Magnesium in PDB 3t5p: Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne

The structure of Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne, PDB code: 3t5p was solved by J.Hou, H.Zheng, M.Chruszcz, D.R.Cooper, O.Onopriyenko, S.Grimshaw, A.Savchenko, W.F.Anderson, W.Minor, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.016, 115.100, 208.018, 90.00, 92.34, 90.00
R / Rfree (%)	20.5 / 24.1

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne (pdb code 3t5p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne, PDB code: 3t5p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


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 A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:48.1 occ:1.00 O A:LYS216 2.0 52.0 1.0 OD1 A:ASP219 2.0 50.3 1.0 O A:THR221 2.0 50.5 1.0 O A:HOH302 2.0 26.2 1.0 O A:HOH303 2.1 24.3 1.0 O A:HOH304 2.2 33.0 1.0 CG A:ASP219 2.9 50.2 1.0 C A:LYS216 3.2 52.7 1.0 C A:THR221 3.2 51.1 1.0 OD2 A:ASP219 3.3 49.6 1.0 N A:THR221 3.9 50.7 1.0 N A:LYS216 4.0 52.5 1.0 CA A:LYS216 4.1 52.8 1.0 CA A:THR221 4.1 51.2 1.0 N A:CYS217 4.2 52.8 1.0 OD2 A:ASP127 4.2 54.9 1.0 N A:ASP219 4.2 51.2 1.0 N A:LEU222 4.2 51.6 1.0 CB A:ASP219 4.3 50.4 1.0 CG2 A:THR221 4.3 50.1 1.0 OD2 A:ASP223 4.3 54.2 1.0 CA A:CYS217 4.3 53.1 1.0 OD1 A:ASN201 4.4 52.2 1.0 CA A:LEU222 4.4 51.8 1.0 O A:ASN201 4.5 52.6 1.0 C A:CYS217 4.5 53.0 1.0 CB A:LYS216 4.5 53.1 1.0 N A:ASP218 4.6 52.6 1.0 CA A:ASP219 4.6 51.0 1.0 N A:GLY220 4.6 51.1 1.0 C A:ASP219 4.8 51.0 1.0 CB A:THR221 4.8 51.3 1.0 CG1 A:VAL215 4.9 53.9 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


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 A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:36.1 occ:1.00 O B:LYS216 1.9 44.8 1.0 O B:HOH303 2.0 33.9 1.0 O B:THR221 2.1 43.2 1.0 O B:HOH302 2.1 32.9 1.0 O B:HOH304 2.1 27.0 1.0 OD1 B:ASP219 2.2 44.0 1.0 CG B:ASP219 3.1 45.0 1.0 C B:LYS216 3.1 45.8 1.0 OD2 B:ASP219 3.3 44.9 1.0 C B:THR221 3.3 43.8 1.0 N B:LYS216 3.8 47.8 1.0 CA B:LYS216 4.0 47.3 1.0 N B:THR221 4.1 43.5 1.0 N B:CYS217 4.1 44.7 1.0 OD2 B:ASP223 4.1 49.8 1.0 CA B:THR221 4.2 44.2 1.0 N B:LEU222 4.2 43.9 1.0 OD1 B:ASN201 4.3 41.4 1.0 CA B:CYS217 4.3 43.8 1.0 O B:ASN201 4.3 43.4 1.0 CA B:LEU222 4.4 43.9 1.0 N B:ASP219 4.4 44.4 1.0 CG2 B:THR221 4.4 44.9 1.0 CB B:ASP219 4.4 45.5 1.0 OD2 B:ASP127 4.5 40.2 1.0 CB B:LYS216 4.5 48.4 1.0 C B:CYS217 4.6 43.6 1.0 CG1 B:VAL215 4.6 47.7 1.0 N B:ASP218 4.7 44.1 1.0 CA B:ASP219 4.8 45.0 1.0 N B:GLY220 4.9 43.7 1.0 C B:VAL215 5.0 48.7 1.0 CB B:THR221 5.0 45.4 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


