Zinc in PDB 3aoh: Rna Polymerase-GFH1 Complex (Crystal Type 1)

All present enzymatic activity of Rna Polymerase-GFH1 Complex (Crystal Type 1):
2.7.7.6;

The structure of Rna Polymerase-GFH1 Complex (Crystal Type 1), PDB code: 3aoh 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)	49.87 / 4.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	192.760, 260.700, 198.560, 90.00, 117.58, 90.00
R / Rfree (%)	26.2 / 31.8

The structure of Rna Polymerase-GFH1 Complex (Crystal Type 1) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Rna Polymerase-GFH1 Complex (Crystal Type 1) (pdb code 3aoh). 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 1), PDB code: 3aoh:
Jump to Zinc binding site number: 1; 2; 3;

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


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 1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:95.0 occ:1.00 SG D:CYS1201 2.5 0.7 1.0 SG D:CYS1194 2.8 0.2 1.0 SG D:CYS1112 2.8 0.5 1.0 CB D:CYS1204 2.8 0.3 1.0 SG D:CYS1204 2.9 0.7 1.0 CB D:CYS1201 3.6 0.5 1.0 N D:CYS1201 3.6 0.9 1.0 CB D:CYS1194 3.9 0.3 1.0 CB D:CYS1112 3.9 0.0 1.0 CA D:CYS1201 4.0 0.5 1.0 CA D:CYS1204 4.0 0.0 1.0 CA D:CYS1194 4.0 0.3 1.0 N D:CYS1204 4.0 0.8 1.0 O D:CYS1201 4.2 0.4 1.0 C D:CYS1201 4.4 0.4 1.0 N D:GLN1195 4.6 0.2 1.0 C D:VAL1200 4.8 0.2 1.0 CG1 D:VAL1200 4.8 93.6 1.0 O D:CYS1112 4.8 0.9 1.0 NH1 D:ARG1189 4.8 0.4 1.0 N D:CYS1112 4.9 0.6 1.0 CA D:CYS1112 4.9 0.2 1.0 C D:CYS1194 4.9 0.8 1.0

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


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 1) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2002 b:95.0 occ:1.00 SG I:CYS1204 2.4 0.6 1.0 SG I:CYS1112 2.6 0.1 1.0 SG I:CYS1194 3.0 0.2 1.0 CA I:CYS1194 3.0 0.3 1.0 SG I:CYS1201 3.2 78.0 1.0 CB I:CYS1194 3.3 0.3 1.0 CB I:CYS1204 3.4 0.2 1.0 N I:GLN1195 3.6 1.0 1.0 C I:CYS1194 3.8 0.9 1.0 O I:THR1193 3.9 0.6 1.0 N I:CYS1194 4.0 0.6 1.0 CB I:CYS1112 4.0 0.6 1.0 C I:THR1193 4.3 0.6 1.0 CB I:CYS1201 4.5 79.9 1.0 O I:SER1190 4.7 0.5 1.0 N I:CYS1201 4.7 0.7 1.0 CA I:CYS1204 4.8 88.4 1.0 O I:CYS1112 4.8 0.5 1.0 NH1 I:ARG1189 4.8 0.9 1.0 CG I:GLN1195 4.8 0.1 1.0 CA I:GLN1195 4.9 0.4 1.0

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


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 1) within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn2003 b:95.0 occ:1.00 SG N:CYS1201 2.5 0.5 1.0 SG N:CYS1112 2.5 0.3 1.0 SG N:CYS1204 3.0 0.5 1.0 CB N:CYS1112 3.1 0.8 1.0 SG N:CYS1194 3.2 0.9 1.0 CB N:CYS1204 3.4 0.1 1.0 CB N:CYS1201 3.6 0.4 1.0 CA N:CYS1194 4.0 0.6 1.0 CB N:CYS1194 4.1 0.0 1.0 O N:CYS1112 4.1 0.2 1.0 CA N:CYS1112 4.2 0.4 1.0 N N:CYS1201 4.3 0.3 1.0 N N:GLN1195 4.3 0.9 1.0 N N:CYS1112 4.4 0.8 1.0 CA N:CYS1201 4.5 0.9 1.0 N N:CYS1204 4.5 0.6 1.0 CA N:CYS1204 4.6 0.8 1.0 C N:CYS1112 4.6 0.5 1.0 NH1 N:ARG1189 4.7 0.1 1.0 C N:CYS1194 4.7 0.1 1.0 O N:THR1193 4.9 0.9 1.0 O N:CYS1201 5.0 0.7 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