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Manganese in PDB 3l7g: Crystal Structure of Organophosphate Anhydrolase/Prolidase

Enzymatic activity of Crystal Structure of Organophosphate Anhydrolase/Prolidase

All present enzymatic activity of Crystal Structure of Organophosphate Anhydrolase/Prolidase:
3.1.8.1; 3.1.8.2; 3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Organophosphate Anhydrolase/Prolidase, PDB code: 3l7g was solved by N.K.Vyas, A.Nickitenko, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.73 / 2.70
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 (%) 20.4 / 25.9

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Organophosphate Anhydrolase/Prolidase (pdb code 3l7g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the Crystal Structure of Organophosphate Anhydrolase/Prolidase, PDB code: 3l7g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in 3l7g

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Manganese binding site 1 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn519

b:26.2
occ:1.00
 O1 A:M44518 1.9 37.8 1.0
OD2 A:ASP255 2.0 23.6 1.0
NE2 A:HIS336 2.1 20.5 1.0
OE2 A:GLU420 2.2 24.6 1.0
OE2 A:GLU381 2.2 40.2 1.0
P A:M44518 3.0 37.0 1.0
CD2 A:HIS336 3.0 18.5 1.0
O2 A:M44518 3.1 37.4 1.0
CG A:ASP255 3.1 21.9 1.0
CE1 A:HIS336 3.1 18.5 1.0
CD A:GLU381 3.2 37.2 1.0
CD A:GLU420 3.2 25.1 1.0
MN A:MN520 3.4 20.8 1.0
OE1 A:GLU381 3.5 37.4 1.0
OE1 A:GLU420 3.6 27.0 1.0
OD1 A:ASP255 3.7 22.1 1.0
OG1 A:THR379 3.7 21.9 1.0
N2 A:M44518 4.0 37.5 1.0
CG2 A:THR379 4.1 23.6 1.0
CB A:THR379 4.2 24.9 1.0
CG A:HIS336 4.2 21.4 1.0
ND1 A:HIS336 4.2 20.4 1.0
N1 A:M44518 4.3 37.7 1.0
NE2 A:HIS343 4.3 21.2 1.0
CB A:ASP255 4.4 20.1 1.0
CG A:GLU381 4.5 34.5 1.0
CD2 A:HIS343 4.5 22.7 1.0
CG A:GLU420 4.5 25.8 1.0
C2 A:M44518 4.8 33.9 1.0
O A:ASP255 4.8 25.1 1.0
C1 A:M44518 4.9 35.5 1.0

Manganese binding site 2 out of 11 in 3l7g

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Manganese binding site 2 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn520

b:20.8
occ:1.00
 OD1 A:ASP255 2.0 22.1 1.0
O1 A:M44518 2.1 37.8 1.0
OE1 A:GLU420 2.1 27.0 1.0
OD1 A:ASP244 2.3 25.5 1.0
OD2 A:ASP244 2.4 28.6 1.0
CG A:ASP244 2.7 27.2 1.0
CG A:ASP255 2.9 21.9 1.0
N1 A:M44518 3.0 37.7 1.0
P A:M44518 3.0 37.0 1.0
CD A:GLU420 3.0 25.1 1.0
OD2 A:ASP255 3.1 23.6 1.0
OE2 A:GLU420 3.3 24.6 1.0
MN A:MN519 3.4 26.2 1.0
OG1 A:THR257 3.4 28.3 1.0
N2 A:M44518 3.9 37.5 1.0
C2 A:M44518 4.0 33.9 1.0
OH A:TYR212 4.0 20.1 1.0
C1 A:M44518 4.1 35.5 1.0
CB A:ASP244 4.2 24.2 1.0
O A:ASP255 4.2 25.1 1.0
O2 A:M44518 4.2 37.4 1.0
CB A:ASP255 4.3 20.1 1.0
C A:ASP255 4.4 21.4 1.0
CG A:GLU420 4.4 25.8 1.0
CZ A:TYR212 4.4 22.6 1.0
OE1 A:GLU381 4.6 37.4 1.0
O A:ILE256 4.6 26.1 1.0
CE2 A:TYR212 4.7 22.6 1.0
CA A:ASP255 4.7 19.9 1.0
OE2 A:GLU381 4.7 40.2 1.0
N A:ILE256 4.8 21.0 1.0
CB A:THR257 4.8 25.2 1.0
C A:ILE256 4.8 24.1 1.0
CD A:GLU381 4.9 37.2 1.0
NE A:ARG418 4.9 29.9 1.0
CB A:GLU420 4.9 26.2 1.0
CA A:ASP244 5.0 24.7 1.0
NH2 A:ARG418 5.0 34.8 1.0

