Atomistry » Manganese » PDB 4z8b-5a56 » 4zwp
Atomistry »
  Manganese »
    PDB 4z8b-5a56 »
      4zwp »

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

Go back to Manganese Binding Sites List in 4zwp
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

Go back to Manganese Binding Sites List in 4zwp
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

Go back to Manganese Binding Sites List in 4zwp
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

Go back to Manganese Binding Sites List in 4zwp
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

Go back to Manganese Binding Sites List in 4zwp
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

Go back to Manganese Binding Sites List in 4zwp
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

Go back to Manganese Binding Sites List in 4zwp
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy