Zinc in PDB 3aoi: Rna Polymerase-GFH1 Complex (Crystal Type 2)

All present enzymatic activity of Rna Polymerase-GFH1 Complex (Crystal Type 2):
2.7.7.6;

The structure of Rna Polymerase-GFH1 Complex (Crystal Type 2), PDB code: 3aoi was solved by S.Tagami, S.Sekine, T.Kumarevel, M.Yamamoto, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 4.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	189.230, 264.510, 193.930, 90.00, 116.68, 90.00
R / Rfree (%)	31.7 / 33.8

The structure of Rna Polymerase-GFH1 Complex (Crystal Type 2) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Rna Polymerase-GFH1 Complex (Crystal Type 2) (pdb code 3aoi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Rna Polymerase-GFH1 Complex (Crystal Type 2), PDB code: 3aoi:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Rna Polymerase-GFH1 Complex (Crystal Type 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase-GFH1 Complex (Crystal Type 2) within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn2001 b:0.6 occ:1.00 SG N:CYS1112 2.1 0.9 1.0 SG N:CYS1194 2.4 0.8 1.0 SG N:CYS1201 2.6 95.3 1.0 CB N:CYS1112 2.8 0.5 1.0 SG N:CYS1204 3.1 0.0 1.0 N N:GLN1195 3.2 0.3 1.0 CB N:CYS1194 3.3 0.9 1.0 CA N:CYS1194 3.4 0.9 1.0 C N:CYS1194 3.8 0.5 1.0 CG N:GLN1195 4.0 0.9 1.0 CB N:CYS1201 4.0 97.2 1.0 N N:THR1196 4.1 0.4 1.0 CA N:CYS1112 4.2 0.6 1.0 CB N:CYS1204 4.2 0.6 1.0 N N:CYS1201 4.3 0.2 1.0 CA N:GLN1195 4.4 0.7 1.0 OG1 N:THR1196 4.4 0.2 1.0 CB N:GLN1195 4.6 1.0 1.0 N N:CYS1112 4.7 1.0 1.0 N N:CYS1194 4.7 0.2 1.0 C N:GLN1195 4.8 0.3 1.0 CA N:CYS1201 4.8 0.8 1.0 CB N:THR1196 4.8 0.4 1.0 C N:CYS1112 4.9 0.6 1.0 O N:CYS1112 5.0 0.3 1.0

Zinc binding site 2 out of 3 in the Rna Polymerase-GFH1 Complex (Crystal Type 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase-GFH1 Complex (Crystal Type 2) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.6 occ:1.00 SG D:CYS1194 2.0 0.8 1.0 SG D:CYS1112 2.3 0.9 1.0 SG D:CYS1204 2.3 0.0 1.0 CB D:CYS1194 3.1 0.9 1.0 SG D:CYS1201 3.1 95.3 1.0 CA D:CYS1194 3.3 0.9 1.0 CB D:CYS1112 3.3 0.5 1.0 CB D:CYS1204 3.4 0.6 1.0 N D:GLN1195 3.7 0.3 1.0 C D:CYS1194 4.0 0.5 1.0 N D:CYS1201 4.1 0.2 1.0 CB D:CYS1201 4.3 97.2 1.0 N D:CYS1194 4.5 0.2 1.0 CA D:CYS1112 4.7 0.6 1.0 CA D:CYS1201 4.7 0.8 1.0 CA D:CYS1204 4.8 0.7 1.0 CG D:GLN1195 4.8 0.9 1.0 N D:THR1196 4.8 0.4 1.0 O D:THR1193 4.8 0.8 1.0 N D:CYS1204 4.9 0.4 1.0 CA D:GLN1195 5.0 0.7 1.0 N D:CYS1112 5.0 1.0 1.0

Zinc binding site 3 out of 3 in the Rna Polymerase-GFH1 Complex (Crystal Type 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase-GFH1 Complex (Crystal Type 2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2003 b:0.6 occ:1.00 SG I:CYS1112 2.1 0.9 1.0 SG I:CYS1204 2.3 0.0 1.0 SG I:CYS1194 2.5 0.8 1.0 CB I:CYS1112 2.9 0.5 1.0 SG I:CYS1201 3.1 95.3 1.0 CA I:CYS1194 3.4 0.9 1.0 CB I:CYS1194 3.5 0.9 1.0 N I:GLN1195 3.6 0.3 1.0 CB I:CYS1204 3.7 0.6 1.0 C I:CYS1194 4.1 0.5 1.0 CA I:CYS1112 4.3 0.6 1.0 CB I:CYS1201 4.4 97.2 1.0 CG I:GLN1195 4.4 0.9 1.0 N I:CYS1201 4.5 0.2 1.0 N I:CYS1194 4.6 0.2 1.0 N I:CYS1112 4.6 1.0 1.0 O I:THR1193 4.8 0.8 1.0 O I:CYS1112 4.8 0.3 1.0 N I:THR1196 4.8 0.4 1.0 CA I:GLN1195 4.8 0.7 1.0 CG2 I:THR1114 4.9 0.4 1.0 C I:CYS1112 4.9 0.6 1.0 CA I:CYS1204 4.9 0.7 1.0 CB I:GLN1195 5.0 1.0 1.0

S.Tagami, S.I.Sekine, T.Kumarevel, N.Hino, Y.Murayama, S.Kamegamori, M.Yamamoto, K.Sakamoto, S.Yokoyama. Crystal Structure of Bacterial Rna Polymerase Bound with A Transcription Inhibitor Protein Nature V. 468 978 2010.
ISSN: ISSN 0028-0836
PubMed: 21124318
DOI: 10.1038/NATURE09573