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Manganese in PDB 4q3r: Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp

Enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp, PDB code: 4q3r 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) 49.23 / 2.17
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 177.488, 177.488, 177.488, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.6

Other elements in 4q3r:

The structure of Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp also contains other interesting chemical elements:

Caesium (Cs) 11 atoms
Chlorine (Cl) 12 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp (pdb code 4q3r). 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 Abhdp, PDB code: 4q3r:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4q3r

Go back to Manganese Binding Sites List in 4q3r
Manganese binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:15.4
occ:1.00
 OD2 A:ASP262 2.1 13.5 1.0
OD2 A:ASP158 2.1 15.7 1.0
OD2 A:ASP154 2.2 16.2 1.0
ND1 A:HIS131 2.2 14.1 1.0
O03 A:XA2407 2.3 20.4 1.0
O01 A:XA2407 2.4 21.4 1.0
B02 A:XA2407 2.9 16.1 1.0
CG A:ASP158 3.0 12.4 1.0
CG A:ASP154 3.2 14.7 1.0
CE1 A:HIS131 3.2 13.3 1.0
CG A:HIS131 3.2 13.6 1.0
CG A:ASP262 3.2 15.8 1.0
OD1 A:ASP158 3.2 18.7 1.0
MN A:MN402 3.3 15.7 1.0
OD1 A:ASP154 3.4 14.5 1.0
CB A:HIS131 3.5 12.3 1.0
CB A:ASP262 3.6 13.3 1.0
O04 A:XA2407 3.9 23.2 1.0
C05 A:XA2407 4.2 17.9 1.0
OD1 A:ASP262 4.3 12.9 1.0
NE2 A:HIS131 4.3 13.9 1.0
CD2 A:HIS131 4.3 12.8 1.0
NE1 A:TRP152 4.4 14.8 1.0
CB A:ASP158 4.4 12.2 1.0
CB A:ASP154 4.5 12.6 1.0
CZ2 A:TRP152 4.6 12.1 1.0
CG A:GLU307 4.6 14.9 1.0
O A:HIS171 4.6 17.6 1.0
OE2 A:GLU307 4.8 21.1 1.0
CA A:ASP262 4.9 12.6 1.0
CE2 A:TRP152 4.9 12.5 1.0
CA A:HIS131 5.0 16.4 1.0

Manganese binding site 2 out of 8 in 4q3r

Go back to Manganese Binding Sites List in 4q3r
Manganese binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:15.7
occ:1.00
 O03 A:XA2407 2.1 20.4 1.0
OD1 A:ASP154 2.2 14.5 1.0
OD2 A:ASP264 2.3 17.3 1.0
ND1 A:HIS156 2.3 11.8 1.0
OD2 A:ASP262 2.4 13.5 1.0
OD1 A:ASP264 2.5 15.2 1.0
CG A:ASP264 2.7 16.0 1.0
O04 A:XA2407 2.9 23.2 1.0
B02 A:XA2407 3.0 16.1 1.0
CG A:ASP262 3.1 15.8 1.0
CE1 A:HIS156 3.2 12.1 1.0
CG A:ASP154 3.2 14.7 1.0
MN A:MN401 3.3 15.4 1.0
CG A:HIS156 3.3 14.9 1.0
OD2 A:ASP154 3.5 16.2 1.0
CB A:HIS156 3.7 13.4 1.0
OD1 A:ASP262 3.7 12.9 1.0
O01 A:XA2407 4.0 21.4 1.0
N A:HIS156 4.1 13.7 1.0
CB A:ASP262 4.1 13.3 1.0
OG1 A:THR276 4.1 32.5 1.0
CB A:ASP264 4.3 14.0 1.0
NE2 A:HIS156 4.3 15.2 1.0
C05 A:XA2407 4.4 17.9 1.0
CD2 A:HIS156 4.4 15.2 1.0
N A:ALA155 4.4 14.8 1.0
C06 A:XA2407 4.5 17.6 1.0
CA A:HIS156 4.5 14.7 1.0
OD1 A:ASP158 4.5 18.7 1.0
O A:HOH517 4.6 19.7 1.0
CB A:ASP154 4.6 12.6 1.0
CB A:ALA155 4.7 12.2 1.0
C A:ALA155 4.9 13.5 1.0
CA A:ALA155 4.9 15.8 1.0
OD2 A:ASP158 4.9 15.7 1.0
CA A:ASP154 5.0 11.6 1.0

