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Manganese in PDB 3l24: Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors

Enzymatic activity of Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors

All present enzymatic activity of Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors:
3.1.8.1; 3.1.8.2; 3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors, PDB code: 3l24 was solved by N.K.Vyas, A.Nichitenko, V.K.Rastogi, S.S.Shah, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.10 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 124.354, 143.934, 219.213, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 27.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors (pdb code 3l24). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors, PDB code: 3l24:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 3l24

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Manganese binding site 1 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn518

b:31.8
occ:1.00
 OD2 A:ASP255 2.1 27.1 1.0
OE2 A:GLU420 2.2 28.6 1.0
NE2 A:HIS336 2.3 24.8 1.0
O11 A:GOA521 2.4 34.9 1.0
OE2 A:GLU381 2.4 43.5 1.0
O12 A:GOA521 2.6 40.7 1.0
C1 A:GOA521 2.7 41.2 1.0
CG A:ASP255 3.1 25.6 1.0
CD A:GLU381 3.2 40.8 1.0
CE1 A:HIS336 3.3 25.8 1.0
OE1 A:GLU381 3.3 37.7 1.0
CD2 A:HIS336 3.3 25.1 1.0
MN A:MN519 3.4 27.5 1.0
CD A:GLU420 3.4 30.1 1.0
OD1 A:ASP255 3.6 22.0 1.0
OE1 A:GLU420 3.8 31.1 1.0
C2 A:GOA521 3.9 39.8 1.0
OG1 A:THR379 4.0 28.9 1.0
O2 A:GOA521 4.0 34.6 1.0
CG2 A:THR379 4.3 25.5 1.0
CB A:ASP255 4.4 25.5 1.0
CB A:THR379 4.4 27.5 1.0
ND1 A:HIS336 4.4 26.5 1.0
CG A:HIS336 4.5 28.4 1.0
NE2 A:HIS343 4.5 30.0 1.0
CG A:GLU420 4.6 32.2 1.0
CG A:GLU381 4.6 36.1 1.0
CD2 A:HIS343 4.8 27.9 1.0
O A:ASP255 5.0 31.6 1.0

Manganese binding site 2 out of 10 in 3l24

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Manganese binding site 2 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn519

b:27.5
occ:1.00
 O11 A:GOA521 1.9 34.9 1.0
OD1 A:ASP255 2.0 22.0 1.0
OE1 A:GLU420 2.2 31.1 1.0
OD1 A:ASP244 2.4 25.9 1.0
OD2 A:ASP244 2.5 24.4 1.0
CG A:ASP244 2.7 24.9 1.0
O2 A:GOA521 2.8 34.6 1.0
C1 A:GOA521 2.8 41.2 1.0
CG A:ASP255 2.9 25.6 1.0
CD A:GLU420 3.0 30.1 1.0
OE2 A:GLU420 3.1 28.6 1.0
C2 A:GOA521 3.1 39.8 1.0
OD2 A:ASP255 3.2 27.1 1.0
MN A:MN518 3.4 31.8 1.0
OG1 A:THR257 3.5 31.1 1.0
OH A:TYR212 3.9 29.6 1.0
O12 A:GOA521 3.9 40.7 1.0
OE1 A:GLU381 4.1 37.7 1.0
CB A:ASP244 4.2 24.0 1.0
CZ A:TYR212 4.3 31.0 1.0
CB A:ASP255 4.3 25.5 1.0
C A:ASP255 4.4 27.7 1.0
O A:ASP255 4.4 31.6 1.0
CG A:GLU420 4.4 32.2 1.0
CE2 A:TYR212 4.5 28.6 1.0
N A:ILE256 4.6 29.4 1.0
CA A:ASP255 4.7 25.1 1.0
O A:ILE256 4.7 30.7 1.0
C A:ILE256 4.8 30.7 1.0
NE A:ARG418 4.8 28.3 1.0
CD A:GLU381 4.9 40.8 1.0
OE2 A:GLU381 4.9 43.5 1.0
CB A:THR257 4.9 31.2 1.0
NH2 A:ARG418 4.9 28.5 1.0
CA A:ASP244 4.9 26.0 1.0

Manganese binding site 3 out of 10 in 3l24

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Manganese binding site 3 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn520

b:36.9
occ:1.00
 O A:HOH675 2.1 20.6 1.0
O A:HOH676 2.1 32.2 1.0
OD1 A:ASP105 2.1 36.4 1.0
OE2 A:GLU107 2.2 31.5 1.0
O A:HOH674 2.3 37.4 1.0
O A:HOH648 2.4 26.9 1.0
CG A:ASP105 3.1 35.4 1.0
CD A:GLU107 3.2 31.8 1.0
OD2 A:ASP105 3.4 38.4 1.0
OE1 A:GLU107 3.6 32.7 1.0
O A:ILE106 4.2 33.4 1.0
CB A:ASP105 4.4 34.4 1.0
C A:ASP105 4.6 34.7 1.0
CG A:GLU107 4.6 31.0 1.0
N A:ILE106 4.7 33.0 1.0
C A:ILE106 4.7 34.3 1.0
CA A:ASP105 4.7 33.0 1.0
O A:ASP105 4.9 33.0 1.0
CE A:LYS79 5.0 44.1 1.0

