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Magnesium in PDB 5c3e: Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble

Enzymatic activity of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble

All present enzymatic activity of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble, PDB code: 5c3e was solved by C.O.Barnes, M.Calero, I.Malik, H.Spahr, Q.Zhang, F.Pullara, C.D.Kaplan, G.Calero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 219.050, 390.940, 278.080, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22

Other elements in 5c3e:

The structure of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble also contains other interesting chemical elements:

Zinc (Zn) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble (pdb code 5c3e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble, PDB code: 5c3e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5c3e

Go back to Magnesium Binding Sites List in 5c3e
Magnesium binding site 1 out of 2 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:82.6
occ:1.00
O2' R:A10 2.3 0.5 1.0
OD1 A:ASP481 2.5 0.0 1.0
C2' R:A10 2.9 0.4 1.0
OD2 A:ASP481 2.9 0.7 1.0
CG A:ASP481 3.0 0.9 1.0
C3' R:A10 3.3 0.3 1.0
OD1 A:ASP483 3.9 0.5 1.0
OD2 A:ASP485 4.0 78.8 1.0
OD2 A:ASP483 4.1 0.7 1.0
C1' R:A10 4.4 0.8 1.0
CG A:ASP483 4.4 0.5 1.0
NH2 A:ARG446 4.5 97.9 1.0
CB A:ASP481 4.5 0.8 1.0
C4' R:A10 4.6 0.1 1.0
N A:ASP481 4.8 0.1 1.0
CG A:ASP485 5.0 76.8 1.0

Magnesium binding site 2 out of 2 in 5c3e

Go back to Magnesium Binding Sites List in 5c3e
Magnesium binding site 2 out of 2 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1804

b:63.3
occ:1.00
O A:LEU1418 3.7 0.3 1.0
O A:THR1394 3.8 76.8 1.0
CA A:GLY1395 3.8 0.8 1.0
CG A:GLU1417 4.0 97.9 1.0
O A:ASN1393 4.1 83.1 1.0
N A:ALA1396 4.1 85.7 1.0
C A:THR1394 4.2 79.6 1.0
N A:GLY1395 4.2 99.8 1.0
C A:LEU1418 4.2 0.1 1.0
CB A:GLU1417 4.3 79.4 1.0
N A:LEU1418 4.3 98.7 1.0
C A:GLY1395 4.4 0.5 1.0
N A:ASP1419 4.7 79.8 1.0
OD1 A:ASP1420 4.8 0.6 1.0
CA A:ASP1419 4.8 76.9 1.0
OE1 A:GLU1417 4.9 1.0 1.0
CA A:GLU1417 4.9 0.0 1.0
CD A:GLU1417 4.9 0.5 1.0
CA A:LEU1418 5.0 95.2 1.0

Reference:

C.O.Barnes, M.Calero, I.Malik, B.W.Graham, H.Spahr, G.Lin, A.E.Cohen, I.S.Brown, Q.Zhang, F.Pullara, M.A.Trakselis, C.D.Kaplan, G.Calero. Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble. Mol.Cell V. 59 258 2015.
ISSN: ISSN 1097-2765
PubMed: 26186291
DOI: 10.1016/J.MOLCEL.2015.06.034
Page generated: Mon Dec 14 20:05:33 2020

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