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Manganese in PDB 4q3p: Crystal Structure of Schistosoma Mansoni Arginase

Enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni Arginase, PDB code: 4q3p 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) 49.48 / 2.50
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 178.384, 178.384, 178.384, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Schistosoma Mansoni Arginase (pdb code 4q3p). 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, PDB code: 4q3p:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4q3p

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Manganese binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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

b:17.3
occ:1.00
 OD1 A:ASP158 2.1 18.1 1.0
OD2 A:ASP262 2.2 12.9 1.0
OD2 A:ASP154 2.2 12.6 1.0
O A:HOH688 2.3 20.5 1.0
ND1 A:HIS131 2.3 16.5 1.0
O A:HOH693 2.5 28.0 1.0
CG A:ASP158 3.0 16.6 1.0
CG A:ASP262 3.2 12.4 1.0
CG A:ASP154 3.2 16.2 1.0
CG A:HIS131 3.2 17.7 1.0
MN A:MN402 3.2 15.1 1.0
CE1 A:HIS131 3.2 16.6 1.0
OD2 A:ASP158 3.3 20.4 1.0
CB A:HIS131 3.5 12.8 1.0
OD1 A:ASP154 3.6 14.9 1.0
CB A:ASP262 3.6 10.2 1.0
OD1 A:ASP262 4.2 10.7 1.0
NE2 A:HIS131 4.4 16.1 1.0
CD2 A:HIS131 4.4 15.8 1.0
O A:HOH695 4.4 28.0 1.0
CB A:ASP158 4.4 13.8 1.0
CB A:ASP154 4.5 13.1 1.0
O A:HIS171 4.5 17.4 1.0
NE1 A:TRP152 4.5 14.2 1.0
CG A:GLU307 4.6 15.1 1.0
CZ2 A:TRP152 4.7 11.6 1.0
OD1 A:ASP264 4.7 15.9 1.0
OE2 A:GLU307 4.9 20.0 1.0
CA A:ASP262 4.9 12.0 1.0
CE2 A:TRP152 5.0 13.9 1.0
CA A:HIS131 5.0 16.3 1.0
OD2 A:ASP264 5.0 15.2 1.0

Manganese binding site 2 out of 8 in 4q3p

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Manganese binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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

b:15.1
occ:1.00
 O A:HOH688 2.1 20.5 1.0
OD1 A:ASP264 2.1 15.9 1.0
OD1 A:ASP154 2.2 14.9 1.0
ND1 A:HIS156 2.3 15.5 1.0
OD2 A:ASP262 2.3 12.9 1.0
OD2 A:ASP264 2.5 15.2 1.0
CG A:ASP264 2.7 15.4 1.0
CG A:ASP154 3.1 16.2 1.0
CE1 A:HIS156 3.2 11.2 1.0
CG A:ASP262 3.2 12.4 1.0
MN A:MN401 3.2 17.3 1.0
OD2 A:ASP154 3.3 12.6 1.0
CG A:HIS156 3.3 16.4 1.0
CB A:HIS156 3.7 12.9 1.0
O A:HOH695 3.7 28.0 1.0
OD1 A:ASP262 3.8 10.7 1.0
O A:HOH693 3.9 28.0 1.0
N A:HIS156 3.9 15.2 1.0
CB A:ASP262 4.1 10.2 1.0
CB A:ASP264 4.2 10.8 1.0
N A:ALA155 4.2 12.0 1.0
OG1 A:THR276 4.2 24.2 1.0
NE2 A:HIS156 4.3 15.2 1.0
CA A:HIS156 4.4 16.4 1.0
CD2 A:HIS156 4.4 16.2 1.0
OD2 A:ASP158 4.4 20.4 1.0
CB A:ASP154 4.5 13.1 1.0
CB A:ALA155 4.7 12.1 1.0
C A:ALA155 4.7 16.1 1.0
OD1 A:ASP158 4.7 18.1 1.0
CA A:ALA155 4.8 16.1 1.0
O A:HOH502 4.8 13.8 1.0
CA A:ASP154 4.9 10.4 1.0
C A:ASP154 5.0 14.8 1.0
CG A:ASP158 5.0 16.6 1.0

Manganese binding site 3 out of 8 in 4q3p

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Manganese binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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

