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Manganese in PDB 4q41: Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Lysine

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

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

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Lysine, PDB code: 4q41 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) 49.22 / 2.20
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 177.448, 177.448, 177.448, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with L- Lysine (pdb code 4q41). 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- Lysine, PDB code: 4q41:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4q41

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


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

b:26.8
occ:1.00
 O A:HOH654 2.1 33.1 1.0
OD1 A:ASP158 2.1 25.1 1.0
OD2 A:ASP154 2.1 23.7 1.0
OD2 A:ASP262 2.2 24.9 1.0
ND1 A:HIS131 2.2 23.3 1.0
O A:HOH655 2.4 32.1 1.0
CG A:ASP158 3.1 26.9 1.0
CG A:ASP154 3.1 23.9 1.0
CE1 A:HIS131 3.2 23.9 1.0
CG A:HIS131 3.2 22.5 1.0
CG A:ASP262 3.2 24.2 1.0
MN A:MN402 3.3 25.9 1.0
OD2 A:ASP158 3.4 26.9 1.0
OD1 A:ASP154 3.4 21.7 1.0
CB A:HIS131 3.5 25.1 1.0
CB A:ASP262 3.6 19.9 1.0
NZ A:LYS403 3.9 44.8 1.0
NE2 A:HIS131 4.3 22.1 1.0
OD1 A:ASP262 4.3 21.2 1.0
CE A:LYS403 4.3 36.6 1.0
CD2 A:HIS131 4.3 22.4 1.0
NE1 A:TRP152 4.4 23.8 1.0
CB A:ASP158 4.4 24.1 1.0
CB A:ASP154 4.5 22.6 1.0
O A:HIS171 4.6 28.2 1.0
CG A:GLU307 4.6 22.6 1.0
CZ2 A:TRP152 4.6 21.5 1.0
OE2 A:GLU307 4.9 27.6 1.0
CE2 A:TRP152 4.9 22.6 1.0
CA A:ASP262 4.9 21.2 1.0
OD1 A:ASP264 4.9 25.9 1.0

Manganese binding site 2 out of 8 in 4q41

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


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

b:25.9
occ:1.00
 O A:HOH654 2.1 33.1 1.0
OD1 A:ASP154 2.2 21.7 1.0
OD1 A:ASP264 2.2 25.9 1.0
ND1 A:HIS156 2.3 25.2 1.0
OD2 A:ASP262 2.4 24.9 1.0
OD2 A:ASP264 2.5 21.8 1.0
CG A:ASP264 2.7 25.4 1.0
CE1 A:HIS156 3.1 25.2 1.0
CG A:ASP154 3.1 23.9 1.0
CG A:ASP262 3.2 24.2 1.0
NZ A:LYS403 3.2 44.8 1.0
MN A:MN401 3.3 26.8 1.0
CG A:HIS156 3.4 24.6 1.0
OD2 A:ASP154 3.5 23.7 1.0
OD1 A:ASP262 3.8 21.2 1.0
CB A:HIS156 3.8 22.8 1.0
N A:HIS156 4.0 20.3 1.0
CB A:ASP262 4.0 19.9 1.0
CE A:LYS403 4.1 36.6 1.0
O A:HOH655 4.1 32.1 1.0
N A:ALA155 4.2 24.5 1.0
CB A:ASP264 4.2 25.4 1.0
OG1 A:THR276 4.2 34.5 1.0
NE2 A:HIS156 4.3 26.0 1.0
CD2 A:HIS156 4.4 28.1 1.0
CB A:ASP154 4.5 22.6 1.0
CA A:HIS156 4.5 23.1 1.0
OD2 A:ASP158 4.6 26.9 1.0
CB A:ALA155 4.6 22.6 1.0
O A:HOH503 4.6 24.3 1.0
CD A:LYS403 4.7 39.9 1.0
CA A:ALA155 4.8 24.8 1.0
C A:ALA155 4.8 23.9 1.0
OD1 A:ASP158 4.8 25.1 1.0
CA A:ASP154 4.9 22.1 1.0
C A:ASP154 5.0 22.9 1.0

