Sodium in PDB 3gti: D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans

The structure of D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans, PDB code: 3gti 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 / 2.42
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.960, 60.960, 205.400, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 26.6

The structure of D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Sodium atom in the D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans (pdb code 3gti). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans, PDB code: 3gti:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:24.3 occ:1.00 O A:ASP357 2.7 27.1 1.0 OG A:SER323 2.8 25.8 1.0 O A:HOH23 3.0 17.4 1.0 CG A:ASN417 3.4 22.0 1.0 CB A:ASN417 3.4 22.2 1.0 OD1 A:ASN417 3.5 23.6 1.0 CB A:SER323 3.5 24.1 1.0 CD1 A:LEU360 3.6 15.4 1.0 C A:ASP357 3.7 28.0 1.0 CA A:ARG358 3.8 24.8 1.0 ND2 A:ASN417 3.9 21.2 1.0 CA A:ASN417 4.1 24.7 1.0 C A:ARG358 4.1 23.5 1.0 N A:ARG358 4.1 26.4 1.0 O A:HOH17 4.3 16.6 1.0 O A:HOH476 4.4 31.6 1.0 O A:ASN417 4.4 25.1 1.0 O A:HOH44 4.4 22.7 1.0 O A:HOH22 4.5 18.1 1.0 C A:ASN417 4.5 24.6 1.0 N A:LEU359 4.6 22.0 1.0 O A:ARG358 4.6 24.4 1.0 CG A:LEU360 4.6 15.2 1.0 CA A:SER323 4.6 23.8 1.0 CD A:ARG358 4.7 25.2 1.0 CA A:ASP357 4.9 28.8 1.0 CB A:ARG358 5.0 25.1 1.0

Sodium binding site 2 out of 3 in the D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:10.5 occ:1.00 N A:GLY171 3.2 19.8 1.0 N A:TYR197 3.3 21.6 1.0 CA A:GLY171 3.3 20.3 1.0 N A:ALA203 3.6 24.4 1.0 CB A:PRO169 3.7 19.0 1.0 CA A:PHE196 3.8 20.8 1.0 CB A:TYR197 3.9 23.3 1.0 C A:GLY171 3.9 20.4 1.0 CA A:GLY202 3.9 25.8 1.0 N A:CYS172 3.9 19.2 1.0 C A:PHE196 4.0 21.4 1.0 CB A:PHE196 4.0 20.8 1.0 CD2 A:PHE196 4.0 24.2 1.0 SG A:CYS172 4.0 20.2 1.0 CG A:PHE196 4.1 22.9 1.0 CA A:TYR197 4.2 20.9 1.0 C A:GLY202 4.3 23.7 1.0 CB A:ALA203 4.3 21.4 1.0 C A:ASN170 4.4 20.2 1.0 C A:PRO169 4.5 18.9 1.0 N A:ASN170 4.5 19.4 1.0 O A:HOH37 4.5 20.2 1.0 CA A:ALA203 4.6 23.8 1.0 CG A:PRO129 4.6 27.6 1.0 CA A:PRO169 4.7 19.2 1.0 O A:PRO169 4.8 21.6 1.0 O A:GLY171 4.8 18.9 1.0 CG A:PRO169 4.8 17.1 1.0 O A:GLY195 4.8 22.1 1.0 CE2 A:PHE196 4.8 25.0 1.0 CB A:CYS172 4.9 17.8 1.0 CA A:ASN170 5.0 21.1 1.0 CD1 A:PHE196 5.0 22.6 1.0 CA A:CYS172 5.0 18.4 1.0

Sodium binding site 3 out of 3 in the D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of D71G/E101G/M234L Mutant in Organophosphorus Hydrolase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5 b:25.6 occ:1.00 O A:GLU151 2.9 29.6 1.0 O A:HOH610 3.0 43.5 1.0 N A:ALA155 3.6 23.3 1.0 CG A:GLU151 3.7 42.2 1.0 O A:HOH578 3.8 41.1 1.0 CB A:ALA155 3.8 22.0 1.0 C A:GLU151 3.8 30.4 1.0 O A:HOH561 3.8 38.5 1.0 CB A:ARG154 3.9 27.3 1.0 CA A:ALA155 3.9 22.8 1.0 O A:HOH477 4.0 32.0 1.0 C A:ARG154 4.1 25.6 1.0 CA A:GLU151 4.2 32.2 1.0 CA A:ARG154 4.5 26.7 1.0 CB A:GLU151 4.6 35.7 1.0 O A:ARG154 4.7 26.0 1.0 CD A:GLU151 4.7 46.2 1.0 N A:THR152 4.9 27.7 1.0 OE2 A:GLU151 4.9 48.5 1.0 N A:ARG154 4.9 26.3 1.0 CG A:ARG154 5.0 30.6 1.0

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