Magnesium in PDB 1smy: Structural Basis For Transcription Regulation By Alarmone Ppgpp

All present enzymatic activity of Structural Basis For Transcription Regulation By Alarmone Ppgpp:
2.7.7.6;

The structure of Structural Basis For Transcription Regulation By Alarmone Ppgpp, PDB code: 1smy was solved by I.Artsimovitch, V.Patlan, S.Sekine, M.N.Vassylyeva, T.Hosaka, K.Ochi, S.Yokoyama, D.G.Vassylyev, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	236.350, 236.350, 249.040, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 26.6

The structure of Structural Basis For Transcription Regulation By Alarmone Ppgpp also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 310; Page 32, Binding sites: 311 - 320; Page 33, Binding sites: 321 - 330; Page 34, Binding sites: 331 - 340; Page 35, Binding sites: 341 - 350; Page 36, Binding sites: 351 - 360; Page 37, Binding sites: 361 - 362;

Binding sites:

The binding sites of Magnesium atom in the Structural Basis For Transcription Regulation By Alarmone Ppgpp (pdb code 1smy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 362 binding sites of Magnesium where determined in the Structural Basis For Transcription Regulation By Alarmone Ppgpp, PDB code: 1smy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9209 b:20.0 occ:1.00 O A:HOH9623 2.4 28.4 1.0 O A:HOH9578 3.2 44.3 1.0 O A:LYS83 3.2 69.3 1.0 O A:LEU85 3.6 62.7 1.0 O A:VAL170 3.6 50.0 1.0 CB A:ALA52 3.7 40.0 1.0 O A:THR51 4.0 41.1 1.0 OD1 A:ASP202 4.1 58.4 1.0 C A:LYS83 4.4 69.5 1.0 CA A:ALA52 4.6 39.5 1.0 C A:LEU85 4.6 63.5 1.0 CB A:VAL170 4.6 46.4 1.0 O A:GLU84 4.7 68.1 1.0 C A:VAL170 4.8 48.1 1.0 NH1 A:ARG175 4.8 81.3 1.0 NH2 A:ARG175 4.8 80.0 1.0 C A:GLU84 4.8 68.0 1.0 C A:THR51 5.0 41.4 1.0 CG2 A:VAL170 5.0 44.6 1.0

Magnesium binding site 2 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9212 b:20.0 occ:1.00 O A:HOH9777 2.5 75.8 1.0 O A:ASP160 2.6 77.6 1.0 N A:ILE162 2.7 70.4 1.0 C A:ARG161 2.8 72.4 1.0 C A:ASP160 2.8 77.5 1.0 CA A:ARG161 3.0 74.1 1.0 N A:ARG161 3.0 76.1 1.0 O A:HOH9705 3.2 55.0 1.0 O A:ARG161 3.4 73.3 1.0 O A:LYS159 3.4 79.6 1.0 CA A:ILE162 3.5 70.0 1.0 C A:LYS159 3.5 79.2 1.0 N A:ASP160 3.8 78.8 1.0 CA A:ASP160 3.9 78.6 1.0 CG2 A:ILE162 4.0 70.9 1.0 CA A:LYS159 4.2 79.3 1.0 CB A:ILE162 4.3 69.7 1.0 CB A:LYS159 4.4 76.0 1.0 CB A:ARG161 4.5 75.3 1.0 C A:ILE162 4.8 70.3 1.0

Magnesium binding site 3 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9224 b:20.0 occ:1.00 O C:HOH2048 2.7 26.1 1.0 O C:HOH9863 2.9 34.4 1.0 CE1 C:PHE628 3.0 83.4 1.0 CZ C:PHE628 3.2 83.3 1.0 CB A:ASP74 3.3 67.3 1.0 OD2 A:ASP74 3.5 73.4 1.0 CG A:ASP74 3.8 71.4 1.0 OD2 C:ASP638 4.0 77.8 1.0 CD1 C:PHE628 4.2 84.4 1.0 O A:HOH9794 4.2 45.6 1.0 CB C:ASP638 4.4 74.4 1.0 CE2 C:PHE628 4.5 84.6 1.0 CG C:ASP638 4.6 77.2 1.0 CA A:ASP74 4.6 64.1 1.0 OD1 A:ASP74 4.9 72.9 1.0

