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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 08:14:41 2020

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