Magnesium in PDB 6p70: X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrbi Promoter Complex

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

The structure of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrbi Promoter Complex, PDB code: 6p70 was solved by Y.Shin, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.06 / 3.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	185.179, 100.845, 294.865, 90.00, 98.81, 90.00
R / Rfree (%)	20.7 / 25.2

The structure of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrbi 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 Pyrbi Promoter Complex (pdb code 6p70). 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 Pyrbi Promoter Complex, PDB code: 6p70:
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 Pyrbi 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 Pyrbi Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:69.2 occ:1.00 O D:LYS840 2.0 75.3 1.0 OE2 B:GLU154 2.7 93.7 1.0 C D:LYS840 3.2 79.5 1.0 OD2 B:ASP168 3.4 91.2 1.0 CD B:GLU154 3.6 99.6 1.0 OE1 B:GLU154 3.7 99.5 1.0 OD1 B:ASP168 4.1 84.1 1.0 CA D:LYS840 4.1 75.4 1.0 O D:LEU839 4.1 72.5 1.0 N D:TYR841 4.1 80.0 1.0 CG B:ASP168 4.2 86.9 1.0 OE1 B:GLU64 4.4 0.5 1.0 CA D:TYR841 4.4 70.0 1.0 N D:VAL842 4.5 70.3 1.0 OE2 B:GLU64 4.7 99.5 1.0 CB B:ALA153 4.9 83.9 1.0 C D:TYR841 4.9 74.0 1.0 CD B:GLU64 5.0 0.2 1.0 CG B:GLU154 5.0 94.0 1.0

Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrbi 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 Pyrbi Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2003 b:50.4 occ:1.00 OD1 D:ASP739 2.1 63.6 1.0 OD1 D:ASP741 2.2 57.9 1.0 OD1 D:ASP743 2.4 55.8 1.0 CG D:ASP739 2.9 64.3 1.0 CG D:ASP741 2.9 64.5 1.0 OD2 D:ASP741 3.0 67.7 1.0 OD2 D:ASP739 3.2 73.5 1.0 CG D:ASP743 3.3 57.9 1.0 OD2 D:ASP743 3.4 58.9 1.0 CB D:ASP739 4.3 51.1 1.0 CB D:ASP741 4.4 60.6 1.0 CB D:ASP743 4.7 46.6 1.0 NH2 D:ARG704 4.7 67.4 1.0 N D:ASP739 4.8 52.5 1.0 N D:ASP743 4.9 50.1 1.0 N D:ASP741 4.9 57.8 1.0 CA D:ASP739 4.9 48.8 1.0 CA D:ASP741 5.0 56.1 1.0

Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrbi 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 Pyrbi Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:0.6 occ:1.00 C7 G:DT17 2.7 0.5 1.0 N4 G:DC18 2.8 0.2 1.0 OD2 F:ASP326 2.9 0.6 1.0 OP2 G:DG16 3.5 96.8 1.0 O4 G:DT17 3.8 0.7 1.0 C5 G:DT17 3.9 0.1 1.0 CG F:ASP326 4.0 1.0 1.0 C4 G:DC18 4.0 0.3 1.0 C4 G:DT17 4.3 0.1 1.0 P G:DG16 4.5 0.1 1.0 OE1 F:GLU324 4.5 0.1 1.0 OD1 F:ASP326 4.7 0.4 1.0 C5 G:DC18 4.7 0.4 1.0 OP1 G:DG16 4.8 0.5 1.0 O F:ASP326 4.8 0.9 1.0 O5' G:DG16 4.9 0.7 1.0 CB F:ASP326 4.9 0.6 1.0 N3 G:DC18 4.9 0.5 1.0

Y.Shin, K.S.Murakami. Structural Basis of Reiterative Transcription From the Pyrg Promoter To Be Published.