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Manganese in PDB 4q40: Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Valine

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

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

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Valine, PDB code: 4q40 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) 49.31 / 1.83
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 177.808, 177.808, 177.808, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Valine (pdb code 4q40). 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- Valine, PDB code: 4q40:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4q40

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


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

b:14.7
occ:1.00
 OD1 A:ASP158 2.1 17.4 1.0
OD2 A:ASP154 2.2 11.1 1.0
OD2 A:ASP262 2.2 15.2 1.0
O A:HOH579 2.2 15.2 1.0
ND1 A:HIS131 2.2 13.4 1.0
O A:HOH581 2.4 22.4 1.0
CG A:ASP158 3.0 13.8 1.0
CG A:ASP154 3.1 12.7 1.0
CG A:HIS131 3.2 15.1 1.0
CG A:ASP262 3.2 12.8 1.0
CE1 A:HIS131 3.2 13.0 1.0
MN A:MN402 3.3 14.0 1.0
OD2 A:ASP158 3.4 16.2 1.0
OD1 A:ASP154 3.4 10.8 1.0
CB A:HIS131 3.4 15.1 1.0
CB A:ASP262 3.6 13.4 1.0
O A:HOH580 3.9 25.0 1.0
OD1 A:ASP262 4.3 12.8 1.0
NE2 A:HIS131 4.3 14.3 1.0
CD2 A:HIS131 4.3 14.1 1.0
CB A:ASP158 4.4 11.8 1.0
NE1 A:TRP152 4.4 14.4 1.0
CB A:ASP154 4.5 9.9 1.0
O A:HIS171 4.5 15.0 1.0
CZ2 A:TRP152 4.6 15.8 1.0
CG A:GLU307 4.6 13.2 1.0
OE2 A:GLU307 4.8 15.1 1.0
OD1 A:ASP264 4.8 13.8 1.0
CE2 A:TRP152 4.9 13.7 1.0
CA A:ASP262 4.9 13.2 1.0
CA A:HIS131 4.9 13.8 1.0
OD2 A:ASP264 5.0 12.5 1.0

Manganese binding site 2 out of 8 in 4q40

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


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

b:14.0
occ:1.00
 O A:HOH579 2.1 15.2 1.0
OD1 A:ASP154 2.1 10.8 1.0
OD1 A:ASP264 2.2 13.8 1.0
ND1 A:HIS156 2.2 12.9 1.0
OD2 A:ASP262 2.3 15.2 1.0
OD2 A:ASP264 2.3 12.5 1.0
CG A:ASP264 2.6 14.2 1.0
CE1 A:HIS156 3.1 15.1 1.0
O A:HOH580 3.1 25.0 1.0
CG A:ASP262 3.1 12.8 1.0
CG A:ASP154 3.2 12.7 1.0
MN A:MN401 3.3 14.7 1.0
CG A:HIS156 3.3 13.9 1.0
OD2 A:ASP154 3.5 11.1 1.0
CB A:HIS156 3.7 12.8 1.0
OD1 A:ASP262 3.8 12.8 1.0
N A:HIS156 4.0 11.2 1.0
CB A:ASP262 4.0 13.4 1.0
CB A:ASP264 4.1 12.6 1.0
OG1 A:THR276 4.2 19.0 1.0
O A:HOH581 4.2 22.4 1.0
NE2 A:HIS156 4.3 14.6 1.0
N A:ALA155 4.3 10.5 1.0
CD2 A:HIS156 4.4 13.4 1.0
CA A:HIS156 4.5 11.8 1.0
CB A:ASP154 4.5 9.9 1.0
OD2 A:ASP158 4.5 16.2 1.0
CB A:ALA155 4.7 12.1 1.0
OD1 A:ASP158 4.8 17.4 1.0
O A:HOH535 4.8 15.3 1.0
C A:ALA155 4.8 13.4 1.0
CA A:ALA155 4.8 12.0 1.0
CA A:ASP154 4.8 9.5 1.0
C A:ASP154 5.0 9.9 1.0

Manganese binding site 3 out of 8 in 4q40

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


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

b:14.2
occ:1.00
 OD1 B:ASP158 2.1 14.3 1.0
O B:HOH680 2.2 16.6 1.0
ND1 B:HIS131 2.2 12.5 1.0
OD2 B:ASP154 2.2 12.9 1.0
OD2 B:ASP262 2.2 12.0 1.0
O B:HOH535 2.4 18.4 1.0
CG B:ASP158 3.0 13.8 1.0
CE1 B:HIS131 3.1 14.4 1.0
CG B:HIS131 3.2 13.3 1.0
CG B:ASP154 3.2 13.3 1.0
CG B:ASP262 3.2 12.4 1.0
MN B:MN402 3.3 13.4 1.0
OD2 B:ASP158 3.4 14.4 1.0
OD1 B:ASP154 3.4 10.9 1.0
CB B:HIS131 3.5 14.9 1.0
CB B:ASP262 3.6 10.5 1.0
O B:HOH536 3.9 23.6 1.0
NE2 B:HIS131 4.2 14.2 1.0
CD2 B:HIS131 4.3 14.2 1.0
OD1 B:ASP262 4.3 12.1 1.0
CB B:ASP158 4.4 12.3 1.0
NE1 B:TRP152 4.4 12.4 1.0
CB B:ASP154 4.5 11.5 1.0
O B:HIS171 4.5 14.3 1.0
CZ2 B:TRP152 4.6 11.4 1.0
CG B:GLU307 4.6 12.3 1.0
OE2 B:GLU307 4.8 14.4 1.0
CE2 B:TRP152 4.9 12.0 1.0
CA B:ASP262 4.9 10.8 1.0
OD1 B:ASP264 4.9 12.9 1.0
CA B:HIS131 5.0 13.6 1.0