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 A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:56.8 occ:1.00 O C:HOH303 1.8 38.0 1.0 O C:HOH304 1.8 45.4 1.0 O C:THR221 1.9 58.4 1.0 O C:LYS216 2.0 58.7 1.0 O C:HOH302 2.2 31.3 1.0 OD1 C:ASP219 2.3 57.8 1.0 C C:THR221 3.2 59.0 1.0 CG C:ASP219 3.2 58.5 1.0 C C:LYS216 3.3 59.2 1.0 OD2 C:ASP219 3.6 58.9 1.0 N C:THR221 4.0 57.3 1.0 N C:LYS216 4.1 61.9 1.0 N C:LEU222 4.1 59.8 1.0 OD1 C:ASN201 4.1 56.2 1.0 CA C:THR221 4.1 58.7 1.0 N C:CYS217 4.2 57.9 1.0 CA C:LYS216 4.2 60.7 1.0 CA C:LEU222 4.2 60.3 1.0 OD2 C:ASP223 4.3 66.0 1.0 CA C:CYS217 4.3 57.1 1.0 OD2 C:ASP127 4.3 53.3 1.0 O C:ASN201 4.3 58.1 1.0 N C:ASP219 4.4 56.5 1.0 CG2 C:THR221 4.4 59.7 1.0 C C:CYS217 4.5 56.4 1.0 CB C:ASP219 4.6 58.0 1.0 N C:ASP218 4.7 56.3 1.0 CB C:LYS216 4.7 61.1 1.0 CG1 C:VAL215 4.7 63.1 1.0 N C:GLY220 4.8 56.4 1.0 CA C:ASN201 4.9 58.8 1.0 CA C:ASP219 4.9 57.0 1.0 CB C:THR221 5.0 60.0 1.0 C C:LEU222 5.0 62.0 1.0 O C:GLY200 5.0 61.9 1.0 O C:CYS217 5.0 55.8 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