Manganese binding site 4 out of 10 in 3l24

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Manganese binding site 4 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn518

b:32.1
occ:1.00
 OD2 B:ASP255 1.9 24.3 1.0
OE2 B:GLU381 2.0 31.1 1.0
NE2 B:HIS336 2.3 29.1 1.0
OE2 B:GLU420 2.3 29.9 1.0
O11 B:GOA522 2.4 49.6 1.0
O12 B:GOA522 2.7 50.4 1.0
C1 B:GOA522 2.7 51.1 1.0
CG B:ASP255 3.0 23.6 1.0
CD B:GLU381 3.0 34.7 1.0
CD2 B:HIS336 3.2 27.7 1.0
CE1 B:HIS336 3.3 29.6 1.0
OE1 B:GLU381 3.3 37.9 1.0
MN B:MN519 3.3 33.1 1.0
CD B:GLU420 3.3 27.5 1.0
OD1 B:ASP255 3.4 20.5 1.0
OE1 B:GLU420 3.7 26.5 1.0
OG1 B:THR379 3.9 27.9 1.0
C2 B:GOA522 3.9 49.0 1.0
O2 B:GOA522 4.1 43.8 1.0
CG2 B:THR379 4.2 21.9 1.0
CB B:ASP255 4.2 22.1 1.0
CB B:THR379 4.2 28.6 1.0
CG B:GLU381 4.3 34.2 1.0
CG B:HIS336 4.3 30.2 1.0
ND1 B:HIS336 4.4 29.2 1.0
NE2 B:HIS343 4.6 39.8 1.0
CG B:GLU420 4.6 26.4 1.0
CD2 B:HIS343 4.9 40.1 1.0
O B:ASP255 4.9 25.5 1.0
CG1 B:VAL342 5.0 26.9 1.0

Manganese binding site 5 out of 10 in 3l24

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Manganese binding site 5 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn519

b:33.1
occ:1.00
 OD1 B:ASP255 2.0 20.5 1.0
O11 B:GOA522 2.1 49.6 1.0
OD2 B:ASP244 2.2 29.1 1.0
OE1 B:GLU420 2.3 26.5 1.0
OD1 B:ASP244 2.3 31.5 1.0
O2 B:GOA522 2.5 43.8 1.0
CG B:ASP244 2.6 28.7 1.0
C1 B:GOA522 2.9 51.1 1.0
CG B:ASP255 2.9 23.6 1.0
C2 B:GOA522 3.1 49.0 1.0
CD B:GLU420 3.1 27.5 1.0
OD2 B:ASP255 3.2 24.3 1.0
OE2 B:GLU420 3.3 29.9 1.0
MN B:MN518 3.3 32.1 1.0
OG1 B:THR257 3.5 26.7 1.0
OH B:TYR212 3.9 30.8 1.0
OE1 B:GLU381 4.0 37.9 1.0
O12 B:GOA522 4.0 50.4 1.0
CB B:ASP244 4.1 27.1 1.0
CB B:ASP255 4.3 22.1 1.0
CZ B:TYR212 4.3 33.9 1.0
C B:ASP255 4.4 23.9 1.0
OE2 B:GLU381 4.5 31.1 1.0
CE2 B:TYR212 4.6 31.5 1.0
O B:ASP255 4.6 25.5 1.0
CG B:GLU420 4.6 26.4 1.0
CD B:GLU381 4.6 34.7 1.0
CA B:ASP255 4.7 23.8 1.0
NE B:ARG418 4.7 31.0 1.0
N B:ILE256 4.7 24.3 1.0
NH2 B:ARG418 4.8 29.1 1.0
CB B:THR257 4.9 24.8 1.0
CA B:ASP244 4.9 25.2 1.0
C B:ILE256 5.0 23.8 1.0

Manganese binding site 6 out of 10 in 3l24

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Manganese binding site 6 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn520

b:57.2
occ:1.00
 O B:HOH627 2.0 31.5 1.0
OE1 C:GLU436 2.2 50.9 1.0
OE2 B:GLU26 2.5 60.5 1.0
O B:HOH602 2.5 27.2 1.0
O C:HOH603 2.7 45.8 1.0
CD B:GLU26 3.1 59.7 1.0
OE1 B:GLU26 3.2 59.1 1.0
CD C:GLU436 3.3 52.9 1.0
O C:HOH605 3.4 60.9 1.0
OE2 C:GLU436 3.8 54.5 1.0
OE2 C:GLU431 4.1 36.6 1.0
O B:ARG25 4.2 57.2 1.0
CG C:GLU431 4.4 38.9 1.0
CD C:GLU431 4.4 38.8 1.0
CG B:GLU26 4.6 59.8 1.0
CG C:GLU436 4.6 52.2 1.0
CA B:GLU26 4.8 60.0 1.0
O C:HOH604 4.9 44.6 1.0
C B:ARG25 4.9 57.3 1.0

