Atomistry » Magnesium » PDB 4pjj-4pyj » 4pv4
Atomistry »
  Magnesium »
    PDB 4pjj-4pyj »
      4pv4 »

Magnesium in PDB 4pv4: Proline Aminopeptidase P II From Yersinia Pestis

Enzymatic activity of Proline Aminopeptidase P II From Yersinia Pestis

All present enzymatic activity of Proline Aminopeptidase P II From Yersinia Pestis:
3.4.11.9;

Protein crystallography data

The structure of Proline Aminopeptidase P II From Yersinia Pestis, PDB code: 4pv4 was solved by J.Osipiuk, N.Maltseva, S.Shatsman, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 1.76
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 124.299, 82.865, 110.091, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Proline Aminopeptidase P II From Yersinia Pestis (pdb code 4pv4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Proline Aminopeptidase P II From Yersinia Pestis, PDB code: 4pv4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4pv4

Go back to Magnesium Binding Sites List in 4pv4
Magnesium binding site 1 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:24.6
occ:1.00
OD1 A:ASP269 2.1 23.9 1.0
OE1 A:GLU405 2.2 21.2 1.0
O A:HOH1083 2.2 39.9 1.0
OD1 A:ASP258 2.3 18.4 1.0
OD2 A:ASP258 2.3 18.5 1.0
CG A:ASP258 2.7 17.5 1.0
CG A:ASP269 3.0 23.9 1.0
MG A:MG502 3.1 20.9 0.7
CD A:GLU405 3.1 21.6 1.0
OE2 A:GLU405 3.2 19.4 1.0
OD2 A:ASP269 3.3 29.7 1.0
OG1 A:THR271 3.5 17.7 1.0
OH A:TYR227 3.9 19.4 1.0
CB A:ASP258 4.2 16.5 1.0
OE1 A:GLU382 4.2 30.6 1.0
C24 A:1PE503 4.2 46.1 1.0
CZ A:TYR227 4.4 20.4 1.0
CB A:ASP269 4.4 17.8 1.0
CG A:GLU405 4.5 17.8 1.0
O A:HOH837 4.5 34.7 1.0
OH4 A:1PE503 4.6 47.1 1.0
NE A:ARG403 4.6 17.3 1.0
C A:ASP269 4.6 18.5 1.0
O A:ILE270 4.7 15.7 1.0
CE2 A:TYR227 4.7 20.4 1.0
C23 A:1PE503 4.7 36.2 1.0
C14 A:1PE503 4.8 48.3 1.0
C A:ILE270 4.8 16.9 1.0
OE2 A:GLU382 4.8 29.0 1.0
N A:ILE270 4.8 17.2 1.0
CA A:ASP269 4.8 17.0 1.0
CD A:GLU382 4.8 27.5 1.0
NH1 A:ARG403 4.8 21.6 1.0
CB A:THR271 4.9 17.7 1.0
O A:ASP269 4.9 18.6 1.0
CA A:ASP258 5.0 16.4 1.0
CB A:GLU405 5.0 18.4 1.0

Magnesium binding site 2 out of 4 in 4pv4

Go back to Magnesium Binding Sites List in 4pv4
Magnesium binding site 2 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:20.9
occ:0.70
O A:HOH1083 2.0 39.9 1.0
OE2 A:GLU405 2.1 19.4 1.0
NE2 A:HIS352 2.2 20.1 1.0
OD2 A:ASP269 2.3 29.7 1.0
OE2 A:GLU382 2.4 29.0 1.0
MG A:MG501 3.1 24.6 1.0
CD A:GLU405 3.1 21.6 1.0
CE1 A:HIS352 3.1 20.3 1.0
CG A:ASP269 3.2 23.9 1.0
CD A:GLU382 3.2 27.5 1.0
CD2 A:HIS352 3.2 20.8 1.0
OE1 A:GLU382 3.3 30.6 1.0
OE1 A:GLU405 3.4 21.2 1.0
OD1 A:ASP269 3.4 23.9 1.0
O A:HOH837 3.5 34.7 1.0
CG2 A:THR380 3.7 18.8 1.0
OG1 A:THR380 3.8 19.9 1.0
CB A:THR380 4.0 17.8 1.0
OH2 A:1PE503 4.1 55.2 1.0
ND1 A:HIS352 4.2 19.7 1.0
CG A:HIS352 4.3 20.3 1.0
CB A:ASP269 4.3 17.8 1.0
CG A:GLU405 4.4 17.8 1.0
CG A:GLU382 4.5 20.2 1.0
CB A:GLU382 4.9 18.9 1.0
CG2 A:VAL358 5.0 21.6 1.0
NE2 A:HIS359 5.0 21.5 1.0

