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Manganese in PDB 4zwo: 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: 4zwo 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) 32.90 / 2.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.391, 67.944, 140.450, 90.00, 110.08, 90.00
R / Rfree (%) 17.2 / 21.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F (pdb code 4zwo). 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: 4zwo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 4zwo

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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:18.4
occ:1.00
 OD2 A:ASP255 2.1 13.9 1.0
OE2 A:GLU420 2.2 19.4 1.0
NE2 A:HIS336 2.3 17.9 1.0
OE2 A:GLU381 2.3 27.8 1.0
O A:HOH602 2.5 19.1 1.0
O12 A:GOA506 2.7 37.1 1.0
CD A:GLU381 3.1 30.9 1.0
CG A:ASP255 3.2 15.1 1.0
C1 A:GOA506 3.2 37.3 1.0
CE1 A:HIS336 3.2 17.5 1.0
CD A:GLU420 3.2 18.2 1.0
CD2 A:HIS336 3.3 18.4 1.0
OE1 A:GLU381 3.3 30.0 1.0
MN A:MN502 3.4 19.1 1.0
O11 A:GOA506 3.6 37.7 1.0
OE1 A:GLU420 3.6 17.3 1.0
OD1 A:ASP255 3.7 15.8 1.0
O2 A:GOA506 3.9 32.8 1.0
OG1 A:THR379 4.0 16.2 1.0
C2 A:GOA506 4.1 35.6 1.0
CG2 A:THR379 4.3 15.1 1.0
CB A:ASP255 4.3 15.6 1.0
ND1 A:HIS336 4.3 17.2 1.0
CB A:THR379 4.4 21.6 1.0
CG A:HIS336 4.4 17.7 1.0
CG A:GLU381 4.4 29.8 1.0
NE2 A:HIS343 4.5 22.3 1.0
CG A:GLU420 4.6 16.8 1.0
CD2 A:HIS343 4.7 20.1 1.0
CG1 A:VAL342 4.9 17.9 1.0

Manganese binding site 2 out of 7 in 4zwo

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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:19.1
occ:1.00
 O A:HOH602 1.9 19.1 1.0
OD1 A:ASP255 2.1 15.8 1.0
OD1 A:ASP244 2.2 14.9 1.0
OE1 A:GLU420 2.2 17.3 1.0
OD2 A:ASP244 2.3 15.1 1.0
O2 A:GOA506 2.5 32.8 1.0
CG A:ASP244 2.5 16.4 1.0
CG A:ASP255 2.9 15.1 1.0
OD2 A:ASP255 3.1 13.9 1.0
CD A:GLU420 3.1 18.2 1.0
OE2 A:GLU420 3.4 19.4 1.0
MN A:MN501 3.4 18.4 1.0
OG1 A:THR257 3.5 17.7 1.0
C2 A:GOA506 3.6 35.6 1.0
C1 A:GOA506 3.7 37.3 1.0
O11 A:GOA506 3.8 37.7 1.0
OE1 A:GLU381 4.0 30.0 1.0
CB A:ASP244 4.1 15.6 1.0
CZ A:PHE212 4.1 15.3 1.0
CB A:ASP255 4.3 15.6 1.0
O12 A:GOA506 4.3 37.1 1.0
C A:ASP255 4.4 16.2 1.0
CE2 A:PHE212 4.5 14.6 1.0
CG A:GLU420 4.5 16.8 1.0
N A:ILE256 4.5 16.9 1.0
O A:ASP255 4.5 14.1 1.0
CA A:ASP255 4.7 16.1 1.0
CD A:GLU381 4.7 30.9 1.0
NE A:ARG418 4.8 15.9 1.0
C A:ILE256 4.8 18.8 1.0
CE1 A:PHE212 4.8 16.0 1.0
OE2 A:GLU381 4.8 27.8 1.0
O A:ILE256 4.8 17.9 1.0
CA A:ASP244 4.8 15.6 1.0
CB A:THR257 4.9 18.1 1.0
CB A:GLU420 4.9 16.1 1.0

Manganese binding site 3 out of 7 in 4zwo

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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:Mn503

b:22.7
occ:1.00
 O A:HOH877 2.8 35.8 1.0
O A:ARG25 2.9 32.1 1.0
ND2 A:ASN27 2.9 38.6 1.0
CG A:ASN27 3.9 38.0 1.0
C A:ARG25 4.1 31.8 1.0
OD1 A:ASN27 4.1 38.5 1.0
O A:HOH632 4.2 25.9 1.0
CA A:GLU26 4.9 29.0 1.0
N A:GLU26 5.0 29.1 1.0