Manganese binding site 3 out of 11 in 3l7g

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Manganese binding site 3 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn521

b:50.8
occ:1.00
 ND1 A:HIS226 2.3 59.1 1.0
CE1 A:HIS226 3.1 60.0 1.0
CG A:HIS226 3.3 55.5 1.0
CB A:HIS226 3.8 48.4 1.0
NE2 A:HIS226 4.2 61.1 1.0
CD2 A:HIS226 4.3 58.1 1.0

Manganese binding site 4 out of 11 in 3l7g

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Manganese binding site 4 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn522

b:39.3
occ:1.00
 OE2 A:GLU107 1.8 43.2 1.0
OD1 A:ASP105 2.3 34.9 1.0
CD A:GLU107 3.0 38.6 1.0
CG A:ASP105 3.1 34.6 1.0
OD2 A:ASP105 3.3 37.5 1.0
OE1 A:GLU107 3.7 40.9 1.0
CG A:GLU107 4.2 35.5 1.0
O A:ILE106 4.4 29.1 1.0
CB A:ASP105 4.6 33.0 1.0
C A:ASP105 4.8 31.3 1.0
O A:ASP105 4.9 31.8 1.0
C A:ILE106 5.0 30.1 1.0

Manganese binding site 5 out of 11 in 3l7g

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Manganese binding site 5 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn519

b:23.0
occ:1.00
 O1 B:M44518 1.8 41.1 1.0
OE2 B:GLU381 2.0 32.5 1.0
OD2 B:ASP255 2.0 16.8 1.0
NE2 B:HIS336 2.1 20.8 1.0
OE2 B:GLU420 2.2 28.4 1.0
CD B:GLU381 2.9 32.6 1.0
P B:M44518 3.0 41.2 1.0
CD2 B:HIS336 3.0 22.7 1.0
CG B:ASP255 3.1 17.3 1.0
CE1 B:HIS336 3.1 21.9 1.0
O2 B:M44518 3.2 39.8 1.0
OE1 B:GLU381 3.2 36.8 1.0
CD B:GLU420 3.3 28.0 1.0
MN B:MN520 3.5 24.9 1.0
OD1 B:ASP255 3.6 20.0 1.0
OG1 B:THR379 3.7 20.8 1.0
OE1 B:GLU420 3.8 28.6 1.0
CG2 B:THR379 4.0 20.9 1.0
N2 B:M44518 4.0 39.9 1.0
CB B:THR379 4.1 23.0 1.0
CG B:HIS336 4.2 23.5 1.0
ND1 B:HIS336 4.2 23.9 1.0
N1 B:M44518 4.2 39.7 1.0
CB B:ASP255 4.2 18.3 1.0
CG B:GLU381 4.3 31.6 1.0
NE2 B:HIS343 4.6 29.4 1.0
CG B:GLU420 4.6 27.4 1.0
C2 B:M44518 4.8 36.7 1.0
CD2 B:HIS343 4.8 28.9 1.0
C1 B:M44518 4.9 38.0 1.0

