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Magnesium in PDB 3l12: Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution

Protein crystallography data

The structure of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution, PDB code: 3l12 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) 27.28 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.409, 136.411, 50.548, 90.00, 118.00, 90.00
R / Rfree (%) 15.6 / 18.7

Other elements in 3l12:

The structure of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution (pdb code 3l12). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution, PDB code: 3l12:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3l12

Go back to Magnesium Binding Sites List in 3l12
Magnesium binding site 1 out of 3 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 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 (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg313

b:12.0
occ:1.00
OE1 A:GLU148 2.0 7.7 1.0
OD1 A:ASP51 2.1 8.9 1.0
O A:HOH327 2.1 6.4 1.0
OE2 A:GLU49 2.1 8.0 1.0
O A:HOH353 2.1 8.4 1.0
O4 A:UNL317 2.2 7.3 1.0
CG A:ASP51 3.1 7.7 1.0
CD A:GLU148 3.1 8.9 1.0
CD A:GLU49 3.1 7.8 1.0
O3 A:UNL317 3.4 15.8 1.0
OE1 A:GLU49 3.4 7.2 1.0
OD2 A:ASP51 3.4 7.8 1.0
O6 A:UNL317 3.6 8.7 1.0
O A:HOH593 3.8 32.0 1.0
O2 A:UNL317 3.8 19.7 1.0
O1 A:UNL317 3.9 12.4 1.0
O5 A:UNL317 3.9 18.1 1.0
CB A:GLU148 3.9 6.5 1.0
OE2 A:GLU148 3.9 10.1 1.0
CG A:GLU148 4.0 7.4 1.0
NE2 A:HIS22 4.1 7.8 1.0
O A:HOH617 4.4 19.3 1.0
CB A:ASP51 4.4 7.7 1.0
CG A:GLU49 4.5 6.2 1.0
ND1 A:HIS64 4.6 19.2 0.5
NE A:ARG23 4.6 7.2 1.0
NH2 A:ARG23 4.6 9.6 1.0
CD2 A:HIS22 4.7 8.4 1.0
O A:PHE50 4.8 6.8 1.0
C A:PHE50 4.9 8.8 1.0

Magnesium binding site 2 out of 3 in 3l12

Go back to Magnesium Binding Sites List in 3l12
Magnesium binding site 2 out of 3 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 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 (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg313

b:11.2
occ:1.00
OE1 B:GLU148 2.0 10.8 1.0
OE2 B:GLU49 2.1 7.8 1.0
OD1 B:ASP51 2.1 9.6 1.0
O B:HOH364 2.1 10.6 1.0
O B:HOH323 2.1 7.3 1.0
O4 B:UNL317 2.1 9.0 1.0
CG B:ASP51 3.1 9.0 1.0
CD B:GLU49 3.1 7.5 1.0
CD B:GLU148 3.2 10.1 1.0
OD2 B:ASP51 3.4 8.4 1.0
O3 B:UNL317 3.4 18.2 1.0
OE1 B:GLU49 3.4 8.2 1.0
O1 B:UNL317 3.6 10.3 1.0
O5 B:UNL317 3.9 17.4 1.0
CB B:GLU148 4.0 9.8 1.0
OE2 B:GLU148 4.0 10.8 1.0
O2 B:UNL317 4.1 18.1 1.0
O B:HOH483 4.1 17.5 1.0
NE2 B:HIS22 4.1 6.9 1.0
CG B:GLU148 4.1 8.6 1.0
O6 B:UNL317 4.2 12.7 1.0
NZ B:LYS150 4.3 6.5 0.4
CB B:ASP51 4.4 9.1 1.0
CG B:GLU49 4.5 7.7 1.0
ND1 B:HIS64 4.5 13.7 1.0
O B:HOH444 4.6 14.0 1.0
CD2 B:HIS22 4.7 6.6 1.0
NE B:ARG23 4.7 6.9 1.0
C B:PHE50 4.9 8.9 1.0
O B:PHE50 4.9 8.7 1.0
CA B:ASP51 5.0 8.8 1.0
N B:ASP51 5.0 6.7 1.0

Magnesium binding site 3 out of 3 in 3l12

Go back to Magnesium Binding Sites List in 3l12
Magnesium binding site 3 out of 3 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 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 (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg314

b:15.8
occ:0.75
NE2 B:HIS79 2.0 14.7 1.0
CE1 B:HIS79 3.0 13.6 1.0
CD2 B:HIS79 3.0 12.4 1.0
O B:HOH624 4.0 33.3 1.0
O B:GLN77 4.1 12.6 0.2
ND1 B:HIS79 4.1 14.7 1.0
CG B:HIS79 4.2 12.5 1.0
O B:GLN77 4.3 13.5 0.8
CB B:GLN77 4.8 19.7 0.8
CB B:GLN77 4.9 13.7 0.2

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Dec 14 08:23:36 2020

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