OD1 C:ASP262 3.7 26.7 1.0
CB C:HIS156 3.8 22.8 1.0
N C:HIS156 4.0 22.4 1.0
CB C:ASP262 4.0 26.3 1.0
O C:HOH634 4.1 36.0 1.0
CB C:ASP264 4.2 23.5 1.0
N C:ALA155 4.2 25.4 1.0
OG1 C:THR276 4.3 36.4 1.0
NE2 C:HIS156 4.3 26.1 1.0
NE C:ORN403 4.5 39.0 1.0
CD2 C:HIS156 4.5 27.4 1.0
CD C:ORN403 4.5 36.5 1.0
CA C:HIS156 4.5 24.0 1.0
CB C:ASP154 4.6 20.5 1.0
OD2 C:ASP158 4.6 29.4 1.0
CB C:ALA155 4.7 24.4 1.0
O C:HOH514 4.8 25.6 1.0
CA C:ALA155 4.8 22.8 1.0
C C:ALA155 4.8 23.7 1.0
OD1 C:ASP158 4.9 25.3 1.0
CA C:ASP154 4.9 26.4 1.0

Manganese binding site 7 out of 8 in 4q42

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Manganese binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:40.2
occ:1.00
 OD1 D:ASP158 2.2 41.0 1.0
ND1 D:HIS131 2.3 40.5 1.0
OD2 D:ASP262 2.3 34.4 1.0
O D:HOH531 2.3 37.1 1.0
OD2 D:ASP154 2.3 35.7 1.0
CG D:ASP158 3.1 39.9 1.0
MN D:MN402 3.1 38.1 1.0
CG D:HIS131 3.2 42.0 1.0
CE1 D:HIS131 3.2 40.2 1.0
OD2 D:ASP158 3.2 40.9 1.0
CG D:ASP154 3.3 40.4 1.0
CG D:ASP262 3.3 41.8 1.0
CB D:HIS131 3.5 38.7 1.0
OD1 D:ASP154 3.5 33.1 1.0
CB D:ASP262 3.7 40.7 1.0
NE2 D:HIS131 4.3 43.8 1.0
CD2 D:HIS131 4.4 42.4 1.0
NE D:ORN403 4.4 53.4 1.0
OD1 D:ASP262 4.4 36.2 1.0
NE1 D:TRP152 4.4 41.6 1.0
CB D:ASP158 4.5 35.0 1.0
CZ2 D:TRP152 4.5 37.5 1.0
CG D:GLU307 4.5 42.3 1.0
O D:HIS171 4.6 44.2 1.0
CB D:ASP154 4.7 34.1 1.0
OD1 D:ASP264 4.8 36.9 1.0
CE2 D:TRP152 4.8 42.6 1.0
OE2 D:GLU307 4.8 35.5 1.0
CA D:HIS131 5.0 42.4 1.0
CB D:HIS156 5.0 35.1 1.0

Manganese binding site 8 out of 8 in 4q42

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Manganese binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Ornithine


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 L- Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:38.1
occ:1.00
 O D:HOH531 2.2 37.1 1.0
OD1 D:ASP264 2.3 36.9 1.0
OD2 D:ASP262 2.3 34.4 1.0
OD1 D:ASP154 2.3 33.1 1.0
OD2 D:ASP264 2.5 35.3 1.0
ND1 D:HIS156 2.5 41.3 1.0
CG D:ASP264 2.7 40.2 1.0
MN D:MN401 3.1 40.2 1.0
CG D:ASP262 3.1 41.8 1.0
CG D:ASP154 3.2 40.4 1.0
CE1 D:HIS156 3.4 40.6 1.0
OD2 D:ASP154 3.5 35.7 1.0
CG D:HIS156 3.5 38.6 1.0
CB D:HIS156 3.8 35.1 1.0
OD1 D:ASP262 3.8 36.2 1.0
CB D:ASP262 4.1 40.7 1.0
N D:HIS156 4.1 34.8 1.0
CB D:ASP264 4.2 32.8 1.0
N D:ALA155 4.3 32.8 1.0
OG1 D:THR276 4.3 44.6 1.0
NE D:ORN403 4.5 53.4 1.0
CA D:HIS156 4.5 41.1 1.0
NE2 D:HIS156 4.6 43.5 1.0
OD2 D:ASP158 4.6 40.9 1.0
CD2 D:HIS156 4.6 46.9 1.0
CB D:ASP154 4.6 34.1 1.0
CB D:ALA155 4.8 35.4 1.0
C D:ALA155 4.9 35.8 1.0
O D:HOH503 4.9 37.2 1.0
CA D:ALA155 4.9 32.5 1.0
OD1 D:ASP158 4.9 41.0 1.0
CD D:ORN403 4.9 50.8 1.0
CA D:ASP154 5.0 34.6 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 20:57:20 2024

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