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Manganese in PDB 4zwu: Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y

Enzymatic activity of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y

All present enzymatic activity of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y:
3.1.8.1; 3.1.8.2; 3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y, PDB code: 4zwu 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) 48.47 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.890, 68.846, 139.394, 90.00, 109.58, 90.00
R / Rfree (%) 17 / 21.9

Other elements in 4zwu:

The structure of Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y also contains other interesting chemical elements:

Barium (Ba) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y (pdb code 4zwu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y, PDB code: 4zwu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4zwu

Go back to Manganese Binding Sites List in 4zwu
Manganese binding site 1 out of 6 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y


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, V342L, I215Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:36.7
occ:1.00
 OD2 A:ASP255 2.2 29.8 1.0
OE2 A:GLU420 2.3 33.5 1.0
NE2 A:HIS336 2.4 32.8 1.0
O A:HOH638 2.4 33.5 1.0
OE2 A:GLU381 2.5 34.0 1.0
O A:HOH774 3.0 39.4 1.0
CD A:GLU381 3.2 37.8 1.0
MN A:MN502 3.3 39.2 1.0
CG A:ASP255 3.3 32.8 1.0
CD2 A:HIS336 3.3 30.9 1.0
OE1 A:GLU381 3.3 39.7 1.0
CE1 A:HIS336 3.3 33.5 1.0
CD A:GLU420 3.3 33.3 1.0
OE1 A:GLU420 3.7 32.0 1.0
OD1 A:ASP255 3.9 32.5 1.0
OG1 A:THR379 4.1 31.9 1.0
CB A:ASP255 4.4 32.4 1.0
NE2 A:HIS343 4.4 42.3 1.0
CG2 A:THR379 4.4 32.3 1.0
ND1 A:HIS336 4.5 34.2 1.0
CG A:HIS336 4.5 33.8 1.0
CG A:GLU381 4.5 36.3 1.0
CB A:THR379 4.5 32.2 1.0
CG A:GLU420 4.6 31.8 1.0
CD2 A:HIS343 4.7 39.3 1.0

Manganese binding site 2 out of 6 in 4zwu

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Manganese binding site 2 out of 6 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y


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, V342L, I215Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:39.2
occ:1.00
 OE1 A:GLU420 2.1 32.0 1.0
O A:HOH638 2.1 33.5 1.0
OD1 A:ASP255 2.2 32.5 1.0
OD1 A:ASP244 2.3 33.1 1.0
OD2 A:ASP244 2.5 32.4 1.0
CG A:ASP244 2.7 32.3 1.0
CG A:ASP255 2.9 32.8 1.0
OD2 A:ASP255 3.0 29.8 1.0
CD A:GLU420 3.0 33.3 1.0
OE2 A:GLU420 3.2 33.5 1.0
MN A:MN501 3.3 36.7 1.0
OG1 A:THR257 3.5 28.9 1.0
OE1 A:GLU381 3.8 39.7 1.0
O A:HOH774 4.0 39.4 1.0
CZ A:PHE212 4.1 35.6 1.0
CB A:ASP244 4.2 28.0 1.0
CB A:ASP255 4.3 32.4 1.0
CG A:GLU420 4.4 31.8 1.0
C A:ASP255 4.5 31.4 1.0
CD A:GLU381 4.6 37.8 1.0
CE2 A:PHE212 4.7 35.0 1.0
CE1 A:PHE212 4.7 38.0 1.0
N A:ILE256 4.7 30.6 1.0
OE2 A:GLU381 4.7 34.0 1.0
O A:ASP255 4.8 31.4 1.0
NE A:ARG418 4.8 28.9 1.0
CA A:ASP255 4.8 31.0 1.0
CB A:GLU420 4.8 30.4 1.0
O A:ILE256 4.9 33.9 1.0
C A:ILE256 4.9 33.5 1.0
CA A:ASP244 4.9 28.0 1.0
CB A:THR257 4.9 28.9 1.0

Manganese binding site 3 out of 6 in 4zwu

Go back to Manganese Binding Sites List in 4zwu
Manganese binding site 3 out of 6 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y


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, V342L, I215Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:0.8
occ:1.00
 OD1 A:ASP29 2.8 60.2 1.0
CG A:ASP29 4.0 55.9 1.0
O A:HOH667 4.0 58.9 1.0
CA A:ASP29 4.1 51.4 1.0
BA A:BA503 4.2 60.3 1.0
O A:LEU28 4.3 49.5 1.0
O A:HOH797 4.4 56.6 1.0
CB A:ASP29 4.6 54.9 1.0
N A:ASP29 4.9 49.7 1.0
O A:ASP29 4.9 49.5 1.0
OD2 A:ASP29 4.9 48.7 1.0
C A:LEU28 4.9 48.9 1.0