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 A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:39.7 occ:1.00 O D:THR221 2.0 52.7 1.0 O D:LYS216 2.0 53.9 1.0 O D:HOH302 2.1 25.3 1.0 O D:HOH303 2.2 27.6 1.0 OD1 D:ASP219 2.2 54.1 1.0 O D:HOH304 2.3 25.1 1.0 CG D:ASP219 3.1 55.9 1.0 C D:THR221 3.2 53.4 1.0 C D:LYS216 3.2 54.6 1.0 OD2 D:ASP219 3.2 56.4 1.0 N D:LYS216 3.9 57.8 1.0 N D:THR221 4.0 53.1 1.0 OD2 D:ASP223 4.1 60.5 1.0 CA D:LYS216 4.1 56.9 1.0 N D:LEU222 4.1 53.5 1.0 CA D:THR221 4.2 54.0 1.0 N D:CYS217 4.2 53.0 1.0 CA D:LEU222 4.2 53.0 1.0 CG2 D:THR221 4.3 56.6 1.0 OD1 D:ASN201 4.3 47.8 1.0 OD2 D:ASP127 4.4 48.2 1.0 O D:ASN201 4.4 50.6 1.0 CA D:CYS217 4.4 51.2 1.0 CB D:ASP219 4.5 56.6 1.0 CB D:LYS216 4.5 58.7 1.0 N D:ASP219 4.5 53.9 1.0 CG1 D:VAL215 4.6 56.6 1.0 C D:CYS217 4.7 51.2 1.0 N D:ASP218 4.8 52.2 1.0 CB D:THR221 4.9 56.4 1.0 N D:GLY220 4.9 53.4 1.0 C D:LEU222 4.9 55.1 1.0 CA D:ASP219 4.9 55.5 1.0 O D:GLY200 4.9 53.0 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg301 b:59.5 occ:1.00 O E:THR221 1.9 56.2 1.0 O E:HOH303 2.0 37.6 1.0 O E:HOH304 2.0 39.6 1.0 O E:LYS216 2.1 56.7 1.0 OD1 E:ASP219 2.1 57.4 1.0 O E:HOH302 2.1 34.8 1.0 CG E:ASP219 3.1 59.2 1.0 C E:THR221 3.1 57.1 1.0 C E:LYS216 3.3 57.4 1.0 OD2 E:ASP219 3.4 59.9 1.0 N E:THR221 3.8 57.2 1.0 CA E:THR221 4.0 58.3 1.0 N E:LYS216 4.1 60.4 1.0 N E:LEU222 4.1 57.3 1.0 OD1 E:ASN201 4.1 51.1 1.0 OD2 E:ASP127 4.2 55.0 1.0 CA E:LYS216 4.2 59.8 1.0 N E:CYS217 4.2 55.9 1.0 CG2 E:THR221 4.3 60.6 1.0 N E:ASP219 4.3 57.4 1.0 CA E:LEU222 4.3 56.6 1.0 CA E:CYS217 4.3 54.1 1.0 OD2 E:ASP223 4.3 63.0 1.0 CB E:ASP219 4.4 60.1 1.0 C E:CYS217 4.5 54.3 1.0 O E:ASN201 4.5 52.9 1.0 CB E:LYS216 4.6 61.7 1.0 N E:ASP218 4.6 55.6 1.0 N E:GLY220 4.7 57.2 1.0 CA E:ASP219 4.7 59.2 1.0 CB E:THR221 4.8 60.9 1.0 C E:ASP219 4.9 59.0 1.0 CG1 E:VAL215 4.9 58.5 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg301 b:58.2 occ:1.00 O F:THR221 1.9 66.8 1.0 O F:HOH302 1.9 37.4 1.0 O F:LYS216 2.1 67.0 1.0 OD1 F:ASP219 2.2 66.1 1.0 O F:HOH303 2.3 28.6 1.0 CG F:ASP219 3.1 67.8 1.0 C F:THR221 3.1 67.6 1.0 OD2 F:ASP219 3.2 69.1 1.0 C F:LYS216 3.3 67.5 1.0 N F:LYS216 3.9 71.9 1.0 N F:THR221 4.0 65.6 1.0 OD2 F:ASP223 4.0 76.7 1.0 N F:LEU222 4.0 68.8 1.0 CA F:THR221 4.1 67.5 1.0 CA F:LEU222 4.1 69.2 1.0 CA F:LYS216 4.1 70.1 1.0 CG2 F:THR221 4.2 70.1 1.0 N F:CYS217 4.3 65.5 1.0 OD1 F:ASN201 4.3 61.7 1.0 CB F:ASP219 4.5 67.4 1.0 O F:ASN201 4.5 64.9 1.0 CA F:CYS217 4.5 63.5 1.0 N F:ASP219 4.6 64.2 1.0 CB F:LYS216 4.6 71.1 1.0 CG1 F:VAL215 4.7 72.7 1.0 OD2 F:ASP127 4.7 59.2 1.0 C F:CYS217 4.8 62.4 1.0 CB F:THR221 4.8 69.7 1.0 C F:LEU222 4.8 72.0 1.0 N F:ASP218 4.9 62.9 1.0 O F:GLY200 4.9 70.4 1.0 N F:GLY220 4.9 63.8 1.0 CA F:ASP219 4.9 65.5 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:43.8 occ:1.00 O G:THR221 1.8 53.2 1.0 O G:HOH304 2.0 16.1 1.0 OD1 G:ASP219 2.1 54.6 1.0 O G:HOH302 2.1 28.9 1.0 O G:HOH303 2.2 29.1 1.0 O G:LYS216 2.2 54.0 1.0 C G:THR221 3.0 54.0 1.0 CG G:ASP219 3.0 56.0 1.0 OD2 G:ASP219 3.4 56.0 1.0 C G:LYS216 3.4 54.6 1.0 N G:THR221 3.7 55.0 1.0 CA G:THR221 3.9 55.4 1.0 N G:LEU222 4.0 54.1 1.0 OD1 G:ASN201 4.2 50.1 1.0 CG2 G:THR221 4.2 56.7 1.0 N G:LYS216 4.2 56.5 1.0 CA G:LEU222 4.2 53.2 1.0 OD2 G:ASP127 4.3 50.8 1.0 