Magnesium in PDB 8u9r: Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser

Enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser

All present enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser:
2.7.7.6;

Protein crystallography data

The structure of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser, PDB code: 8u9r was solved by P.Arjunan, G.Calero, C.D.Kaplan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 3.34
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 217.195, 387.44, 276.955, 90, 90, 90
R / Rfree (%) 25.5 / 26.1

Other elements in 8u9r:

The structure of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser (pdb code 8u9r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser, PDB code: 8u9r:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8u9r

Go back to Magnesium Binding Sites List in 8u9r
Magnesium binding site 1 out of 3 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1804

b:94.9
occ:1.00
 O2A A:ATP1806 1.9 113.1 1.0
OD1 A:ASP481 2.1 122.2 1.0
OD1 A:ASP485 2.2 82.5 1.0
OD1 A:ASP483 2.2 99.1 1.0
CG A:ASP481 2.5 121.0 1.0
OD2 A:ASP481 2.5 112.5 1.0
CG A:ASP485 3.3 76.8 1.0
CG A:ASP483 3.3 96.5 1.0
PA A:ATP1806 3.4 129.8 1.0
C3' R:G10 3.6 93.6 1.0
OD2 A:ASP485 3.7 79.5 1.0
CB A:ASP481 3.8 100.1 1.0
O A:ASP483 3.9 84.9 1.0
OD2 A:ASP483 3.9 103.2 1.0
MG A:MG1805 4.0 105.0 1.0
N A:ASP481 4.2 98.7 1.0
O1A A:ATP1806 4.2 129.3 1.0
O5' A:ATP1806 4.2 122.1 1.0
C4' R:G10 4.3 87.6 1.0
O A:ASP481 4.3 95.4 1.0
CA A:ASP481 4.4 95.9 1.0
O3A A:ATP1806 4.4 127.9 1.0
O2B A:ATP1806 4.4 122.0 1.0
C A:ASP481 4.4 94.0 1.0
NZ B:LYS987 4.5 97.7 1.0
CB A:ASP483 4.5 87.9 1.0
C5' R:G10 4.5 89.2 1.0
C4' A:ATP1806 4.5 121.3 1.0
CB A:ASP485 4.6 67.5 1.0
N A:ASP483 4.6 82.3 1.0
C2' R:G10 4.7 97.8 1.0
C A:ASP483 4.8 80.7 1.0
C5' A:ATP1806 4.8 121.9 1.0
O2' R:G10 4.8 91.0 1.0
CA A:ASP483 4.9 81.8 1.0

Magnesium binding site 2 out of 3 in 8u9r

Go back to Magnesium Binding Sites List in 8u9r
Magnesium binding site 2 out of 3 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1805

b:105.0
occ:1.00
 OD2 A:ASP483 2.0 103.2 1.0
O2B A:ATP1806 2.2 122.0 1.0
OD2 A:ASP481 2.3 112.5 1.0
CG A:ASP483 2.5 96.5 1.0
OD1 A:ASP483 2.8 99.1 1.0
NH2 B:ARG1020 3.3 77.5 1.0
OD2 B:ASP837 3.4 112.0 1.0
CG A:ASP481 3.4 121.0 1.0
PB A:ATP1806 3.7 128.3 1.0
O3G A:ATP1806 3.8 133.7 1.0
CB A:ASP483 3.8 87.9 1.0
CB B:ASP837 3.9 99.5 1.0
CB A:ASP481 3.9 100.1 1.0
MG A:MG1804 4.0 94.9 1.0
O2A A:ATP1806 4.0 113.1 1.0
CG B:ASP837 4.1 107.3 1.0
O3A A:ATP1806 4.1 127.9 1.0
CZ B:ARG1020 4.3 83.3 1.0
O3B A:ATP1806 4.3 129.4 1.0
NE B:ARG1020 4.4 95.5 1.0
OD1 A:ASP481 4.4 122.2 1.0
CE B:LYS987 4.5 91.9 1.0
CG B:LYS987 4.7 70.1 1.0
PA A:ATP1806 4.7 129.8 1.0
PG A:ATP1806 4.7 133.2 1.0
CD B:LYS987 4.8 76.1 1.0
NZ B:LYS987 4.8 97.7 1.0
O1B A:ATP1806 4.8 127.2 1.0

Magnesium binding site 3 out of 3 in 8u9r

Go back to Magnesium Binding Sites List in 8u9r
Magnesium binding site 3 out of 3 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:92.1
occ:1.00
 O1A A:ATP1806 2.7 129.3 1.0
OE1 B:GLU529 3.7 94.1 1.0
PA A:ATP1806 4.1 129.8 1.0
NZ B:LYS987 4.1 97.7 1.0
OH B:TYR769 4.3 105.3 1.0
OP2 R:G10 4.4 100.1 1.0
C5' A:ATP1806 4.4 121.9 1.0
O3A A:ATP1806 4.5 127.9 1.0
O5' A:ATP1806 4.6 122.1 1.0
CE2 B:TYR769 4.6 105.3 1.0
CZ B:TYR769 4.6 106.4 1.0
O5' R:G10 4.6 93.1 1.0
C8 A:ATP1806 4.7 116.9 1.0
CD B:GLU529 4.7 95.9 1.0
N7 A:ATP1806 4.8 117.8 1.0
P R:G10 5.0 95.0 1.0

Reference:

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
Page generated: Fri Oct 4 21:14:24 2024

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