Magnesium in PDB 5voi: X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex

All present enzymatic activity of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex:
2.7.7.6;

The structure of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex, PDB code: 5voi was solved by K.S.Murakami, Y.Shin, C.L.Turnbough Jr, V.Molodtsov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.180, 103.474, 294.444, 90.00, 99.14, 90.00
R / Rfree (%)	19.2 / 23.6

The structure of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex (pdb code 5voi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex, PDB code: 5voi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2003 b:44.0 occ:1.00 OD1 D:ASP739 2.1 48.7 1.0 OD1 D:ASP741 2.2 55.0 1.0 OD1 D:ASP743 2.2 42.7 1.0 OD2 D:ASP741 2.6 50.5 1.0 CG D:ASP741 2.8 39.2 1.0 OD2 D:ASP743 2.9 33.0 1.0 CG D:ASP743 2.9 34.9 1.0 CG D:ASP739 3.0 44.9 1.0 OD2 D:ASP739 3.3 56.8 1.0 CB D:ASP741 4.3 26.2 1.0 CB D:ASP739 4.4 26.9 1.0 CB D:ASP743 4.4 22.3 1.0 N D:ASP739 4.6 31.1 1.0 O D:ASP739 4.7 38.7 1.0 C D:ASP739 4.7 22.7 1.0 NH2 D:ARG704 4.8 20.4 1.0 CA D:ASP739 4.8 27.5 1.0 N D:ASP743 4.8 25.0 1.0 N D:ASP741 4.8 28.6 1.0 CA D:ASP741 5.0 27.2 1.0

Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2004 b:52.7 occ:1.00 O D:LYS840 2.2 97.0 1.0 OE2 B:GLU154 3.1 93.8 1.0 C D:LYS840 3.3 70.6 1.0 OE1 B:GLU64 3.8 93.6 1.0 OD2 B:ASP168 3.8 61.4 1.0 CD B:GLU154 4.0 96.6 1.0 OD1 B:ASP168 4.1 58.6 1.0 CA D:LYS840 4.1 73.3 1.0 O D:LEU839 4.2 67.0 1.0 OE2 B:GLU64 4.2 0.2 1.0 OE1 B:GLU154 4.2 98.9 1.0 CG B:ASP168 4.3 63.8 1.0 N D:TYR841 4.4 56.9 1.0 CD B:GLU64 4.4 94.5 1.0 CA D:TYR841 4.7 59.8 1.0 N D:VAL842 4.8 61.5 1.0 CB B:ALA153 4.8 57.6 1.0

Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:91.2 occ:1.00 OD2 F:ASP326 3.6 0.8 1.0 N6 G:DA18 3.6 75.1 1.0 N6 G:DA17 3.7 68.9 1.0 N7 G:DA16 4.1 52.0 1.0 OP2 G:DA16 4.1 86.9 1.0 OE1 F:GLU324 4.4 0.7 1.0 CG F:ASP326 4.5 99.5 1.0 CB F:ASP326 4.5 78.2 1.0 C8 G:DA16 4.6 51.3 1.0 N7 G:DA17 4.6 48.0 1.0 C6 G:DA18 4.6 68.3 1.0 C6 G:DA17 4.8 61.4 1.0 N1 G:DA18 4.9 85.7 1.0

K.S.Murakami, Y.Shin, C.L.Turnbough, V.Molodtsov. X-Ray Crystal Structure of A Reiterative Transcription Complex Reveals An Atypical Rna Extension Pathway. Proc. Natl. Acad. Sci. V. 114 8211 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28652344
DOI: 10.1073/PNAS.1702741114