Manganese binding site 7 out of 10 in 3l24

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Manganese binding site 7 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn521

b:75.7
occ:1.00
 ND1 B:HIS226 2.2 58.7 1.0
CE1 B:HIS226 2.9 58.9 1.0
CG B:HIS226 3.4 56.7 1.0
CB B:HIS226 3.9 51.7 1.0
NE2 B:HIS226 4.1 59.1 1.0
CD2 B:HIS226 4.3 58.6 1.0

Manganese binding site 8 out of 10 in 3l24

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Manganese binding site 8 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


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 the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn518

b:39.9
occ:1.00
 OD2 C:ASP255 2.0 26.8 1.0
OE2 C:GLU420 2.0 43.7 1.0
OE2 C:GLU381 2.1 52.4 1.0
O12 C:GOA521 2.4 52.3 1.0
NE2 C:HIS336 2.5 36.3 1.0
O11 C:GOA521 2.7 49.2 1.0
C1 C:GOA521 2.8 51.9 1.0
CG C:ASP255 3.0 32.6 1.0
CD C:GLU381 3.1 53.5 1.0
CD C:GLU420 3.1 45.7 1.0
MN C:MN519 3.2 39.1 1.0
CD2 C:HIS336 3.3 35.9 1.0
OD1 C:ASP255 3.4 28.1 1.0
OE1 C:GLU381 3.5 54.3 1.0
CE1 C:HIS336 3.6 36.1 1.0
OE1 C:GLU420 3.6 45.7 1.0
OG1 C:THR379 3.9 41.7 1.0
O2 C:GOA521 3.9 49.7 1.0
C2 C:GOA521 3.9 51.3 1.0
CB C:ASP255 4.2 31.1 1.0
CG C:GLU381 4.3 51.9 1.0
CB C:THR379 4.4 42.0 1.0
CG C:GLU420 4.4 44.0 1.0
CG C:HIS336 4.5 38.2 1.0
CG2 C:THR379 4.5 42.1 1.0
NE2 C:HIS343 4.5 48.5 1.0
ND1 C:HIS336 4.6 36.5 1.0
O C:ASP255 4.7 34.9 1.0
CD2 C:HIS343 4.8 46.8 1.0
CG1 C:VAL342 5.0 31.7 1.0

Manganese binding site 9 out of 10 in 3l24

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Manganese binding site 9 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn519

b:39.1
occ:1.00
 OD1 C:ASP255 2.0 28.1 1.0
O11 C:GOA521 2.1 49.2 1.0
OE1 C:GLU420 2.2 45.7 1.0
OD2 C:ASP244 2.5 34.2 1.0
OD1 C:ASP244 2.5 28.3 1.0
O2 C:GOA521 2.6 49.7 1.0
C1 C:GOA521 2.8 51.9 1.0
CG C:ASP244 2.8 31.9 1.0
CG C:ASP255 2.9 32.6 1.0
C2 C:GOA521 3.0 51.3 1.0
CD C:GLU420 3.1 45.7 1.0
OE2 C:GLU420 3.2 43.7 1.0
OD2 C:ASP255 3.2 26.8 1.0
MN C:MN518 3.2 39.9 1.0
OG1 C:THR257 3.5 41.7 1.0
O12 C:GOA521 3.7 52.3 1.0
OH C:TYR212 3.8 33.6 1.0
OE1 C:GLU381 4.2 54.3 1.0
O C:ASP255 4.2 34.9 1.0
CZ C:TYR212 4.3 34.4 1.0
CB C:ASP244 4.3 31.6 1.0
CB C:ASP255 4.3 31.1 1.0
C C:ASP255 4.4 33.7 1.0
CE2 C:TYR212 4.4 32.7 1.0
OE2 C:GLU381 4.5 52.4 1.0
CG C:GLU420 4.5 44.0 1.0
CD C:GLU381 4.7 53.5 1.0
NE C:ARG418 4.7 47.2 1.0
CA C:ASP255 4.7 30.9 1.0
NH2 C:ARG418 4.7 47.4 1.0
N C:ILE256 4.8 35.1 1.0
O C:ILE256 4.9 38.3 1.0
CB C:THR257 4.9 38.1 1.0
C C:ILE256 4.9 36.9 1.0

Manganese binding site 10 out of 10 in 3l24

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Manganese binding site 10 out of 10 in the Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn520

b:94.1
occ:1.00
 ND1 C:HIS226 2.3 73.0 1.0
CE1 C:HIS226 3.3 73.2 1.0
CG C:HIS226 3.3 71.5 1.0
CB C:HIS226 3.6 67.8 1.0
NE2 C:HIS226 4.4 74.1 1.0
CD2 C:HIS226 4.5 72.7 1.0

Reference:

N.K.Vyas, A.Nickitenko, V.K.Rastogi, S.S.Shah, F.A.Quiocho. Structural Insights Into the Dual Activities of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase. Biochemistry V. 49 547 2010.
ISSN: ISSN 0006-2960
PubMed: 20000741
DOI: 10.1021/BI9011989
Page generated: Sat Oct 5 16:46:30 2024

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