b:17.6
occ:1.00
 OD2 B:ASP158 2.1 21.8 1.0
OD2 B:ASP262 2.1 15.7 1.0
OD2 B:ASP154 2.2 15.9 1.0
ND1 B:HIS131 2.3 17.5 1.0
O B:HOH669 2.3 22.0 1.0
O B:HOH650 2.5 25.5 1.0
CG B:ASP158 3.0 16.2 1.0
CG B:ASP262 3.1 18.1 1.0
MN B:MN402 3.1 16.2 1.0
CE1 B:HIS131 3.2 21.8 1.0
CG B:ASP154 3.2 18.0 1.0
CG B:HIS131 3.2 20.1 1.0
OD1 B:ASP158 3.2 19.2 1.0
CB B:HIS131 3.5 18.0 1.0
OD1 B:ASP154 3.6 15.2 1.0
CB B:ASP262 3.6 13.4 1.0
OD1 B:ASP262 4.2 16.3 1.0
NE2 B:HIS131 4.3 16.6 1.0
CB B:ASP158 4.3 13.6 1.0
CD2 B:HIS131 4.4 13.3 1.0
NE1 B:TRP152 4.5 14.7 1.0
O B:HIS171 4.5 17.5 1.0
OD2 B:ASP264 4.6 18.1 1.0
CB B:ASP154 4.6 18.7 1.0
O B:HOH672 4.6 23.0 1.0
CG B:GLU307 4.6 16.4 1.0
CZ2 B:TRP152 4.7 14.6 1.0
OE2 B:GLU307 4.9 15.3 1.0
CA B:ASP262 4.9 13.1 1.0
CE2 B:TRP152 4.9 12.4 1.0
OD1 B:ASP264 5.0 20.0 1.0

Manganese binding site 4 out of 8 in 4q3p

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Manganese binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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

b:16.2
occ:1.00
 OD2 B:ASP264 1.9 18.1 1.0
O B:HOH669 2.0 22.0 1.0
OD1 B:ASP154 2.2 15.2 1.0
OD2 B:ASP262 2.3 15.7 1.0
ND1 B:HIS156 2.4 15.2 1.0
OD1 B:ASP264 2.5 20.0 1.0
CG B:ASP264 2.6 18.6 1.0
CG B:ASP154 3.1 18.0 1.0
CG B:ASP262 3.1 18.1 1.0
MN B:MN401 3.1 17.6 1.0
CE1 B:HIS156 3.2 14.0 1.0
OD2 B:ASP154 3.3 15.9 1.0
CG B:HIS156 3.4 15.3 1.0
O B:HOH672 3.6 23.0 1.0
OD1 B:ASP262 3.7 16.3 1.0
CB B:HIS156 3.8 17.2 1.0
O B:HOH650 3.9 25.5 1.0
N B:HIS156 4.0 15.9 1.0
CB B:ASP262 4.0 13.4 1.0
CB B:ASP264 4.1 15.6 1.0
OG1 B:THR276 4.2 27.5 1.0
N B:ALA155 4.2 15.8 1.0
OD1 B:ASP158 4.3 19.2 1.0
NE2 B:HIS156 4.4 16.9 1.0
CA B:HIS156 4.5 17.9 1.0
CD2 B:HIS156 4.5 17.8 1.0
CB B:ASP154 4.5 18.7 1.0
CB B:ALA155 4.6 13.8 1.0
OD2 B:ASP158 4.7 21.8 1.0
C B:ALA155 4.7 19.9 1.0
CA B:ALA155 4.7 17.6 1.0
O B:HOH625 4.8 15.2 1.0
CA B:ASP154 4.9 12.6 1.0
CG B:ASP158 4.9 16.2 1.0

Manganese binding site 5 out of 8 in 4q3p

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Manganese binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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

b:23.4
occ:1.00
 OD2 C:ASP262 2.1 24.4 1.0
OD1 C:ASP158 2.2 20.9 1.0
OD2 C:ASP154 2.2 16.9 1.0
O C:HOH598 2.3 24.7 1.0
ND1 C:HIS131 2.3 19.2 1.0
O C:HOH597 2.4 27.0 1.0
CG C:ASP158 3.0 22.9 1.0
CG C:ASP262 3.1 21.5 1.0
CG C:HIS131 3.2 21.4 1.0
MN C:MN402 3.2 25.0 1.0
CG C:ASP154 3.2 22.3 1.0
OD2 C:ASP158 3.3 29.5 1.0
CE1 C:HIS131 3.3 24.4 1.0
CB C:HIS131 3.4 22.0 1.0
CB C:ASP262 3.5 21.6 1.0
OD1 C:ASP154 3.6 26.8 1.0
O C:HOH599 4.1 29.1 1.0
OD1 C:ASP262 4.2 22.9 1.0
CD2 C:HIS131 4.3 22.7 1.0
NE2 C:HIS131 4.4 21.6 1.0
CB C:ASP158 4.4 20.0 1.0
O C:HIS171 4.5 29.1 1.0
CB C:ASP154 4.5 21.5 1.0
NE1 C:TRP152 4.5 23.1 1.0
CG C:GLU307 4.5 21.9 1.0
CZ2 C:TRP152 4.7 20.4 1.0
OE2 C:GLU307 4.7 23.2 1.0
OD1 C:ASP264 4.8 25.5 1.0
CA C:ASP262 4.8 22.0 1.0
CA C:HIS131 4.9 24.6 1.0
CE2 C:TRP152 5.0 20.9 1.0