Magnesium binding site 3 out of 4 in 4pv4

Go back to Magnesium Binding Sites List in 4pv4
Magnesium binding site 3 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:26.8
occ:1.00
OE2 B:GLU405 2.2 19.0 1.0
NE2 B:HIS352 2.2 20.2 1.0
OD2 B:ASP269 2.3 29.2 1.0
OE2 B:GLU382 2.5 26.7 1.0
O B:HOH844 2.5 38.8 1.0
MG B:MG502 3.1 24.8 1.0
CD B:GLU405 3.1 20.8 1.0
CD2 B:HIS352 3.1 19.8 1.0
CG B:ASP269 3.1 25.2 1.0
CD B:GLU382 3.2 27.7 1.0
CE1 B:HIS352 3.2 19.8 1.0
OE1 B:GLU382 3.3 29.7 1.0
OE1 B:GLU405 3.4 23.2 1.0
OD1 B:ASP269 3.5 23.8 1.0
O B:HOH781 3.6 33.7 1.0
CG2 B:THR380 3.6 17.8 1.0
OG1 B:THR380 3.8 18.9 1.0
CB B:THR380 4.0 18.4 1.0
ND1 B:HIS352 4.3 19.7 1.0
CG B:HIS352 4.3 19.1 1.0
CB B:ASP269 4.3 19.9 1.0
CG B:GLU405 4.5 18.9 1.0
CG B:GLU382 4.5 21.2 1.0
C11 B:P6G503 4.8 44.6 1.0
CB B:GLU382 4.9 20.1 1.0

Magnesium binding site 4 out of 4 in 4pv4

Go back to Magnesium Binding Sites List in 4pv4
Magnesium binding site 4 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:24.8
occ:1.00
OD1 B:ASP269 2.2 23.8 1.0
O B:HOH844 2.2 38.8 1.0
OE1 B:GLU405 2.2 23.2 1.0
OD2 B:ASP258 2.3 19.7 1.0
OD1 B:ASP258 2.4 20.4 1.0
CG B:ASP258 2.7 19.9 1.0
CG B:ASP269 3.0 25.2 1.0
CD B:GLU405 3.1 20.8 1.0
MG B:MG501 3.1 26.8 1.0
OE2 B:GLU405 3.2 19.0 1.0
OD2 B:ASP269 3.3 29.2 1.0
OG1 B:THR271 3.5 17.9 1.0
C12 B:P6G503 3.8 46.1 1.0
OH B:TYR227 3.9 17.8 1.0
C11 B:P6G503 4.1 44.6 1.0
O13 B:P6G503 4.1 36.2 1.0
CB B:ASP258 4.2 18.7 1.0
OE1 B:GLU382 4.2 29.7 1.0
CZ B:TYR227 4.4 20.0 1.0
CB B:ASP269 4.4 19.9 1.0
O B:HOH781 4.5 33.7 1.0
CG B:GLU405 4.5 18.9 1.0
C14 B:P6G503 4.5 41.0 1.0
NE B:ARG403 4.6 19.4 1.0
C B:ASP269 4.7 17.7 1.0
O B:ILE270 4.7 17.8 1.0
CE2 B:TYR227 4.7 19.7 1.0
C B:ILE270 4.8 17.0 1.0
O16 B:P6G503 4.8 40.7 1.0
CA B:ASP269 4.8 18.3 1.0
CD B:GLU382 4.9 27.7 1.0
N B:ILE270 4.9 17.3 1.0
OE2 B:GLU382 4.9 26.7 1.0
O B:ASP269 4.9 18.0 1.0
CB B:THR271 4.9 18.1 1.0
NH1 B:ARG403 4.9 23.3 1.0
CB B:GLU405 5.0 18.4 1.0
CA B:ASP258 5.0 18.1 1.0

Reference:

J.Osipiuk, N.Maltseva, S.Shatsman, W.F.Anderson, A.Joachimiak. Proline Aminopeptidase P II From Yersinia Pestis To Be Published.
Page generated: Tue Aug 20 01:41:11 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