Zinc 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:

Magnesium

(Mg)

362 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis For Transcription Regulation By Alarmone Ppgpp, PDB code: 1smy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn9102 b:0.3 occ:1.00 SG D:CYS76 2.4 0.9 1.0 SG D:CYS60 2.4 1.0 1.0 SG D:CYS73 2.4 0.5 1.0 SG D:CYS58 2.4 0.5 1.0 CB D:CYS73 3.5 0.0 1.0 CB D:CYS76 3.8 0.0 1.0 CB D:CYS60 3.8 0.5 1.0 CB D:CYS58 3.8 0.5 1.0 O D:CYS76 3.9 0.9 1.0 N D:CYS60 4.0 0.4 1.0 CA D:CYS60 4.4 0.9 1.0 CG D:LYS62 4.4 0.8 1.0 C D:CYS76 4.5 0.9 1.0 N D:GLY61 4.5 0.6 1.0 CA D:CYS76 4.6 0.4 1.0 N D:ALA59 4.6 0.9 1.0 CG2 D:VAL78 4.7 0.1 1.0 N D:LYS62 4.8 0.7 1.0 CB D:LYS62 4.8 0.8 1.0 N D:CYS76 4.8 0.2 1.0 CB D:VAL78 4.8 0.1 1.0 C D:CYS60 5.0 0.5 1.0 O D:HOH2359 5.0 60.1 1.0 CA D:CYS73 5.0 0.7 1.0

Zinc binding site 2 out of 4 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn9103 b:87.1 occ:1.00 SG D:CYS1112 2.3 90.2 1.0 SG D:CYS1201 2.3 85.2 1.0 SG D:CYS1204 2.3 85.7 1.0 SG D:CYS1194 2.4 89.3 1.0 CB D:CYS1204 3.2 79.7 1.0 CB D:CYS1112 3.3 88.8 1.0 CB D:CYS1201 3.6 78.2 1.0 CB D:CYS1194 3.6 84.0 1.0 O D:HOH2009 3.8 37.6 1.0 CA D:CYS1194 3.8 82.3 1.0 N D:CYS1201 3.9 74.0 1.0 OG1 D:THR1196 4.1 92.2 1.0 NH1 D:ARG1189 4.2 52.2 1.0 N D:GLN1195 4.2 88.2 1.0 CA D:CYS1201 4.3 73.8 1.0 N D:CYS1204 4.4 75.2 1.0 CA D:CYS1204 4.4 76.6 1.0 CA D:CYS1112 4.5 89.2 1.0 MG D:MG9312 4.5 20.0 1.0 C D:CYS1194 4.6 84.5 1.0 O D:CYS1112 4.6 89.7 1.0 N D:CYS1112 4.7 89.5 1.0 C D:CYS1201 4.9 71.6 1.0 N D:CYS1194 4.9 77.9 1.0 C D:VAL1200 4.9 74.1 1.0 C D:CYS1112 5.0 89.1 1.0

Zinc binding site 3 out of 4 in the Structural Basis For Transcription Regulation By Alarmone Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn9104 b:0.6 occ:1.00 SG N:CYS76 2.4 0.8 1.0 SG N:CYS73 2.4 1.0 1.0 SG N:CYS60 2.4 0.6 1.0 SG N:CYS58 2.5 0.3 1.0 CB N:CYS73 3.6 0.8 1.0 CB N:CYS76 3.7 0.3 1.0 CB N:CYS60 3.7 0.7 1.0 O N:CYS76 3.9 0.2 1.0 CB N:CYS58 4.0 0.8 1.0 N N:CYS60 4.0 0.8 1.0 C N:CYS76 4.4 0.8 1.0 CA N:CYS76 4.4 0.7 1.0 CA N:CYS60 4.4 0.6 1.0 N N:GLY61 4.6 0.7 1.0 N N:CYS76 4.6 0.9 1.0 N N:ALA59 4.7 0.3 1.0 CG2 N:VAL78 4.8 92.5 1.0 CG N:LYS62 4.8 0.7 1.0 CB N:LYS62 4.8 0.5 1.0 N N:LYS62 4.8 0.3 1.0 CB N:VAL78 4.9 92.4 1.0 C N:CYS60 5.0 0.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For Transcription Regulation By Alarmone Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn9105 b:80.4 occ:1.00 SG N:CYS1201 2.3 80.1 1.0 SG N:CYS1112 2.4 80.1 1.0 SG N:CYS1194 2.4 79.2 1.0 SG N:CYS1204 2.4 79.7 1.0 O N:HOH9487 3.1 23.4 1.0 CB N:CYS1204 3.3 78.7 1.0 CB N:CYS1112 3.3 79.7 1.0 CB N:CYS1194 3.4 76.8 1.0 CA N:CYS1194 3.6 75.9 1.0 CB N:CYS1201 3.6 74.7 1.0 NH2 N:ARG1189 3.7 57.1 1.0 N N:CYS1201 3.8 72.0 1.0 O N:HOH2611 3.9 84.3 1.0 N N:GLN1195 4.0 79.8 1.0 CA N:CYS1201 4.3 71.9 1.0 OG1 N:THR1196 4.3 82.0 1.0 C N:CYS1194 4.4 77.5 1.0 CA N:CYS1204 4.5 77.9 1.0 N N:CYS1204 4.5 77.1 1.0 CA N:CYS1112 4.6 80.3 1.0 N N:CYS1194 4.8 72.6 1.0 O N:CYS1112 4.8 81.0 1.0 CZ N:ARG1189 4.8 56.1 1.0 N N:CYS1112 4.8 79.9 1.0 C N:VAL1200 4.8 72.9 1.0 N N:THR1196 4.9 83.8 1.0 C N:CYS1201 4.9 70.4 1.0 CA N:VAL1200 5.0 73.9 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