Manganese binding site 3 out of 8 in 4q3r

Go back to Manganese Binding Sites List in 4q3r
Manganese binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:11.9
occ:1.00
 OD2 B:ASP158 2.1 16.7 1.0
OD2 B:ASP262 2.2 11.1 1.0
OD2 B:ASP154 2.2 12.1 1.0
ND1 B:HIS131 2.3 12.7 1.0
O04 B:XA2409 2.3 19.2 1.0
O03 B:XA2409 2.4 19.1 1.0
B02 B:XA2409 2.9 15.5 1.0
CG B:ASP158 3.0 15.4 1.0
CG B:ASP154 3.2 13.6 1.0
CE1 B:HIS131 3.2 13.5 1.0
CG B:HIS131 3.2 14.3 1.0
CG B:ASP262 3.2 13.7 1.0
MN B:MN402 3.3 11.8 1.0
OD1 B:ASP158 3.3 15.2 1.0
OD1 B:ASP154 3.4 13.2 1.0
CB B:HIS131 3.5 17.0 1.0
CB B:ASP262 3.6 12.0 1.0
O01 B:XA2409 3.9 25.5 1.0
C05 B:XA2409 4.2 19.6 1.0
NE2 B:HIS131 4.3 15.0 1.0
CD2 B:HIS131 4.3 13.8 1.0
OD1 B:ASP262 4.3 15.4 1.0
NE1 B:TRP152 4.4 12.4 1.0
CB B:ASP158 4.4 14.9 1.0
CZ2 B:TRP152 4.6 12.3 1.0
CB B:ASP154 4.6 12.2 1.0
CG B:GLU307 4.6 13.8 1.0
O B:HIS171 4.6 16.2 1.0
CE2 B:TRP152 4.8 12.1 1.0
OE2 B:GLU307 4.8 17.8 1.0
CA B:ASP262 4.9 11.3 1.0
OD2 B:ASP264 5.0 16.6 1.0

Manganese binding site 4 out of 8 in 4q3r

Go back to Manganese Binding Sites List in 4q3r
Manganese binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:11.8
occ:1.00
 O04 B:XA2409 2.0 19.2 1.0
OD2 B:ASP264 2.2 16.6 1.0
OD1 B:ASP154 2.3 13.2 1.0
ND1 B:HIS156 2.3 15.1 1.0
OD2 B:ASP262 2.4 11.1 1.0
OD1 B:ASP264 2.6 15.7 1.0
CG B:ASP264 2.7 17.2 1.0
O01 B:XA2409 2.9 25.5 1.0
B02 B:XA2409 3.0 15.5 1.0
CG B:ASP262 3.1 13.7 1.0
CE1 B:HIS156 3.2 14.6 1.0
CG B:ASP154 3.2 13.6 1.0
MN B:MN401 3.3 11.9 1.0
CG B:HIS156 3.4 15.8 1.0
OD2 B:ASP154 3.5 12.1 1.0
OD1 B:ASP262 3.7 15.4 1.0
CB B:HIS156 3.8 14.1 1.0
O03 B:XA2409 4.0 19.1 1.0
CB B:ASP262 4.1 12.0 1.0
N B:HIS156 4.1 12.8 1.0
OG1 B:THR276 4.2 24.4 1.0
CB B:ASP264 4.2 14.7 1.0
N B:ALA155 4.3 13.2 1.0
NE2 B:HIS156 4.3 14.9 1.0
C05 B:XA2409 4.3 19.6 1.0
C06 B:XA2409 4.4 16.8 1.0
OD1 B:ASP158 4.5 15.2 1.0
CD2 B:HIS156 4.5 15.0 1.0
O B:HOH507 4.5 14.7 1.0
CA B:HIS156 4.6 12.7 1.0
CB B:ASP154 4.6 12.2 1.0
CB B:ALA155 4.7 13.0 1.0
OD2 B:ASP158 4.9 16.7 1.0
CA B:ALA155 4.9 13.8 1.0
C B:ALA155 4.9 12.6 1.0
CA B:ASP154 5.0 12.4 1.0