Manganese binding site 3 out of 8 in 4q41

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


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

b:28.8
occ:1.00
 O B:HOH637 2.0 28.9 1.0
ND1 B:HIS131 2.1 26.8 1.0
OD1 B:ASP158 2.2 28.1 1.0
OD2 B:ASP262 2.2 29.0 1.0
OD2 B:ASP154 2.2 24.2 1.0
O B:HOH638 2.7 34.2 1.0
CE1 B:HIS131 3.1 26.6 1.0
CG B:ASP158 3.1 28.2 1.0
CG B:ASP154 3.1 24.3 1.0
CG B:ASP262 3.1 28.6 1.0
CG B:HIS131 3.1 29.6 1.0
MN B:MN402 3.3 27.8 1.0
OD1 B:ASP154 3.3 24.1 1.0
OD2 B:ASP158 3.4 27.9 1.0
CB B:HIS131 3.5 28.5 1.0
CB B:ASP262 3.5 24.5 1.0
NZ B:LYS403 4.1 41.5 1.0
NE2 B:HIS131 4.2 29.9 1.0
OD1 B:ASP262 4.2 25.6 1.0
CD2 B:HIS131 4.3 27.4 1.0
NE1 B:TRP152 4.4 25.2 1.0
CB B:ASP158 4.5 27.3 1.0
CB B:ASP154 4.5 20.4 1.0
O B:HIS171 4.6 33.5 1.0
CZ2 B:TRP152 4.6 25.8 1.0
CG B:GLU307 4.6 25.0 1.0
CE B:LYS403 4.7 45.4 1.0
OD1 B:ASP264 4.7 29.4 1.0
CA B:ASP262 4.8 24.9 1.0
CE2 B:TRP152 4.9 25.4 1.0
OE2 B:GLU307 4.9 31.3 1.0
ND1 B:HIS156 5.0 25.1 1.0
CA B:HIS131 5.0 30.2 1.0

Manganese binding site 4 out of 8 in 4q41

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


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

b:27.8
occ:1.00
 OD1 B:ASP264 2.1 29.4 1.0
OD1 B:ASP154 2.2 24.1 1.0
ND1 B:HIS156 2.2 25.1 1.0
O B:HOH637 2.3 28.9 1.0
OD2 B:ASP262 2.3 29.0 1.0
OD2 B:ASP264 2.4 27.4 1.0
CG B:ASP264 2.6 29.8 1.0
CE1 B:HIS156 3.0 27.5 1.0
CG B:ASP262 3.1 28.6 1.0
CG B:ASP154 3.2 24.3 1.0
NZ B:LYS403 3.2 41.5 1.0
MN B:MN401 3.3 28.8 1.0
CG B:HIS156 3.3 28.3 1.0
OD2 B:ASP154 3.6 24.2 1.0
OD1 B:ASP262 3.7 25.6 1.0
CB B:HIS156 3.7 24.6 1.0
CB B:ASP262 4.0 24.5 1.0
N B:HIS156 4.0 22.0 1.0
CB B:ASP264 4.1 27.1 1.0
O B:HOH638 4.2 34.2 1.0
NE2 B:HIS156 4.2 25.5 1.0
N B:ALA155 4.2 25.6 1.0
OG1 B:THR276 4.3 38.7 1.0
CE B:LYS403 4.3 45.4 1.0
CD2 B:HIS156 4.3 29.2 1.0
CA B:HIS156 4.5 25.2 1.0
CB B:ASP154 4.6 20.4 1.0
OD2 B:ASP158 4.6 27.9 1.0
O B:HOH514 4.6 31.0 1.0
CB B:ALA155 4.7 24.2 1.0
CA B:ALA155 4.8 23.1 1.0
C B:ALA155 4.8 27.4 1.0
OD1 B:ASP158 4.8 28.1 1.0
CD B:LYS403 4.9 44.3 1.0
CA B:ASP154 4.9 24.3 1.0
C B:ASP154 5.0 22.6 1.0

Manganese binding site 5 out of 8 in 4q41

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


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

b:41.1
occ:1.00
 OD1 C:ASP158 2.0 39.5 1.0
OD2 C:ASP262 2.2 38.2 1.0
ND1 C:HIS131 2.2 43.7 1.0
OD2 C:ASP154 2.2 37.4 1.0
O C:HOH545 2.3 38.9 1.0
CG C:ASP158 2.9 37.6 1.0
CE1 C:HIS131 3.1 44.3 1.0
OD2 C:ASP158 3.2 41.7 1.0
CG C:HIS131 3.2 43.6 1.0
CG C:ASP262 3.2 42.6 1.0
CG C:ASP154 3.2 41.0 1.0
MN C:MN402 3.2 41.0 1.0
CB C:HIS131 3.5 41.7 1.0
OD1 C:ASP154 3.5 36.2 1.0
CB C:ASP262 3.6 39.7 1.0
NE2 C:HIS131 4.3 41.3 1.0
OD1 C:ASP262 4.3 40.8 1.0
CB C:ASP158 4.3 36.6 1.0
CD2 C:HIS131 4.3 41.9 1.0
NE1 C:TRP152 4.4 41.9 1.0
O C:HIS171 4.5 40.5 1.0
CB C:ASP154 4.6 37.8 1.0
CZ2 C:TRP152 4.6 37.5 1.0
CG C:GLU307 4.7 41.1 1.0
CE2 C:TRP152 4.9 41.6 1.0
CA C:ASP262 4.9 41.0 1.0
OE2 C:GLU307 4.9 40.5 1.0
OD1 C:ASP264 5.0 43.1 1.0