Magnesium binding site 4 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9227 b:20.0 occ:1.00 O A:GLU121 2.5 72.1 1.0 C A:GLU121 2.9 71.5 1.0 CG A:MET123 2.9 66.8 1.0 CB A:ARG88 3.1 62.6 1.0 N A:MET123 3.1 66.7 1.0 SD A:MET123 3.2 69.3 1.0 CG A:GLU121 3.3 75.1 1.0 OE1 A:GLU121 3.3 76.6 1.0 N A:ILE122 3.3 70.0 1.0 CB A:GLU121 3.4 73.3 1.0 CE A:MET123 3.4 68.3 1.0 N A:ARG88 3.5 61.2 1.0 CA A:ILE122 3.6 68.9 1.0 C A:ILE122 3.6 68.5 1.0 CD A:GLU121 3.7 75.8 1.0 CA A:GLU121 3.7 71.9 1.0 CA A:ARG88 3.8 61.7 1.0 C A:VAL87 3.8 61.3 1.0 CB A:MET123 3.9 66.3 1.0 CA A:MET123 4.0 65.8 1.0 CD A:ARG88 4.0 62.7 1.0 CG A:ARG88 4.2 63.2 1.0 O A:ARG88 4.2 62.0 1.0 CA A:VAL87 4.2 61.1 1.0 N A:GLU121 4.4 72.5 1.0 O A:VAL87 4.5 62.3 1.0 O A:VAL86 4.5 63.4 1.0 O A:ILE122 4.5 70.5 1.0 C A:ARG88 4.5 62.1 1.0 OE2 A:GLU121 4.8 75.6 1.0

Magnesium binding site 5 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9254 b:20.0 occ:1.00 CG A:ASN212 2.8 59.8 1.0 ND2 A:ASN212 2.8 58.6 1.0 OD1 A:ASN212 2.9 60.4 1.0 O A:HOH9610 3.1 29.2 1.0 CB A:ASN212 3.5 60.6 1.0 CA A:ASN212 4.0 62.4 1.0 O B:PHE225 4.0 66.7 1.0 CD1 A:LEU208 4.9 60.7 1.0 N A:ASN212 4.9 61.5 1.0

Magnesium binding site 6 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9268 b:20.0 occ:1.00 O A:HOH9637 2.5 37.2 1.0 O A:HOH9749 2.7 36.1 1.0 MG A:MG9437 3.6 20.0 1.0 O A:HOH9811 3.9 40.8 1.0 OH B:TYR224 4.3 73.1 1.0 O A:SER4 4.8 0.2 1.0

Magnesium binding site 7 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9273 b:20.0 occ:1.00 O A:HOH9801 2.5 67.6 1.0 O A:HOH9627 2.5 46.6 1.0 O A:HOH9651 2.7 31.3 1.0 CB A:GLU59 3.0 80.8 1.0 ND2 A:ASN139 3.0 56.0 1.0 CB A:ASN139 3.3 57.0 1.0 O A:HOH9841 3.4 51.8 1.0 CG A:ASN139 3.6 57.2 1.0 CA A:GLU59 3.6 79.8 1.0 NH2 A:ARG137 4.2 68.3 1.0 OE1 A:GLU59 4.2 86.0 1.0 CG A:GLU59 4.3 83.0 1.0 C A:GLU59 4.4 81.2 1.0 CD A:GLU59 4.6 84.3 1.0 CA A:ASN139 4.6 57.2 1.0 O A:ASN139 4.6 58.5 1.0 N A:GLU59 4.8 75.6 1.0 OD1 A:ASN139 4.8 58.1 1.0 O A:GLU59 4.8 82.0 1.0 N A:ASN139 4.9 58.8 1.0

Magnesium binding site 8 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9295 b:20.0 occ:1.00 CE A:LYS107 2.9 70.9 1.0 OD1 A:ASP113 3.6 70.4 1.0 CG A:LYS107 3.6 69.3 1.0 CD A:LYS107 3.8 70.7 1.0 NZ A:LYS107 3.9 71.8 1.0 OD2 A:ASP113 3.9 72.1 1.0 O A:GLU108 4.0 63.5 1.0 CG A:ASP113 4.2 71.0 1.0 C A:GLU108 4.6 63.4 1.0 O A:HOH9603 4.8 41.8 1.0 N A:GLU108 4.9 65.7 1.0

Magnesium binding site 9 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9318 b:20.0 occ:1.00 OD1 A:ASN124 4.0 75.8 1.0 CG A:ASN124 5.0 72.7 1.0

Magnesium binding site 10 out of 362 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9327 b:20.0 occ:1.00 MG A:MG9464 2.5 20.0 1.0 O A:HOH9580 3.5 31.0 1.0 CD1 A:TRP200 3.5 59.5 1.0 NE1 A:TRP200 3.7 59.3 1.0 CG A:TRP200 4.3 58.7 1.0 CE2 A:TRP200 4.5 59.1 1.0 NE A:ARG176 4.7 60.3 1.0 CD A:ARG176 4.8 58.6 1.0 CD2 A:TRP200 4.8 58.9 1.0 CZ A:ARG176 4.9 62.1 1.0 CB A:TRP200 5.0 58.0 1.0 CG A:ARG176 5.0 59.8 1.0

I.Artsimovitch, V.Patlan, S.Sekine, M.N.Vassylyeva, T.Hosaka, K.Ochi, S.Yokoyama, D.G.Vassylyev. Structural Basis For Transcription Regulation By Alarmone Ppgpp Cell(Cambridge,Mass.) V. 117 299 2004.
ISSN: ISSN 0092-8674
PubMed: 15109491
DOI: 10.1016/S0092-8674(04)00401-5