Manganese binding site 6 out of 11 in 3l7g

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Manganese binding site 6 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn520

b:24.9
occ:1.00
 OE1 B:GLU420 2.0 28.6 1.0
OD1 B:ASP255 2.0 20.0 1.0
OD1 B:ASP244 2.2 19.7 1.0
O1 B:M44518 2.2 41.1 1.0
OD2 B:ASP244 2.4 21.5 1.0
CG B:ASP244 2.6 22.0 1.0
CD B:GLU420 2.7 28.0 1.0
CG B:ASP255 2.9 17.3 1.0
OE2 B:GLU420 2.9 28.4 1.0
N1 B:M44518 3.0 39.7 1.0
P B:M44518 3.1 41.2 1.0
OD2 B:ASP255 3.2 16.8 1.0
MN B:MN519 3.5 23.0 1.0
OG1 B:THR257 3.5 24.1 1.0
OH B:TYR212 3.7 23.1 1.0
C2 B:M44518 4.0 36.7 1.0
N2 B:M44518 4.0 39.9 1.0
C1 B:M44518 4.1 38.0 1.0
CB B:ASP244 4.1 22.4 1.0
CG B:GLU420 4.1 27.4 1.0
CB B:ASP255 4.2 18.3 1.0
C B:ASP255 4.2 19.0 1.0
O B:ASP255 4.3 18.1 1.0
O2 B:M44518 4.3 39.8 1.0
CZ B:TYR212 4.4 23.7 1.0
CA B:ASP255 4.4 19.1 1.0
OE1 B:GLU381 4.4 36.8 1.0
OE2 B:GLU381 4.5 32.5 1.0
N B:ILE256 4.5 18.6 1.0
CE2 B:TYR212 4.8 22.1 1.0
CD B:GLU381 4.8 32.6 1.0
C B:ILE256 4.8 20.2 1.0
CB B:THR257 4.8 22.0 1.0
CA B:ASP244 4.8 22.3 1.0
CB B:GLU420 4.9 26.3 1.0
O B:ILE256 4.9 21.2 1.0
NE B:ARG418 4.9 23.9 1.0
N B:THR257 5.0 19.8 1.0

Manganese binding site 7 out of 11 in 3l7g

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Manganese binding site 7 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn521

b:47.1
occ:1.00
 OE1 B:GLU26 2.0 57.1 1.0
O C:HOH636 2.1 18.4 1.0
OE1 C:GLU436 2.2 43.8 1.0
CD B:GLU26 2.9 54.9 1.0
OE2 B:GLU26 3.1 54.1 1.0
CD C:GLU436 3.3 44.9 1.0
OE2 C:GLU431 3.6 33.6 1.0
OE2 C:GLU436 3.6 45.0 1.0
O B:ARG25 3.8 53.9 1.0
CG B:GLU26 4.3 53.5 1.0
CD C:GLU431 4.5 32.3 1.0
CG C:GLU436 4.6 44.0 1.0
CA B:GLU26 4.6 54.9 1.0
C B:ARG25 4.7 53.3 1.0
O C:HOH625 4.9 33.3 1.0
CG C:GLU431 4.9 32.7 1.0
CB B:GLU26 5.0 53.4 1.0
CB C:GLU436 5.0 42.1 1.0

Manganese binding site 8 out of 11 in 3l7g

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Manganese binding site 8 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn522

b:57.0
occ:1.00
 ND1 B:HIS226 2.2 57.1 1.0
CE1 B:HIS226 2.7 56.7 1.0
CG B:HIS226 3.3 54.6 1.0
NE2 B:HIS226 3.9 57.1 1.0
CB B:HIS226 3.9 49.5 1.0
CD2 B:HIS226 4.2 56.9 1.0

