Manganese in PDB 9bvt: Rna Pol II - High Mn(+2) Concentration

All present enzymatic activity of Rna Pol II - High Mn(+2) Concentration:
2.7.7.6;

The structure of Rna Pol II - High Mn(+2) Concentration, PDB code: 9bvt was solved by G.Calero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 3.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	221.19, 393.97, 283.28, 90, 90, 90
R / Rfree (%)	22 / 24.9

The structure of Rna Pol II - High Mn(+2) Concentration also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Manganese atom in the Rna Pol II - High Mn(+2) Concentration (pdb code 9bvt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Rna Pol II - High Mn(+2) Concentration, PDB code: 9bvt:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1803 b:30.0 occ:1.00 O3' X:A10 1.8 84.3 1.0 OD1 A:ASP483 1.9 81.5 1.0 OD1 A:ASP485 2.1 138.0 1.0 OD1 A:ASP481 2.2 81.0 1.0 CG A:ASP483 2.6 135.2 1.0 CG A:ASP481 2.6 104.8 1.0 CG A:ASP485 2.9 128.4 1.0 OD2 A:ASP481 2.9 86.6 1.0 OD2 A:ASP483 2.9 85.9 1.0 OD2 A:ASP485 3.0 91.5 1.0 C3' X:A10 3.0 160.5 1.0 C4' X:A10 3.3 169.8 1.0 CB A:ASP481 3.8 131.1 1.0 O A:ASP481 3.8 97.0 1.0 CB A:ASP483 3.9 136.6 1.0 C5' X:A10 4.0 207.3 1.0 N A:ASP483 4.0 149.0 1.0 C A:ASP483 4.0 89.6 1.0 O A:ASP483 4.1 122.5 1.0 CA A:ASP483 4.2 93.5 1.0 C A:ASP481 4.2 123.1 1.0 C2' X:A10 4.2 185.5 1.0 O2' X:A10 4.2 174.5 1.0 MN A:MN1804 4.2 30.0 0.8 CB A:ASP485 4.3 136.6 1.0 CA A:ASP481 4.3 110.7 1.0 N A:ASP481 4.3 116.0 1.0 O5' X:A10 4.4 216.8 1.0 NZ B:LYS987 4.4 170.6 1.0 N A:GLY484 4.5 80.7 1.0 N A:ASP485 4.6 79.7 1.0 OD2 B:ASP837 4.6 88.1 1.0 O4' X:A10 4.6 189.4 1.0 CE B:LYS987 4.8 159.2 1.0 C1' X:A10 4.8 174.9 1.0 CA A:ASP485 4.9 95.3 1.0

Manganese binding site 2 out of 2 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1804 b:30.0 occ:0.78 OD2 A:ASP481 2.3 86.6 1.0 OD2 A:ASP483 2.5 85.9 1.0 OD2 B:ASP837 2.6 88.1 1.0 CG A:ASP483 3.3 135.2 1.0 CG A:ASP481 3.4 104.8 1.0 CG B:ASP837 3.7 158.7 1.0 OD1 A:ASP483 3.7 81.5 1.0 CB A:ASP481 4.1 131.1 1.0 MN A:MN1803 4.2 30.0 1.0 OD1 B:ASP837 4.3 175.9 1.0 CB A:ASP483 4.4 136.6 1.0 OD1 A:ASP481 4.4 81.0 1.0 NZ B:LYS987 4.6 170.6 1.0 NH1 B:ARG1020 4.7 186.7 1.0 O3' X:A10 4.7 84.3 1.0 CB B:ASP837 4.7 161.1 1.0

G.Lin, C.O.Barnes, S.Weiss, B.Dutagaci, C.Qiu, M.Feig, J.Song, A.Lyubimov, A.E.Cohen, C.D.Kaplan, G.Calero. Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser. Proc.Natl.Acad.Sci.Usa V. 121 27121 2024.
ISSN: ESSN 1091-6490
PubMed: 39190355
DOI: 10.1073/PNAS.2318527121