Magnesium 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:

Zinc

(Zn)

3 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of Rna Polymerase-GFH1 Complex (Crystal Type 2) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2004 b:0.6 occ:1.00 OD1 D:ASP739 1.9 97.2 1.0 O3' Q:G16 2.2 0.4 1.0 CG D:ASP739 2.4 97.6 1.0 OD2 D:ASP739 2.5 0.4 1.0 OD2 D:ASP741 3.1 0.1 1.0 OD1 D:ASP741 3.2 0.5 1.0 OD2 D:ASP743 3.4 0.8 1.0 OD1 D:ASP743 3.4 0.1 1.0 C3' Q:G16 3.4 0.4 1.0 CG D:ASP741 3.4 0.5 1.0 O2' Q:G16 3.6 0.2 1.0 CB D:ASP739 3.8 97.5 1.0 CG D:ASP743 3.8 0.6 1.0 C2' Q:G16 4.0 0.4 1.0 C4' Q:G16 4.2 0.4 1.0 N D:ASP739 4.4 0.8 1.0 CA D:ASP739 4.6 0.1 1.0 OD1 X:ASP44 4.8 0.2 1.0 CB D:ASP741 4.8 0.0 1.0 O D:ASP739 4.9 0.8 1.0 C D:ASP739 4.9 0.7 1.0 C5' Q:G16 4.9 0.4 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of Rna Polymerase-GFH1 Complex (Crystal Type 2) within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg2005 b:0.6 occ:1.00 O3' S:G16 1.6 0.4 1.0 C3' S:G16 2.4 0.4 1.0 C5' S:G16 3.1 0.4 1.0 C4' S:G16 3.2 0.4 1.0 OD1 I:ASP739 3.3 97.2 1.0 OD1 I:ASP743 3.5 0.1 1.0 C2' S:G16 3.8 0.4 1.0 OD1 I:ASP741 3.9 0.5 1.0 OD2 I:ASP741 3.9 0.1 1.0 CG I:ASP739 3.9 97.6 1.0 OD2 I:ASP739 4.0 0.4 1.0 O5' S:G16 4.1 0.4 1.0 OD2 I:ASP743 4.2 0.8 1.0 CG I:ASP743 4.3 0.6 1.0 CG I:ASP741 4.3 0.5 1.0 O4' S:G16 4.4 0.4 1.0 O2' S:G16 4.4 0.4 1.0 NH2 I:ARG704 4.5 0.6 1.0 C1' S:G16 4.7 0.4 1.0 OP1 S:G16 4.8 0.4 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 3 of Rna Polymerase-GFH1 Complex (Crystal Type 2) within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg2006 b:0.6 occ:1.00 OD1 N:ASP739 2.0 97.2 1.0 CG N:ASP739 2.3 97.6 1.0 OD2 N:ASP739 2.6 0.4 1.0 CB N:ASP739 3.4 97.5 1.0 OD1 N:ASP743 3.8 0.1 1.0 OD1 N:ASP741 3.9 0.5 1.0 OD2 N:ASP741 3.9 0.1 1.0 OD2 N:ASP743 4.0 0.8 1.0 O3' U:G16 4.0 0.4 1.0 N N:ASP739 4.1 0.8 1.0 CG N:ASP741 4.2 0.5 1.0 CG N:ASP743 4.3 0.6 1.0 CA N:ASP739 4.3 0.1 1.0 OD1 Z:ASP44 4.5 0.1 1.0 C N:ASP739 4.9 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