Manganese binding site 6 out of 8 in 4q3p

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Manganese binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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

b:25.0
occ:1.00
 OD1 C:ASP154 2.2 26.8 1.0
O C:HOH598 2.2 24.7 1.0
OD1 C:ASP264 2.2 25.5 1.0
OD2 C:ASP262 2.3 24.4 1.0
ND1 C:HIS156 2.4 21.2 1.0
OD2 C:ASP264 2.5 26.3 1.0
CG C:ASP264 2.7 24.4 1.0
CG C:ASP154 3.0 22.3 1.0
CG C:ASP262 3.1 21.5 1.0
MN C:MN401 3.2 23.4 1.0
OD2 C:ASP154 3.2 16.9 1.0
CE1 C:HIS156 3.3 24.9 1.0
O C:HOH599 3.3 29.1 1.0
CG C:HIS156 3.4 20.5 1.0
CB C:HIS156 3.7 18.9 1.0
OD1 C:ASP262 3.7 22.9 1.0
N C:HIS156 3.9 23.0 1.0
O C:HOH597 3.9 27.0 1.0
CB C:ASP262 4.0 21.6 1.0
OG1 C:THR276 4.2 27.5 1.0
CB C:ASP264 4.2 20.7 1.0
N C:ALA155 4.2 23.7 1.0
NE2 C:HIS156 4.4 25.4 1.0
OD2 C:ASP158 4.4 29.5 1.0
CA C:HIS156 4.4 21.5 1.0
CB C:ASP154 4.4 21.5 1.0
CD2 C:HIS156 4.5 25.3 1.0
CB C:ALA155 4.8 24.1 1.0
C C:ALA155 4.8 25.8 1.0
OD1 C:ASP158 4.8 20.9 1.0
CA C:ALA155 4.9 21.2 1.0
CA C:ASP154 4.9 17.9 1.0
O C:HOH501 4.9 23.0 1.0
C C:ASP154 5.0 25.7 1.0

Manganese binding site 7 out of 8 in 4q3p

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Manganese binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn400

b:57.7
occ:1.00
 ND1 D:HIS131 2.1 65.5 1.0
OD1 D:ASP158 2.2 58.3 1.0
OD2 D:ASP262 2.4 57.2 1.0
OD2 D:ASP154 2.4 55.9 1.0
CE1 D:HIS131 2.9 59.5 1.0
CG D:ASP158 3.0 64.5 1.0
MN D:MN401 3.1 59.8 1.0
CG D:HIS131 3.2 69.3 1.0
OD2 D:ASP158 3.2 65.0 1.0
CG D:ASP154 3.4 52.1 1.0
CG D:ASP262 3.4 58.8 1.0
OD1 D:ASP154 3.6 56.5 1.0
CB D:HIS131 3.7 71.7 1.0
CB D:ASP262 3.9 58.5 1.0
NE2 D:HIS131 4.1 58.4 1.0
CD2 D:HIS131 4.3 65.7 1.0
O D:HIS171 4.3 65.2 1.0
CB D:ASP158 4.4 63.2 1.0
OD1 D:ASP262 4.5 61.7 1.0
NE1 D:TRP152 4.5 64.4 1.0
CZ2 D:TRP152 4.6 61.0 1.0
CG D:GLU307 4.7 66.5 1.0
CB D:ASP154 4.7 61.7 1.0
OD1 D:ASP264 4.8 59.3 1.0
CE2 D:TRP152 4.9 60.8 1.0
OE2 D:GLU307 4.9 52.9 1.0
OD2 D:ASP264 4.9 58.8 1.0

Manganese binding site 8 out of 8 in 4q3p

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Manganese binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase


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

b:59.8
occ:1.00
 OD1 D:ASP154 2.4 56.5 1.0
OD2 D:ASP262 2.5 57.2 1.0
OD2 D:ASP264 2.5 58.8 1.0
ND1 D:HIS156 2.6 52.3 1.0
OD1 D:ASP264 2.6 59.3 1.0
CG D:ASP264 2.9 57.9 1.0
MN D:MN400 3.1 57.7 1.0
CG D:ASP154 3.2 52.1 1.0
CG D:ASP262 3.3 58.8 1.0
OD2 D:ASP154 3.4 55.9 1.0
CE1 D:HIS156 3.5 55.5 1.0
CG D:HIS156 3.5 57.0 1.0
CB D:HIS156 3.8 58.9 1.0
N D:HIS156 4.0 56.0 1.0
OD1 D:ASP262 4.0 61.7 1.0
OG1 D:THR276 4.0 68.9 1.0
CB D:ASP262 4.1 58.5 1.0
OD2 D:ASP158 4.3 65.0 1.0
N D:ALA155 4.4 56.1 1.0
CB D:ASP264 4.4 59.5 1.0
CA D:HIS156 4.5 60.7 1.0
NE2 D:HIS156 4.6 63.9 1.0
CD2 D:HIS156 4.7 61.3 1.0
CB D:ASP154 4.7 61.7 1.0
OD1 D:ASP158 4.8 58.3 1.0
CB D:ALA155 4.8 47.2 1.0
C D:ALA155 4.9 54.3 1.0
ND1 D:HIS131 4.9 65.5 1.0
CA D:ALA155 4.9 52.9 1.0
CG D:ASP158 5.0 64.5 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 20:52:01 2024

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