Manganese binding site 4 out of 8 in 4q40

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


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

b:13.4
occ:1.00
 OD1 B:ASP154 2.1 10.9 1.0
O B:HOH680 2.1 16.6 1.0
OD1 B:ASP264 2.2 12.9 1.0
OD2 B:ASP262 2.2 12.0 1.0
ND1 B:HIS156 2.3 13.4 1.0
OD2 B:ASP264 2.4 12.7 1.0
CG B:ASP264 2.6 12.2 1.0
CG B:ASP262 3.1 12.4 1.0
CE1 B:HIS156 3.1 13.4 1.0
O B:HOH536 3.1 23.6 1.0
CG B:ASP154 3.1 13.3 1.0
MN B:MN401 3.3 14.2 1.0
CG B:HIS156 3.3 12.0 1.0
OD2 B:ASP154 3.5 12.9 1.0
CB B:HIS156 3.7 10.7 1.0
OD1 B:ASP262 3.7 12.1 1.0
CB B:ASP262 4.0 10.5 1.0
N B:HIS156 4.0 10.8 1.0
CB B:ASP264 4.2 10.8 1.0
OG1 B:THR276 4.2 16.6 1.0
O B:HOH535 4.2 18.4 1.0
NE2 B:HIS156 4.3 13.2 1.0
N B:ALA155 4.3 10.3 1.0
CD2 B:HIS156 4.4 12.4 1.0
CA B:HIS156 4.5 11.0 1.0
CB B:ASP154 4.5 11.5 1.0
OD2 B:ASP158 4.5 14.4 1.0
CB B:ALA155 4.7 10.7 1.0
O B:HOH527 4.7 14.2 1.0
OD1 B:ASP158 4.8 14.3 1.0
C B:ALA155 4.8 13.4 1.0
CA B:ASP154 4.9 9.9 1.0
CA B:ALA155 4.9 12.3 1.0

Manganese binding site 5 out of 8 in 4q40

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


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

b:22.0
occ:1.00
 OD1 C:ASP158 2.1 22.0 1.0
OD2 C:ASP154 2.1 19.3 1.0
OD2 C:ASP262 2.2 20.3 1.0
O C:HOH546 2.2 21.7 1.0
ND1 C:HIS131 2.3 19.8 1.0
O C:HOH547 2.4 27.5 1.0
CG C:ASP158 3.0 21.5 1.0
CG C:ASP154 3.1 20.4 1.0
CG C:HIS131 3.2 21.7 1.0
CG C:ASP262 3.2 21.4 1.0
MN C:MN403 3.2 22.2 1.0
CE1 C:HIS131 3.2 21.4 1.0
OD2 C:ASP158 3.3 22.7 1.0
CB C:HIS131 3.4 23.3 1.0
OD1 C:ASP154 3.5 18.7 1.0
CB C:ASP262 3.6 22.7 1.0
O C:HOH664 4.1 31.1 1.0
OD1 C:ASP262 4.3 22.5 1.0
CD2 C:HIS131 4.3 22.8 1.0
NE2 C:HIS131 4.3 22.9 1.0
CB C:ASP158 4.4 19.7 1.0
NE1 C:TRP152 4.4 19.8 1.0
O C:HIS171 4.5 22.1 1.0
CB C:ASP154 4.5 17.4 1.0
CZ2 C:TRP152 4.6 21.6 1.0
CG C:GLU307 4.6 21.2 1.0
OE2 C:GLU307 4.8 23.2 1.0
CE2 C:TRP152 4.9 21.0 1.0
CA C:ASP262 4.9 20.8 1.0
CA C:HIS131 4.9 21.4 1.0