Manganese binding site 5 out of 8 in 4q3r

Go back to Manganese Binding Sites List in 4q3r
Manganese binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:25.7
occ:1.00
 OD2 C:ASP154 2.1 17.5 1.0
O01 C:XA2407 2.1 26.7 1.0
OD2 C:ASP158 2.1 23.2 1.0
OD2 C:ASP262 2.2 23.4 1.0
ND1 C:HIS131 2.2 21.1 1.0
O03 C:XA2407 2.4 24.0 1.0
B02 C:XA2407 2.8 19.2 1.0
CG C:ASP158 3.1 20.3 1.0
CG C:ASP154 3.1 19.4 1.0
CE1 C:HIS131 3.1 20.7 1.0
CG C:HIS131 3.2 21.1 1.0
CG C:ASP262 3.2 21.8 1.0
MN C:MN402 3.3 25.3 1.0
OD1 C:ASP158 3.3 26.3 1.0
OD1 C:ASP154 3.4 20.2 1.0
CB C:HIS131 3.5 21.0 1.0
CB C:ASP262 3.6 18.7 1.0
O04 C:XA2407 3.8 28.4 1.0
C05 C:XA2407 4.1 25.0 1.0
NE2 C:HIS131 4.2 19.8 1.0
CD2 C:HIS131 4.3 21.1 1.0
OD1 C:ASP262 4.3 26.0 1.0
NE1 C:TRP152 4.4 22.1 1.0
CB C:ASP158 4.4 20.0 1.0
CB C:ASP154 4.4 17.3 1.0
O C:HIS171 4.5 25.0 1.0
CG C:GLU307 4.6 20.4 1.0
CZ2 C:TRP152 4.6 22.3 1.0
OE2 C:GLU307 4.8 25.9 1.0
CE2 C:TRP152 4.9 17.8 1.0
CA C:ASP262 4.9 19.4 1.0
OD2 C:ASP264 5.0 23.3 1.0
CA C:HIS131 5.0 18.6 1.0

Manganese binding site 6 out of 8 in 4q3r

Go back to Manganese Binding Sites List in 4q3r
Manganese binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:25.3
occ:1.00
 O03 C:XA2407 2.0 24.0 1.0
OD1 C:ASP154 2.2 20.2 1.0
OD2 C:ASP264 2.2 23.3 1.0
ND1 C:HIS156 2.3 20.6 1.0
OD2 C:ASP262 2.4 23.4 1.0
OD1 C:ASP264 2.5 24.2 1.0
CG C:ASP264 2.7 20.7 1.0
O04 C:XA2407 2.8 28.4 1.0
B02 C:XA2407 2.9 19.2 1.0
CG C:ASP154 3.1 19.4 1.0
CG C:ASP262 3.1 21.8 1.0
CE1 C:HIS156 3.2 20.3 1.0
MN C:MN401 3.3 25.7 1.0
CG C:HIS156 3.4 18.1 1.0
OD2 C:ASP154 3.4 17.5 1.0
OD1 C:ASP262 3.6 26.0 1.0
CB C:HIS156 3.7 18.4 1.0
O01 C:XA2407 3.9 26.7 1.0
N C:HIS156 4.1 18.6 1.0
CB C:ASP262 4.1 18.7 1.0
OG1 C:THR276 4.2 36.3 1.0
CB C:ASP264 4.2 20.2 1.0
N C:ALA155 4.3 21.6 1.0
C05 C:XA2407 4.3 25.0 1.0
C06 C:XA2407 4.3 21.9 1.0
NE2 C:HIS156 4.3 21.1 1.0
CD2 C:HIS156 4.5 19.4 1.0
CB C:ASP154 4.5 17.3 1.0
CA C:HIS156 4.5 16.8 1.0
OD1 C:ASP158 4.5 26.3 1.0
O C:HOH506 4.6 26.5 1.0
CB C:ALA155 4.8 18.4 1.0
OD2 C:ASP158 4.9 23.2 1.0
CA C:ASP154 4.9 22.1 1.0
C C:ALA155 4.9 19.3 1.0
CA C:ALA155 4.9 18.0 1.0