Manganese binding site 6 out of 8 in 4q41

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


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

b:41.0
occ:1.00
 O C:HOH545 2.1 38.9 1.0
OD1 C:ASP264 2.2 43.1 1.0
OD1 C:ASP154 2.3 36.2 1.0
OD2 C:ASP262 2.3 38.2 1.0
ND1 C:HIS156 2.3 37.7 1.0
OD2 C:ASP264 2.5 41.8 1.0
CG C:ASP264 2.7 42.3 1.0
CG C:ASP262 3.1 42.6 1.0
CE1 C:HIS156 3.2 39.2 1.0
CG C:ASP154 3.2 41.0 1.0
MN C:MN401 3.2 41.1 1.0
CG C:HIS156 3.4 40.3 1.0
OD2 C:ASP154 3.4 37.4 1.0
OD1 C:ASP262 3.7 40.8 1.0
CB C:HIS156 3.8 37.1 1.0
CB C:ASP262 4.0 39.7 1.0
N C:HIS156 4.0 37.7 1.0
OG1 C:THR276 4.2 46.6 1.0
CB C:ASP264 4.2 41.2 1.0
N C:ALA155 4.3 37.9 1.0
NE2 C:HIS156 4.4 41.6 1.0
OD2 C:ASP158 4.4 41.7 1.0
CD2 C:HIS156 4.5 40.9 1.0
CA C:HIS156 4.5 34.6 1.0
CB C:ALA155 4.6 39.2 1.0
CB C:ASP154 4.6 37.8 1.0
CA C:ALA155 4.8 38.3 1.0
OD1 C:ASP158 4.8 39.5 1.0
C C:ALA155 4.8 38.4 1.0
O C:HOH506 4.8 41.6 1.0
CA C:ASP154 4.9 42.0 1.0

Manganese binding site 7 out of 8 in 4q41

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


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

b:48.5
occ:0.75
 OD1 D:ASP158 2.0 53.9 1.0
ND1 D:HIS131 2.2 58.2 1.0
OD2 D:ASP262 2.2 52.6 1.0
OD2 D:ASP154 2.4 50.9 1.0
CG D:ASP158 2.9 61.1 1.0
MN D:MN401 3.0 53.5 0.9
CE1 D:HIS131 3.1 57.0 1.0
OD2 D:ASP158 3.1 61.6 1.0
CG D:HIS131 3.2 63.4 1.0
CG D:ASP262 3.2 56.0 1.0
CG D:ASP154 3.3 54.5 1.0
OD1 D:ASP154 3.5 54.9 1.0
CB D:HIS131 3.5 65.0 1.0
CB D:ASP262 3.6 51.4 1.0
O D:HOH522 3.6 65.0 1.0
NE2 D:HIS131 4.2 61.3 1.0
CD2 D:HIS131 4.3 63.5 1.0
OD1 D:ASP262 4.3 53.4 1.0
CB D:ASP158 4.3 60.9 1.0
NE1 D:TRP152 4.5 59.4 1.0
CZ2 D:TRP152 4.6 63.2 1.0
CB D:ASP154 4.6 56.4 1.0
O D:HIS171 4.6 66.5 1.0
CG D:GLU307 4.7 63.4 1.0
OD1 D:ASP264 4.7 58.5 1.0
CE2 D:TRP152 4.9 60.5 1.0
OD2 D:ASP264 4.9 57.2 1.0
CA D:ASP262 4.9 55.1 1.0
ND1 D:HIS156 4.9 56.1 1.0

Manganese binding site 8 out of 8 in 4q41

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


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

b:53.5
occ:0.90
 OD2 D:ASP262 2.2 52.6 1.0
OD1 D:ASP264 2.3 58.5 1.0
ND1 D:HIS156 2.3 56.1 1.0
OD1 D:ASP154 2.4 54.9 1.0
OD2 D:ASP264 2.6 57.2 1.0
CG D:ASP264 2.8 58.3 1.0
O D:HOH522 2.9 65.0 1.0
MN D:MN400 3.0 48.5 0.8
CG D:ASP262 3.1 56.0 1.0
CE1 D:HIS156 3.2 60.8 1.0
CG D:ASP154 3.3 54.5 1.0
CG D:HIS156 3.4 58.5 1.0
OD2 D:ASP154 3.5 50.9 1.0
OD1 D:ASP262 3.8 53.4 1.0
CB D:HIS156 3.8 56.0 1.0
CB D:ASP262 4.1 51.4 1.0
N D:HIS156 4.1 53.5 1.0
OG1 D:THR276 4.1 72.6 1.0
OD2 D:ASP158 4.3 61.6 1.0
CB D:ASP264 4.3 56.6 1.0
NE2 D:HIS156 4.3 61.9 1.0
N D:ALA155 4.4 52.9 1.0
CD2 D:HIS156 4.5 59.0 1.0
CA D:HIS156 4.6 57.7 1.0
OD1 D:ASP158 4.6 53.9 1.0
CB D:ASP154 4.7 56.4 1.0
CB D:ALA155 4.8 54.2 1.0
CG D:ASP158 4.9 61.1 1.0
C D:ALA155 4.9 56.9 1.0
CA D:ALA155 4.9 53.3 1.0
O D:HOH506 4.9 58.6 1.0
ND1 D:HIS131 5.0 58.2 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 20:57:08 2024

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