Manganese binding site 4 out of 7 in 4zwo

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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:Mn504

b:37.5
occ:1.00
 O A:HOH632 1.8 25.9 1.0
O A:GLU24 2.6 29.0 1.0
OD1 A:ASN27 3.0 38.5 1.0
C A:GLU24 3.7 33.2 1.0
CG A:ASN27 4.1 38.0 1.0
CA A:GLU24 4.3 33.0 1.0
CB A:GLU24 4.7 36.8 1.0
N A:ARG25 4.7 32.2 1.0
CA A:ASN27 4.7 29.9 1.0
N A:ASN27 4.9 29.3 1.0
CB A:ASN27 4.9 29.6 1.0
ND2 A:ASN27 4.9 38.6 1.0
CA A:ARG25 5.0 33.8 1.0

Manganese binding site 5 out of 7 in 4zwo

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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
A:Mn505

b:41.2
occ:1.00
 O A:HOH622 2.2 21.3 1.0
O A:HOH861 2.5 46.5 1.0
O A:ASP309 2.8 32.6 1.0
O A:HOH923 2.8 37.4 1.0
C A:ASP309 3.8 31.6 1.0
OD1 A:ASN311 4.3 40.2 1.0
O A:HOH903 4.5 61.4 1.0
CA A:ASP309 4.6 31.4 1.0
N A:PHE310 4.7 29.4 1.0
CA A:PHE310 4.7 29.5 1.0
CB A:ASP309 4.8 30.6 1.0

Manganese binding site 6 out of 7 in 4zwo

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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:Mn501

b:20.6
occ:1.00
 O B:HOH603 2.0 39.3 1.0
OD1 B:ASP255 2.1 17.0 1.0
OD1 B:ASP244 2.1 17.1 1.0
OE1 B:GLU420 2.3 15.9 1.0
OD2 B:ASP244 2.3 17.3 1.0
CG B:ASP244 2.5 18.2 1.0
O2 B:GOA504 2.5 30.5 1.0
CG B:ASP255 2.9 16.7 1.0
CD B:GLU420 3.1 16.6 1.0
OD2 B:ASP255 3.2 17.4 1.0
OE2 B:GLU420 3.3 17.9 1.0
OG1 B:THR257 3.4 15.8 1.0
MN B:MN502 3.4 19.5 1.0
O11 B:GOA504 3.6 36.5 1.0
C2 B:GOA504 3.6 32.8 1.0
C1 B:GOA504 3.6 34.2 1.0
OE1 B:GLU381 4.0 18.3 1.0
CB B:ASP244 4.0 18.1 1.0
CZ B:PHE212 4.1 16.2 1.0
O12 B:GOA504 4.3 32.2 1.0
CB B:ASP255 4.3 15.8 1.0
C B:ASP255 4.4 18.9 1.0
CE1 B:PHE212 4.5 16.3 1.0
CG B:GLU420 4.6 16.1 1.0
N B:ILE256 4.6 18.9 1.0
O B:ASP255 4.6 18.9 1.0
O B:ILE256 4.7 19.2 1.0
CA B:ASP255 4.7 17.1 1.0
C B:ILE256 4.8 18.4 1.0
CA B:ASP244 4.8 18.0 1.0
NE B:ARG418 4.8 17.3 1.0
CE2 B:PHE212 4.8 16.2 1.0
CD B:GLU381 4.8 18.1 1.0
CB B:THR257 4.8 16.0 1.0
OE2 B:GLU381 5.0 16.8 1.0
CB B:GLU420 5.0 16.3 1.0

Manganese binding site 7 out of 7 in 4zwo

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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:Mn502

b:19.5
occ:1.00
 OD2 B:ASP255 2.2 17.4 1.0
NE2 B:HIS336 2.2 14.3 1.0
OE2 B:GLU420 2.2 17.9 1.0
OE2 B:GLU381 2.4 16.8 1.0
O12 B:GOA504 2.5 32.2 1.0
O B:HOH603 2.7 39.3 1.0
C1 B:GOA504 3.1 34.2 1.0
CD B:GLU381 3.1 18.1 1.0
CE1 B:HIS336 3.2 15.1 1.0
CG B:ASP255 3.2 16.7 1.0
CD2 B:HIS336 3.2 15.7 1.0
OE1 B:GLU381 3.3 18.3 1.0
CD B:GLU420 3.3 16.6 1.0
MN B:MN501 3.4 20.6 1.0
O11 B:GOA504 3.6 36.5 1.0
OE1 B:GLU420 3.7 15.9 1.0
OD1 B:ASP255 3.7 17.0 1.0
OG1 B:THR379 4.0 21.1 1.0
C2 B:GOA504 4.0 32.8 1.0
O2 B:GOA504 4.0 30.5 1.0
CG2 B:THR379 4.2 21.3 1.0
ND1 B:HIS336 4.3 17.4 1.0
CB B:THR379 4.3 20.8 1.0
CB B:ASP255 4.3 15.8 1.0
CG B:HIS336 4.4 16.9 1.0
NE2 B:HIS343 4.4 19.2 1.0
CG B:GLU381 4.5 17.1 1.0
CG B:GLU420 4.6 16.1 1.0
CD2 B:HIS343 4.6 18.7 1.0
CG1 B:VAL342 5.0 14.1 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 23:15:43 2024

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