Atomistry » Magnesium » PDB 3hp6-3hwx » 3htw
Atomistry »
  Magnesium »
    PDB 3hp6-3hwx »
      3htw »

Magnesium in PDB 3htw: Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound

Protein crystallography data

The structure of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound, PDB code: 3htw was solved by R.Hawwa, S.Larsen, K.Ratia, A.Mesecar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.292, 61.292, 206.011, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 26

Other elements in 3htw:

The structure of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Arsenic (As) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound (pdb code 3htw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound, PDB code: 3htw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3htw

Go back to Magnesium Binding Sites List in 3htw
Magnesium binding site 1 out of 7 in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg425

b:71.5
occ:1.00
O A:HOH44 2.7 36.5 1.0
O A:HOH18 4.4 30.0 1.0
O A:HOH532 4.7 60.3 1.0

Magnesium binding site 2 out of 7 in 3htw

Go back to Magnesium Binding Sites List in 3htw
Magnesium binding site 2 out of 7 in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg426

b:79.4
occ:1.00
O A:ASP395 3.8 33.1 1.0
NH1 A:ARG402 4.2 50.5 1.0
CB A:ASP399 4.5 35.9 1.0
CZ A:ARG402 4.5 53.1 1.0
CA A:ASP395 4.6 32.7 1.0
C A:ASP395 4.6 33.3 1.0
N A:ASP399 4.7 33.0 1.0
NH2 A:ARG402 4.7 52.3 1.0
CA A:ASP399 4.8 33.4 1.0
CB A:PRO398 4.8 33.3 1.0

Magnesium binding site 3 out of 7 in 3htw

Go back to Magnesium Binding Sites List in 3htw
Magnesium binding site 3 out of 7 in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3

b:74.3
occ:1.00
NH1 A:ARG402 3.3 50.5 1.0
NH2 A:ARG402 3.4 52.3 1.0
CZ A:ARG402 3.8 53.1 1.0

Magnesium binding site 4 out of 7 in 3htw

Go back to Magnesium Binding Sites List in 3htw
Magnesium binding site 4 out of 7 in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4

b:72.4
occ:1.00
O A:HOH66 3.0 42.0 1.0
CG2 A:THR406 3.7 35.1 1.0
NH2 A:ARG401 3.8 47.9 1.0
CA A:THR406 3.8 36.5 1.0
CB A:THR406 3.9 37.6 1.0
O A:ILE405 4.4 37.5 1.0
N A:THR406 4.4 36.4 1.0
CZ A:ARG401 4.5 47.2 1.0
O A:HOH495 4.5 54.2 1.0
NE A:ARG401 4.6 47.0 1.0
C A:ILE405 4.7 37.1 1.0
O A:GLY404 4.7 40.1 1.0
N A:GLU407 4.7 38.1 1.0
C A:THR406 4.8 36.7 1.0

Magnesium binding site 5 out of 7 in 3htw

Go back to Magnesium Binding Sites List in 3htw
Magnesium binding site 5 out of 7 in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5

b:70.1
occ:1.00
O A:HOH76 2.7 40.9 1.0
O A:GLY294 3.0 40.4 1.0
N A:ASP296 3.5 34.0 1.0
CB A:ASP296 3.6 34.4 1.0
OE1 A:GLN266 3.7 42.1 1.0
CA A:ASP296 3.9 34.4 1.0
CG A:ARG267 4.1 40.9 1.0
C A:ALA295 4.1 34.8 1.0
C A:GLY294 4.2 40.7 1.0
CA A:ARG267 4.3 38.1 1.0
CA A:ALA295 4.4 36.6 1.0
O A:HOH40 4.5 38.5 1.0
CG A:ASP296 4.6 33.9 1.0
CB A:ARG267 4.7 37.4 1.0
CD A:GLN266 4.7 37.2 1.0
N A:ALA295 4.8 38.4 1.0
O A:ALA295 4.8 34.8 1.0
N A:ARG267 4.8 36.5 1.0
OD2 A:ASP296 4.9 35.5 1.0

Magnesium binding site 6 out of 7 in 3htw

Go back to Magnesium Binding Sites List in 3htw
Magnesium binding site 6 out of 7 in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6

b:57.5
occ:1.00
O A:HOH78 2.5 49.0 1.0
O A:HOH82 2.6 54.3 1.0
OD2 A:ASP296 3.1 35.5 1.0
O A:HOH441 4.1 45.2 1.0
CG A:ASP296 4.1 33.9 1.0
CG A:ARG299 4.1 39.8 1.0
CB A:ALA298 4.2 38.0 1.0
CD A:ARG299 4.2 40.3 1.0
O A:HOH40 4.4 38.5 1.0
OD1 A:ASP296 4.5 35.1 1.0
NE A:ARG299 5.0 43.1 1.0

Magnesium binding site 7 out of 7 in 3htw

Go back to Magnesium Binding Sites List in 3htw
Magnesium binding site 7 out of 7 in the Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Organophosphorus Hydrolase From Deinococcus Radiodurans with Cacodylate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:65.4
occ:1.00
NE A:ARG402 2.6 50.6 1.0
OD1 A:ASP399 3.0 40.6 1.0
NH2 A:ARG402 3.3 52.3 1.0
CZ A:ARG402 3.3 53.1 1.0
CD A:ARG402 3.6 46.7 1.0
CG A:ARG402 3.6 45.2 1.0
NE A:ARG403 3.8 42.5 1.0
CG A:ARG403 3.8 40.2 1.0
CG A:ASP399 4.1 37.7 1.0
CZ A:ARG403 4.2 44.1 1.0
NH2 A:ARG403 4.3 44.9 1.0
CD A:ARG403 4.4 40.3 1.0
OD2 A:ASP399 4.4 45.1 1.0
O A:ASP399 4.5 33.2 1.0
NH1 A:ARG402 4.5 50.5 1.0

Reference:

R.Hawwa, S.D.Larsen, K.Ratia, A.D.Mesecar. Structure-Based and Random Mutagenesis Approaches Increase the Organophosphate-Degrading Activity of A Phosphotriesterase Homologue From Deinococcus Radiodurans. J.Mol.Biol. V. 393 36 2009.
ISSN: ISSN 0022-2836
PubMed: 19631223
DOI: 10.1016/J.JMB.2009.06.083
Page generated: Wed Aug 14 15:21:00 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