Manganese binding site 9 out of 11 in 3l7g

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Manganese binding site 9 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn519

b:34.4
occ:1.00
 O2 C:M44518 1.8 49.9 1.0
OE2 C:GLU381 2.0 47.8 1.0
OE2 C:GLU420 2.0 36.8 1.0
OD2 C:ASP255 2.1 23.5 1.0
NE2 C:HIS336 2.3 34.3 1.0
CD C:GLU381 3.0 49.7 1.0
CD2 C:HIS336 3.0 30.5 1.0
P C:M44518 3.1 47.8 1.0
CD C:GLU420 3.1 38.1 1.0
CG C:ASP255 3.1 26.4 1.0
MN C:MN520 3.3 33.8 1.0
O1 C:M44518 3.4 48.6 1.0
CE1 C:HIS336 3.4 31.9 1.0
OE1 C:GLU381 3.5 51.6 1.0
OE1 C:GLU420 3.5 37.0 1.0
OD1 C:ASP255 3.6 24.7 1.0
OG1 C:THR379 3.7 43.1 1.0
N2 C:M44518 4.1 48.3 1.0
CB C:THR379 4.1 43.6 1.0
N1 C:M44518 4.2 46.4 1.0
CG C:HIS336 4.2 32.7 1.0
CG C:GLU381 4.3 50.0 1.0
ND1 C:HIS336 4.4 32.4 1.0
CG2 C:THR379 4.4 44.0 1.0
CB C:ASP255 4.4 25.2 1.0
CG C:GLU420 4.4 38.1 1.0
NE2 C:HIS343 4.6 39.7 1.0
O C:ASP255 4.6 28.2 1.0
C2 C:M44518 4.7 44.1 1.0
CD2 C:HIS343 4.8 40.6 1.0
C1 C:M44518 4.9 45.4 1.0

Manganese binding site 10 out of 11 in 3l7g

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Manganese binding site 10 out of 11 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase


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 Organophosphate Anhydrolase/Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn520

b:33.8
occ:1.00
 O2 C:M44518 2.1 49.9 1.0
OD1 C:ASP255 2.2 24.7 1.0
OE1 C:GLU420 2.2 37.0 1.0
OD1 C:ASP244 2.3 30.4 1.0
OD2 C:ASP244 2.4 29.0 1.0
N1 C:M44518 2.7 46.4 1.0
CG C:ASP244 2.7 30.4 1.0
P C:M44518 2.8 47.8 1.0
CG C:ASP255 3.0 26.4 1.0
CD C:GLU420 3.1 38.1 1.0
OD2 C:ASP255 3.3 23.5 1.0
MN C:MN519 3.3 34.4 1.0
OE2 C:GLU420 3.3 36.8 1.0
OG1 C:THR257 3.6 33.7 1.0
N2 C:M44518 3.7 48.3 1.0
C1 C:M44518 3.8 45.4 1.0
C2 C:M44518 3.9 44.1 1.0
OH C:TYR212 4.1 30.3 1.0
O1 C:M44518 4.1 48.6 1.0
CB C:ASP244 4.2 29.6 1.0
O C:ASP255 4.2 28.2 1.0
CB C:ASP255 4.5 25.2 1.0
CZ C:TYR212 4.5 31.5 1.0
C C:ASP255 4.5 26.7 1.0
OE2 C:GLU381 4.5 47.8 1.0
CG C:GLU420 4.5 38.1 1.0
OE1 C:GLU381 4.5 51.6 1.0
CE2 C:TYR212 4.6 30.1 1.0
NE C:ARG418 4.7 43.6 1.0
NH2 C:ARG418 4.7 44.2 1.0
CD C:GLU381 4.8 49.7 1.0
C3 C:M44518 4.8 45.7 1.0
CA C:ASP255 4.8 25.9 1.0
O C:ILE256 4.9 29.6 1.0
CB C:THR257 4.9 30.3 1.0
C4 C:M44518 4.9 48.2 1.0
CA C:ASP244 5.0 28.3 1.0
C C:ILE256 5.0 28.0 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 16:48:37 2024

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