Magnesium in PDB 3ks6: Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution

The structure of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution, PDB code: 3ks6 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.427, 99.797, 134.656, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.5

The structure of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution (pdb code 3ks6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution, PDB code: 3ks6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg251 b:17.7 occ:1.00 OE1 A:GLU104 2.0 21.8 1.0 OE2 A:GLU34 2.1 18.1 1.0 OD1 A:ASP36 2.1 17.6 1.0 O A:HOH290 2.1 20.8 1.0 O A:HOH256 2.1 16.2 1.0 O1 A:UNL250 2.2 24.3 1.0 CD A:GLU34 3.0 18.0 1.0 CG A:ASP36 3.1 21.8 1.0 CD A:GLU104 3.2 17.4 1.0 OE1 A:GLU34 3.3 18.2 1.0 OD2 A:ASP36 3.4 20.8 1.0 CB A:GLU104 3.8 17.0 1.0 OXT A:ACT253 3.9 21.9 1.0 OE2 A:GLU104 4.0 20.0 1.0 O2 A:UNL250 4.1 46.8 1.0 O A:HOH271 4.1 19.4 1.0 CG A:GLU104 4.1 13.9 1.0 NE2 A:HIS7 4.2 19.1 1.0 O3 A:UNL250 4.3 32.8 1.0 O A:HOH359 4.3 26.3 1.0 CG A:GLU34 4.4 14.4 1.0 CB A:ASP36 4.4 19.1 1.0 O4 A:UNL250 4.5 27.2 1.0 CD2 A:HIS7 4.5 19.3 1.0 CD2 A:HIS49 4.6 19.1 1.0 C A:ACT253 4.7 29.0 1.0 C A:PHE35 4.9 17.8 1.0 CH3 A:ACT253 4.9 32.4 1.0 O A:PHE35 4.9 19.2 1.0 N A:ASP36 4.9 14.6 1.0 CD A:LYS106 5.0 20.7 0.5

Magnesium binding site 2 out of 4 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg251 b:18.3 occ:1.00 OE1 B:GLU104 2.0 21.8 1.0 O B:HOH265 2.1 26.9 1.0 OD1 B:ASP36 2.1 23.0 1.0 O B:HOH263 2.1 19.2 1.0 OE2 B:GLU34 2.1 21.9 1.0 O1 B:UNL250 2.2 23.0 1.0 CD B:GLU34 3.1 18.5 1.0 CG B:ASP36 3.1 23.5 1.0 CD B:GLU104 3.2 25.9 1.0 OE1 B:GLU34 3.4 18.2 1.0 OD2 B:ASP36 3.4 21.5 1.0 O2 B:UNL250 3.7 49.5 1.0 CB B:GLU104 3.8 18.1 1.0 OXT B:ACT252 3.9 31.7 1.0 O B:HOH278 4.0 20.9 1.0 CG B:GLU104 4.0 17.3 1.0 OE2 B:GLU104 4.0 21.1 1.0 O B:HOH333 4.2 25.7 1.0 NE2 B:HIS7 4.2 20.6 1.0 CG B:GLU34 4.4 17.4 1.0 CB B:ASP36 4.5 22.9 1.0 O4 B:UNL250 4.5 21.2 1.0 CD2 B:HIS49 4.6 25.0 1.0 CD2 B:HIS7 4.7 18.6 1.0 CH3 B:ACT252 4.7 38.9 1.0 C B:ACT252 4.7 35.6 1.0 O3 B:UNL250 4.7 30.7 1.0 C B:PHE35 4.9 20.6 1.0 CD B:LYS106 4.9 29.5 1.0 O B:PHE35 4.9 19.9 1.0 N B:ASP36 4.9 21.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg251 b:17.5 occ:1.00 OE1 C:GLU104 2.0 21.5 1.0 OD1 C:ASP36 2.0 20.6 1.0 O C:HOH276 2.1 21.5 1.0 OE2 C:GLU34 2.1 21.5 1.0 O C:HOH261 2.2 18.6 1.0 O1 C:UNL250 2.2 20.3 1.0 CG C:ASP36 3.1 18.0 1.0 CD C:GLU34 3.1 24.0 1.0 CD C:GLU104 3.1 21.4 1.0 OD2 C:ASP36 3.3 21.3 1.0 OE1 C:GLU34 3.4 16.8 1.0 CB C:GLU104 3.8 18.3 1.0 O C:ACT252 3.9 27.0 1.0 OE2 C:GLU104 4.0 19.7 1.0 CG C:GLU104 4.0 17.2 1.0 O C:HOH299 4.1 24.1 1.0 O C:HOH254 4.2 16.6 1.0 NE2 C:HIS7 4.3 21.7 1.0 O2 C:UNL250 4.4 50.9 1.0 O3 C:UNL250 4.4 32.2 1.0 CB C:ASP36 4.4 19.4 1.0 CG C:GLU34 4.4 19.2 1.0 CD2 C:HIS49 4.5 17.3 1.0 CH3 C:ACT252 4.5 34.4 1.0 C C:ACT252 4.6 28.7 1.0 O4 C:UNL250 4.6 25.8 1.0 CD2 C:HIS7 4.7 20.3 1.0 C C:PHE35 4.8 18.3 1.0 O C:PHE35 4.9 17.5 1.0 N C:ASP36 4.9 18.3 1.0 CD C:LYS106 4.9 25.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) at 1.80 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg251 b:18.6 occ:1.00 OE1 D:GLU104 2.0 17.6 1.0 OD1 D:ASP36 2.0 19.6 1.0 OE2 D:GLU34 2.1 23.9 1.0 O D:HOH282 2.1 22.6 1.0 O2 D:UNL250 2.2 23.8 1.0 O D:HOH278 2.2 21.8 1.0 CG D:ASP36 3.1 17.0 1.0 CD D:GLU34 3.1 21.4 1.0 CD D:GLU104 3.1 22.6 1.0 OD2 D:ASP36 3.4 21.3 1.0 OE1 D:GLU34 3.4 19.2 1.0 CB D:GLU104 3.8 18.8 1.0 O D:ACT252 3.9 32.1 1.0 OE2 D:GLU104 3.9 24.6 1.0 O D:HOH284 4.0 22.9 1.0 CG D:GLU104 4.0 20.7 1.0 O D:HOH310 4.2 25.9 1.0 NE2 D:HIS7 4.2 22.6 1.0 O3 D:UNL250 4.2 35.3 1.0 CB D:ASP36 4.4 19.2 1.0 CG D:GLU34 4.4 19.1 1.0 CD2 D:HIS49 4.5 20.3 1.0 O1 D:UNL250 4.6 27.6 1.0 CD2 D:HIS7 4.7 26.4 1.0 C D:ACT252 4.7 36.7 1.0 CD D:LYS106 4.8 26.3 1.0 C D:PHE35 4.9 22.5 1.0 O D:PHE35 4.9 21.2 1.0 CH3 D:ACT252 4.9 39.9 1.0 N D:ASP36 5.0 21.8 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.