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Manganese in PDB 4zwp: Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F

Enzymatic activity of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F

All present enzymatic activity of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, PDB code: 4zwp was solved by C.M.Daczkowski, S.D.Pegan, S.P.Harvey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.493, 68.179, 142.479, 90.00, 110.50, 90.00
R / Rfree (%) 17.3 / 22.6

Other elements in 4zwp:

The structure of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F also contains other interesting chemical elements:

Barium (Ba) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F (pdb code 4zwp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, PDB code: 4zwp:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 4zwp

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Manganese binding site 1 out of 7 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F


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 Organophosphate Anhydrolase/Prolidase Mutant Y212F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:27.1
occ:1.00
 OD2 A:ASP255 2.1 22.8 1.0
OE2 A:GLU420 2.3 32.7 1.0
NE2 A:HIS336 2.3 30.0 1.0
OE2 A:GLU381 2.4 29.9 1.0
O2 A:M44508 2.5 49.6 1.0
O1 A:M44508 2.7 38.7 1.0
CG A:ASP255 3.1 22.0 1.0
CD A:GLU381 3.2 29.9 1.0
CD A:GLU420 3.2 32.7 1.0
CE1 A:HIS336 3.2 29.3 1.0
P A:M44508 3.3 77.8 1.0
CD2 A:HIS336 3.3 29.6 1.0
MN A:MN502 3.3 29.4 1.0
OE1 A:GLU381 3.3 32.6 1.0
OE1 A:GLU420 3.5 34.7 1.0
OD1 A:ASP255 3.6 22.8 1.0
OG1 A:THR379 3.9 27.9 1.0
CG2 A:THR379 4.1 28.6 1.0
CB A:THR379 4.3 27.8 1.0
CB A:ASP255 4.3 20.4 1.0
ND1 A:HIS336 4.4 28.5 1.0
CG A:HIS336 4.4 29.0 1.0
C1 A:M44508 4.5 80.5 1.0
N1 A:M44508 4.5 81.0 1.0
CG A:GLU381 4.5 27.7 1.0
CG A:GLU420 4.5 29.9 1.0
C2 A:M44508 4.5 80.0 1.0
N2 A:M44508 4.5 42.6 1.0
NE2 A:HIS343 4.7 32.7 1.0
CD2 A:HIS343 4.9 32.9 1.0
O A:ASP255 5.0 22.4 1.0

Manganese binding site 2 out of 7 in 4zwp

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Manganese binding site 2 out of 7 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F


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 Mutant Y212F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:29.4
occ:1.00
 OD1 A:ASP255 2.0 22.8 1.0
OE1 A:GLU420 2.1 34.7 1.0
O2 A:M44508 2.2 49.6 1.0
OD2 A:ASP244 2.2 30.6 1.0
OD1 A:ASP244 2.4 27.7 1.0
CG A:ASP244 2.6 28.0 1.0
CG A:ASP255 2.9 22.0 1.0
CD A:GLU420 3.0 32.7 1.0
C1 A:M44508 3.1 80.5 1.0
OD2 A:ASP255 3.1 22.8 1.0
OE2 A:GLU420 3.3 32.7 1.0
MN A:MN501 3.3 27.1 1.0
OG1 A:THR257 3.4 27.8 1.0
P A:M44508 3.6 77.8 1.0
C2 A:M44508 3.7 80.0 1.0
N1 A:M44508 3.9 81.0 1.0
C3 A:M44508 3.9 80.7 1.0
OE1 A:GLU381 3.9 32.6 1.0
CB A:ASP244 4.1 25.5 1.0
CZ A:PHE212 4.2 22.7 1.0
CB A:ASP255 4.3 20.4 1.0
C A:ASP255 4.3 22.4 1.0
O1 A:M44508 4.3 38.7 1.0
CG A:GLU420 4.4 29.9 1.0
O A:ASP255 4.5 22.4 1.0
N A:ILE256 4.5 23.4 1.0
CA A:ASP255 4.7 20.9 1.0
CD A:GLU381 4.7 29.9 1.0
C A:ILE256 4.7 24.7 1.0
NE A:ARG418 4.8 28.6 1.0
CE1 A:PHE212 4.8 23.4 1.0
CE2 A:PHE212 4.8 22.3 1.0
O A:ILE256 4.8 25.1 1.0
OE2 A:GLU381 4.8 29.9 1.0
CB A:THR257 4.8 27.4 1.0
CA A:ASP244 4.9 25.2 1.0
CB A:GLU420 4.9 29.5 1.0
N2 A:M44508 4.9 42.6 1.0
C4 A:M44508 4.9 42.7 1.0
N A:THR257 5.0 25.3 1.0

Manganese binding site 3 out of 7 in 4zwp

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Manganese binding site 3 out of 7 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F


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 Mutant Y212F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:45.9
occ:1.00
 O A:HOH624 2.0 36.7 1.0
O A:HOH620 2.7 30.9 1.0
O A:LEU28 2.9 41.3 1.0
OD1 A:ASP29 3.8 50.0 1.0
C A:LEU28 3.8 44.3 1.0
CA A:ASP29 4.0 45.3 1.0
N A:ASP29 4.3 44.6 1.0
CD1 A:ILE23 4.4 38.7 1.0
O A:ASP29 4.7 45.4 1.0
C A:ASP29 4.7 44.0 1.0
CG A:ASP29 4.8 49.2 1.0
O A:HOH741 4.9 59.7 1.0
CB A:ASP29 4.9 46.3 1.0