Manganese binding site 7 out of 8 in 4q3r

Go back to Manganese Binding Sites List in 4q3r
Manganese binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:42.1
occ:1.00
 OD2 D:ASP262 2.1 44.5 1.0
ND1 D:HIS131 2.2 47.2 1.0
O04 D:XA2404 2.2 45.4 1.0
OD2 D:ASP158 2.2 46.9 1.0
OD2 D:ASP154 2.4 44.2 1.0
O03 D:XA2404 2.6 48.8 1.0
B02 D:XA2404 2.9 52.3 1.0
CE1 D:HIS131 3.1 46.7 1.0
CG D:ASP158 3.1 49.9 1.0
CG D:ASP262 3.1 46.6 1.0
CG D:HIS131 3.2 53.8 1.0
MN D:MN402 3.2 44.5 1.0
CG D:ASP154 3.3 46.5 1.0
OD1 D:ASP158 3.3 49.2 1.0
OD1 D:ASP154 3.4 44.6 1.0
CB D:HIS131 3.5 51.5 1.0
CB D:ASP262 3.5 44.5 1.0
O01 D:XA2404 4.1 53.3 1.0
C05 D:XA2404 4.2 60.1 1.0
OD1 D:ASP262 4.2 43.9 1.0
NE2 D:HIS131 4.2 51.8 1.0
CD2 D:HIS131 4.3 52.5 1.0
OD2 D:ASP264 4.5 54.3 1.0
NE1 D:TRP152 4.5 48.1 1.0
CB D:ASP158 4.5 52.0 1.0
CG D:GLU307 4.5 52.9 1.0
CB D:ASP154 4.7 45.4 1.0
CZ2 D:TRP152 4.7 50.4 1.0
O D:HIS171 4.7 58.5 1.0
CA D:ASP262 4.8 46.1 1.0
CE2 D:TRP152 4.9 51.0 1.0
CA D:HIS131 5.0 58.0 1.0
OE2 D:GLU307 5.0 49.2 1.0
ND1 D:HIS156 5.0 45.2 1.0

Manganese binding site 8 out of 8 in 4q3r

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Manganese binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni Arginase in Complex with Inhibitor Abhdp


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

b:44.5
occ:1.00
 OD2 D:ASP264 1.9 54.3 1.0
O04 D:XA2404 1.9 45.4 1.0
OD2 D:ASP262 2.3 44.5 1.0
ND1 D:HIS156 2.3 45.2 1.0
OD1 D:ASP154 2.4 44.6 1.0
CG D:ASP264 2.8 49.1 1.0
B02 D:XA2404 3.0 52.3 1.0
O01 D:XA2404 3.0 53.3 1.0
CE1 D:HIS156 3.1 49.0 1.0
CB D:ASP264 3.1 49.0 1.0
CG D:ASP262 3.1 46.6 1.0
MN D:MN401 3.2 42.1 1.0
CG D:HIS156 3.4 46.7 1.0
CG D:ASP154 3.4 46.5 1.0
OD2 D:ASP154 3.7 44.2 1.0
OD1 D:ASP262 3.7 43.9 1.0
CB D:HIS156 3.8 46.2 1.0
O03 D:XA2404 3.9 48.8 1.0
OD1 D:ASP264 4.0 59.4 1.0
CB D:ASP262 4.1 44.5 1.0
N D:HIS156 4.1 42.6 1.0
NE2 D:HIS156 4.3 52.5 1.0
C05 D:XA2404 4.3 60.1 1.0
C06 D:XA2404 4.4 54.6 1.0
N D:ALA155 4.4 41.2 1.0
OD1 D:ASP158 4.4 49.2 1.0
CD2 D:HIS156 4.4 51.0 1.0
CA D:ASP264 4.6 45.0 1.0
CA D:HIS156 4.6 46.4 1.0
CB D:ASP154 4.8 45.4 1.0
CB D:ALA155 4.8 42.2 1.0
OD2 D:ASP158 4.8 46.9 1.0
C D:ALA155 4.9 44.2 1.0
CA D:ALA155 5.0 45.0 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 20:53:04 2024

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