Manganese binding site 4 out of 6 in 4zwu

Go back to Manganese Binding Sites List in 4zwu
Manganese binding site 4 out of 6 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y


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, V342L, I215Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:35.9
occ:1.00
 O B:HOH607 1.9 45.2 1.0
OD1 B:ASP244 2.1 32.6 1.0
OD1 B:ASP255 2.2 31.6 1.0
OE1 B:GLU420 2.3 28.0 1.0
OD2 B:ASP244 2.4 32.6 1.0
CG B:ASP244 2.5 30.4 1.0
O2 B:GOA501 2.7 58.2 1.0
CG B:ASP255 3.0 31.0 1.0
CD B:GLU420 3.2 31.3 1.0
OD2 B:ASP255 3.2 33.0 1.0
OE2 B:GLU420 3.4 31.4 1.0
OG1 B:THR257 3.4 28.7 1.0
MN B:MN504 3.4 36.0 1.0
C2 B:GOA501 3.9 59.1 1.0
C1 B:GOA501 4.0 57.8 1.0
OE1 B:GLU381 4.0 32.8 1.0
CB B:ASP244 4.1 27.6 1.0
CZ B:PHE212 4.1 33.0 1.0
O12 B:GOA501 4.3 60.7 1.0
O11 B:GOA501 4.3 53.4 1.0
CB B:ASP255 4.4 31.2 1.0
C B:ASP255 4.5 28.6 1.0
CG B:GLU420 4.6 31.0 1.0
N B:ILE256 4.7 26.6 1.0
O B:ASP255 4.7 30.4 1.0
CE1 B:PHE212 4.7 34.9 1.0
CE2 B:PHE212 4.7 30.6 1.0
O B:ILE256 4.8 31.3 1.0
CD B:GLU381 4.8 33.0 1.0
CA B:ASP244 4.8 28.4 1.0
NE B:ARG418 4.8 30.1 1.0
CA B:ASP255 4.8 29.4 1.0
C B:ILE256 4.8 29.5 1.0
CB B:THR257 4.8 27.9 1.0
OE2 B:GLU381 4.9 33.0 1.0
CB B:GLU420 5.0 30.4 1.0

Manganese binding site 5 out of 6 in 4zwu

Go back to Manganese Binding Sites List in 4zwu
Manganese binding site 5 out of 6 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y


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, V342L, I215Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:36.0
occ:1.00
 OD2 B:ASP255 2.2 33.0 1.0
OE2 B:GLU420 2.3 31.4 1.0
OE2 B:GLU381 2.3 33.0 1.0
NE2 B:HIS336 2.3 31.4 1.0
O B:HOH607 2.4 45.2 1.0
O11 B:GOA501 2.5 53.4 1.0
CD B:GLU381 3.1 33.0 1.0
C1 B:GOA501 3.2 57.8 1.0
CG B:ASP255 3.3 31.0 1.0
CE1 B:HIS336 3.3 30.5 1.0
OE1 B:GLU381 3.3 32.8 1.0
CD2 B:HIS336 3.3 31.5 1.0
CD B:GLU420 3.3 31.3 1.0
MN B:MN503 3.4 35.9 1.0
OE1 B:GLU420 3.7 28.0 1.0
OD1 B:ASP255 3.8 31.6 1.0
O2 B:GOA501 3.8 58.2 1.0
O12 B:GOA501 3.9 60.7 1.0
C2 B:GOA501 4.0 59.1 1.0
OG1 B:THR379 4.1 33.3 1.0
CG2 B:THR379 4.3 30.3 1.0
ND1 B:HIS336 4.4 31.4 1.0
CB B:THR379 4.4 30.9 1.0
CG B:GLU381 4.4 31.0 1.0
CB B:ASP255 4.4 31.2 1.0
NE2 B:HIS343 4.5 37.9 1.0
CG B:HIS336 4.5 30.5 1.0
CG B:GLU420 4.6 31.0 1.0
CD2 B:HIS343 4.7 35.3 1.0

Manganese binding site 6 out of 6 in 4zwu

Go back to Manganese Binding Sites List in 4zwu
Manganese binding site 6 out of 6 in the Crystal Structure of Organophosphate Anhydrolase/Prolidase Mutant Y212F, V342L, I215Y


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, V342L, I215Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn505

b:0.8
occ:1.00
 OE2 B:GLU10 2.9 63.1 1.0
CD B:GLU10 4.1 56.6 1.0
OE1 B:GLU10 4.7 57.5 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 23:16:16 2024

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