Manganese binding site 6 out of 8 in 4q40

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


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- Valine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:22.2
occ:1.00
 O C:HOH546 2.1 21.7 1.0
OD1 C:ASP154 2.2 18.7 1.0
ND1 C:HIS156 2.3 20.5 1.0
OD2 C:ASP262 2.3 20.3 1.0
OD1 C:ASP264 2.3 24.2 1.0
OD2 C:ASP264 2.4 23.5 1.0
CG C:ASP264 2.7 25.4 1.0
CG C:ASP154 3.1 20.4 1.0
CG C:ASP262 3.1 21.4 1.0
CE1 C:HIS156 3.1 21.4 1.0
O C:HOH664 3.2 31.1 1.0
MN C:MN402 3.2 22.0 1.0
CG C:HIS156 3.3 17.6 1.0
OD2 C:ASP154 3.4 19.3 1.0
CB C:HIS156 3.7 18.6 1.0
OD1 C:ASP262 3.7 22.5 1.0
N C:HIS156 4.0 18.8 1.0
CB C:ASP262 4.0 22.7 1.0
O C:HOH547 4.2 27.5 1.0
CB C:ASP264 4.2 19.5 1.0
N C:ALA155 4.2 19.1 1.0
OG1 C:THR276 4.2 24.3 1.0
NE2 C:HIS156 4.3 21.6 1.0
CD2 C:HIS156 4.4 20.1 1.0
CA C:HIS156 4.5 20.3 1.0
CB C:ASP154 4.5 17.4 1.0
OD2 C:ASP158 4.6 22.7 1.0
CB C:ALA155 4.7 20.7 1.0
O C:HOH545 4.8 22.6 1.0
CA C:ALA155 4.8 18.0 1.0
C C:ALA155 4.8 21.1 1.0
OD1 C:ASP158 4.8 22.0 1.0
CA C:ASP154 4.9 22.3 1.0
C C:ASP154 5.0 20.8 1.0

Manganese binding site 7 out of 8 in 4q40

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


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

b:31.4
occ:1.00
 O D:HOH510 2.2 29.9 1.0
OD1 D:ASP158 2.2 31.9 1.0
ND1 D:HIS131 2.2 30.5 1.0
OD2 D:ASP154 2.3 26.9 1.0
OD2 D:ASP262 2.3 31.2 1.0
O D:HOH511 2.5 35.0 1.0
CG D:ASP158 3.0 32.7 1.0
CG D:HIS131 3.2 33.0 1.0
CE1 D:HIS131 3.2 31.7 1.0
CG D:ASP262 3.2 34.0 1.0
CG D:ASP154 3.2 33.4 1.0
OD2 D:ASP158 3.2 30.8 1.0
MN D:MN402 3.3 30.8 1.0
CB D:HIS131 3.4 35.5 1.0
OD1 D:ASP154 3.5 29.5 1.0
CB D:ASP262 3.6 31.2 1.0
O D:HOH552 3.9 39.5 1.0
NE2 D:HIS131 4.3 36.0 1.0
CD2 D:HIS131 4.3 34.9 1.0
OD1 D:ASP262 4.3 29.3 1.0
NE1 D:TRP152 4.4 30.4 1.0
CB D:ASP158 4.4 29.8 1.0
CZ2 D:TRP152 4.5 33.6 1.0
O D:HIS171 4.5 35.8 1.0
CG D:GLU307 4.6 32.8 1.0
CB D:ASP154 4.6 30.4 1.0
CE2 D:TRP152 4.8 33.8 1.0
OE2 D:GLU307 4.8 33.4 1.0
CA D:ASP262 4.9 30.8 1.0
OD1 D:ASP264 4.9 32.5 1.0
CA D:HIS131 4.9 33.8 1.0
OD2 D:ASP264 5.0 29.3 1.0

Manganese binding site 8 out of 8 in 4q40

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


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

b:30.8
occ:1.00
 O D:HOH510 2.1 29.9 1.0
OD2 D:ASP262 2.2 31.2 1.0
OD1 D:ASP264 2.3 32.5 1.0
OD1 D:ASP154 2.3 29.5 1.0
ND1 D:HIS156 2.3 31.0 1.0
OD2 D:ASP264 2.4 29.3 1.0
CG D:ASP264 2.7 33.0 1.0
CG D:ASP262 3.1 34.0 1.0
O D:HOH552 3.2 39.5 1.0
CE1 D:HIS156 3.2 34.3 1.0
CG D:ASP154 3.2 33.4 1.0
MN D:MN401 3.3 31.4 1.0
CG D:HIS156 3.4 33.0 1.0
OD2 D:ASP154 3.5 26.9 1.0
CB D:HIS156 3.7 31.5 1.0
OD1 D:ASP262 3.7 29.3 1.0
CB D:ASP262 4.0 31.2 1.0
N D:HIS156 4.0 29.7 1.0
OG1 D:THR276 4.2 36.0 1.0
CB D:ASP264 4.2 29.4 1.0
O D:HOH511 4.2 35.0 1.0
N D:ALA155 4.3 27.6 1.0
NE2 D:HIS156 4.4 31.8 1.0
CD2 D:HIS156 4.5 34.3 1.0
CA D:HIS156 4.5 32.1 1.0
OD2 D:ASP158 4.5 30.8 1.0
CB D:ALA155 4.6 27.9 1.0
CB D:ASP154 4.6 30.4 1.0
O D:HOH527 4.7 30.2 1.0
CA D:ALA155 4.8 28.9 1.0
C D:ALA155 4.8 30.8 1.0
OD1 D:ASP158 4.9 31.9 1.0
CA D:ASP154 5.0 29.7 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 20:55:47 2024

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