Manganese binding site 4 out of 7 in 4zwp

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Manganese binding site 4 out of 7 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F


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 Organophosphate Anhydrolase/Prolidase Mutant Y212F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:34.9
occ:1.00
 OD1 A:ASP29 2.7 50.0 1.0
O A:HOH697 2.7 30.8 1.0
O A:HOH620 2.8 30.9 1.0
CG A:ASP29 3.5 49.2 1.0
OD2 A:ASP29 3.5 50.6 1.0
CB A:ASP29 4.9 46.3 1.0

Manganese binding site 5 out of 7 in 4zwp

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Manganese binding site 5 out of 7 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F


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 Mutant Y212F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:26.2
occ:1.00
 O2 B:M44504 1.7 47.9 1.0
OE1 B:GLU420 2.1 23.5 1.0
OD1 B:ASP255 2.1 22.9 1.0
OD1 B:ASP244 2.2 22.7 1.0
OD2 B:ASP244 2.2 19.0 1.0
CG B:ASP244 2.5 21.4 1.0
CD B:GLU420 2.9 22.8 1.0
OE2 B:GLU420 3.0 24.7 1.0
CG B:ASP255 3.1 21.5 1.0
P B:M44504 3.1 80.0 1.0
C4 B:M44504 3.2 74.6 1.0
OG1 B:THR257 3.3 25.4 1.0
MN B:MN502 3.4 28.7 1.0
OD2 B:ASP255 3.4 20.8 1.0
N2 B:M44504 3.6 75.0 1.0
C6 B:M44504 3.7 74.4 1.0
N1 B:M44504 3.9 55.7 1.0
CB B:ASP244 4.0 20.5 1.0
OE1 B:GLU381 4.1 29.2 1.0
O1 B:M44504 4.2 31.3 1.0
CZ B:PHE212 4.3 22.7 1.0
CG B:GLU420 4.3 21.3 1.0
C5 B:M44504 4.4 74.6 1.0
CB B:ASP255 4.5 22.0 1.0
C B:ASP255 4.5 24.1 1.0
O B:ASP255 4.6 24.9 1.0
OE2 B:GLU381 4.7 28.9 1.0
O B:ILE256 4.7 26.7 1.0
N B:ILE256 4.7 23.9 1.0
CD B:GLU381 4.7 28.2 1.0
NE B:ARG418 4.7 26.0 1.0
CB B:THR257 4.7 23.8 1.0
C B:ILE256 4.8 24.8 1.0
CA B:ASP255 4.8 22.9 1.0
CE2 B:PHE212 4.8 22.3 1.0
CA B:ASP244 4.8 19.8 1.0
CE1 B:PHE212 4.9 22.3 1.0
CB B:GLU420 4.9 18.5 1.0
NH2 B:ARG418 4.9 28.1 1.0

Manganese binding site 6 out of 7 in 4zwp

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Manganese binding site 6 out of 7 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F


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 Mutant Y212F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:28.7
occ:1.00
 OE2 B:GLU420 2.1 24.7 1.0
OD2 B:ASP255 2.2 20.8 1.0
OE2 B:GLU381 2.2 28.9 1.0
O2 B:M44504 2.3 47.9 1.0
NE2 B:HIS336 2.3 23.5 1.0
O1 B:M44504 2.6 31.3 1.0
CG B:ASP255 3.1 21.5 1.0
P B:M44504 3.1 80.0 1.0
CD B:GLU381 3.1 28.2 1.0
CE1 B:HIS336 3.2 23.7 1.0
CD B:GLU420 3.3 22.8 1.0
CD2 B:HIS336 3.3 23.6 1.0
MN B:MN501 3.4 26.2 1.0
OE1 B:GLU381 3.4 29.2 1.0
OD1 B:ASP255 3.4 22.9 1.0
OE1 B:GLU420 3.7 23.5 1.0
N1 B:M44504 3.9 55.7 1.0
OG1 B:THR379 4.0 23.4 1.0
CG2 B:THR379 4.1 23.8 1.0
C6 B:M44504 4.2 74.4 1.0
CB B:THR379 4.3 24.7 1.0
CB B:ASP255 4.3 22.0 1.0
CG B:GLU381 4.4 26.1 1.0
ND1 B:HIS336 4.4 24.3 1.0
CG B:HIS336 4.5 23.9 1.0
NE2 B:HIS343 4.5 33.0 1.0
N2 B:M44504 4.5 75.0 1.0
CG B:GLU420 4.5 21.3 1.0
CD2 B:HIS343 4.6 32.2 1.0
C4 B:M44504 4.7 74.6 1.0

Manganese binding site 7 out of 7 in 4zwp

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Manganese binding site 7 out of 7 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F


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 Mutant Y212F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:46.6
occ:1.00
 O B:HOH729 3.2 46.8 1.0
OE2 B:GLU10 3.2 49.9 1.0
CD B:GLU10 3.7 48.4 1.0
OE1 B:GLU10 3.7 50.0 1.0
CG B:GLU10 4.9 44.6 1.0

Reference:

C.M.Daczkowski, S.D.Pegan, S.P.Harvey. Engineering the Organophosphorus Acid Anhydrolase Enzyme For Increased Catalytic Efficiency and Broadened Stereospecificity on Russian Vx. Biochemistry V. 54 6423 2015.
ISSN: ISSN 0006-2960
PubMed: 26418828
DOI: 10.1021/ACS.BIOCHEM.5B00624
Page generated: Sat Oct 5 23:15:46 2024

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