N G:ASP219 4.3 55.3 1.0 CA G:LYS216 4.3 56.3 1.0 OD2 G:ASP223 4.3 58.1 1.0 CB G:ASP219 4.4 57.0 1.0 N G:CYS217 4.4 53.5 1.0 CA G:CYS217 4.5 52.4 1.0 C G:CYS217 4.6 52.8 1.0 N G:GLY220 4.6 55.7 1.0 CB G:THR221 4.7 57.1 1.0 O G:ASN201 4.7 51.1 1.0 CA G:ASP219 4.7 56.7 1.0 N G:ASP218 4.7 53.7 1.0 CB G:LYS216 4.8 58.2 1.0 C G:ASP219 4.8 56.9 1.0 C G:GLY220 4.9 56.1 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg301 b:73.2 occ:1.00 O H:HOH302 1.9 31.9 1.0 O H:LYS216 2.0 78.5 1.0 O H:THR221 2.1 75.2 1.0 OD1 H:ASP219 2.4 76.7 1.0 CG H:ASP219 3.0 78.6 1.0 OD2 H:ASP219 3.0 79.4 1.0 C H:LYS216 3.1 80.0 1.0 C H:THR221 3.4 75.2 1.0 N H:LYS216 3.5 83.4 1.0 OD2 H:ASP223 3.6 84.0 1.0 CA H:LYS216 3.8 82.8 1.0 N H:LEU222 4.2 75.4 1.0 N H:CYS217 4.3 79.0 1.0 CG2 H:THR221 4.3 78.1 1.0 CB H:LYS216 4.3 84.2 1.0 CG1 H:VAL215 4.3 82.4 1.0 CA H:LEU222 4.3 75.5 1.0 N H:THR221 4.4 74.5 1.0 CA H:THR221 4.4 75.4 1.0 CB H:ASP219 4.5 79.2 1.0 O H:ASN201 4.5 76.4 1.0 CA H:CYS217 4.6 77.0 1.0 C H:VAL215 4.6 85.2 1.0 N H:ASP219 4.7 76.8 1.0 OD1 H:ASN201 4.7 72.2 1.0 OD2 H:ASP127 4.8 69.7 1.0 C H:LEU222 4.8 77.5 1.0 CG H:ASP223 4.9 83.8 1.0 CA H:VAL215 4.9 86.0 1.0 O H:GLY200 4.9 77.4 1.0 C H:CYS217 4.9 76.0 1.0 CB H:THR221 5.0 77.3 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg301 b:60.0 occ:1.00 O I:LYS216 1.8 58.7 1.0 O I:HOH302 2.0 36.3 1.0 OD1 I:ASP219 2.1 59.0 1.0 O I:HOH304 2.1 32.7 1.0 O I:THR221 2.2 59.2 1.0 O I:HOH303 2.2 35.4 1.0 CG I:ASP219 2.9 60.0 1.0 C I:LYS216 3.0 59.1 1.0 OD2 I:ASP219 3.2 60.6 1.0 C I:THR221 3.4 60.3 1.0 N I:LYS216 3.8 62.3 1.0 CA I:LYS216 3.9 61.0 1.0 N I:CYS217 4.0 57.3 1.0 N I:THR221 4.1 59.2 1.0 OD2 I:ASP127 4.2 53.5 1.0 CA I:CYS217 4.2 56.1 1.0 N I:ASP219 4.2 57.4 1.0 CB I:ASP219 4.3 59.8 1.0 OD2 I:ASP223 4.3 66.9 1.0 CA I:THR221 4.3 60.7 1.0 OD1 I:ASN201 4.3 55.5 1.0 CB I:LYS216 4.3 62.1 1.0 N I:LEU222 4.4 61.3 1.0 O I:ASN201 4.4 57.0 1.0 C I:CYS217 4.4 55.7 1.0 CG2 I:THR221 4.4 62.3 1.0 N I:ASP218 4.5 56.2 1.0 CA I:LEU222 4.5 61.1 1.0 CA I:ASP219 4.7 58.6 1.0 CG1 I:VAL215 4.7 62.9 1.0 N I:GLY220 4.7 57.8 1.0 C I:ASP219 4.9 58.9 1.0 C I:VAL215 5.0 63.4 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg301 b:69.6 occ:1.00 O J:THR221 1.9 72.1 1.0 O J:LYS216 2.0 73.3 1.0 OD1 J:ASP219 2.1 74.0 1.0 O J:HOH324 2.2 67.8 1.0 O J:HOH323 2.2 69.6 1.0 O J:HOH322 2.2 71.7 1.0 CG J:ASP219 3.0 76.2 1.0 C J:THR221 3.2 72.8 1.0 OD2 J:ASP219 3.2 77.1 1.0 C J:LYS216 3.2 74.1 1.0 N J:THR221 3.9 73.0 1.0 N J:LYS216 4.0 77.8 1.0 CA J:THR221 4.0 73.9 1.0 CA J:LYS216 4.1 76.9 1.0 N J:LEU222 4.1 72.7 1.0 N J:CYS217 4.2 72.2 1.0 OD1 J:ASN201 4.2 66.0 1.0 CG2 J:THR221 4.3 77.2 1.0 N J:ASP219 4.3 73.8 1.0 OD2 J:ASP223 4.3 80.0 1.0 CB J:ASP219 4.3 77.3 1.0 OD2 J:ASP127 4.3 67.0 1.0 CA J:LEU222 4.3 72.0 1.0 CA J:CYS217 4.4 69.9 1.0 CB J:LYS216 4.5 79.2 1.0 C J:CYS217 4.5 69.7 1.0 O J:ASN201 4.6 69.0 1.0 N J:ASP218 4.6 71.3 1.0 CA J:ASP219 4.7 75.9 1.0 N J:GLY220 4.7 73.5 1.0 CB J:THR221 4.8 76.8 1.0 C J:ASP219 4.8 75.7 1.0 CG1 J:VAL215 4.9 76.2 1.0

J.Hou, H.Zheng, M.Chruszcz, D.R.Cooper, O.Onopriyenko, S.Grimshaw, A.Savchenko, W.F.Anderson, W.Minor, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of A Putative Diacylglycerol Kinase From Bacillus Anthracis Str. Sterne To Be Published.