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Magnesium in PDB 4y7n: The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.

Enzymatic activity of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.

All present enzymatic activity of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.:
2.7.7.6;

Protein crystallography data

The structure of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y7n was solved by L.Wang, J.Chong, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.88 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.181, 222.614, 192.829, 90.00, 101.59, 90.00
R / Rfree (%) 20.7 / 25

Other elements in 4y7n:

The structure of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. (pdb code 4y7n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y7n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4y7n

Go back to Magnesium Binding Sites List in 4y7n
Magnesium binding site 1 out of 2 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:42.8
occ:1.00
OD1 A:ASP481 2.1 72.6 1.0
O3' R:G9 2.1 56.3 1.0
OD2 A:ASP485 2.2 62.9 1.0
OD2 A:ASP481 2.4 69.6 1.0
OD1 A:ASP483 2.5 58.2 1.0
OD1 A:ASP485 2.5 66.8 1.0
CG A:ASP481 2.5 72.3 1.0
CG A:ASP485 2.7 63.5 1.0
O2' R:G9 2.8 56.4 1.0
C3' R:G9 3.2 56.9 1.0
CG A:ASP483 3.4 62.5 1.0
OD2 A:ASP483 3.5 65.1 1.0
C2' R:G9 3.5 54.7 1.0
O2A T:G2P101 3.6 89.0 1.0
C4' R:G9 3.7 53.3 1.0
CB A:ASP481 4.0 69.1 1.0
CB A:ASP485 4.1 62.6 1.0
N A:ASP481 4.4 67.8 1.0
NH2 A:ARG446 4.6 57.9 1.0
O4' R:G9 4.6 54.0 1.0
C5' T:G2P101 4.7 81.6 1.0
C1' R:G9 4.7 49.8 1.0
O A:ASP481 4.7 62.9 1.0
C5' R:G9 4.7 49.6 1.0
CA A:ASP481 4.8 64.1 1.0
CB A:ASP483 4.8 60.5 1.0
O1A T:G2P101 4.8 81.1 1.0
N A:ASP485 4.8 59.9 1.0
PA T:G2P101 4.8 94.3 1.0
C A:ASP481 4.8 63.2 1.0
N A:ASP483 4.9 61.3 1.0
CA A:ASP485 4.9 59.2 1.0

Magnesium binding site 2 out of 2 in 4y7n

Go back to Magnesium Binding Sites List in 4y7n
Magnesium binding site 2 out of 2 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1804

b:87.9
occ:1.00
O3G T:G2P101 2.5 0.8 1.0
C5' T:G2P101 2.8 81.6 1.0
O1B T:G2P101 3.2 0.9 1.0
O5' T:G2P101 3.3 82.4 1.0
O3B T:G2P101 3.6 0.5 1.0
PG T:G2P101 3.7 0.5 1.0
PB T:G2P101 3.9 0.8 1.0
O2A T:G2P101 4.0 89.0 1.0
C4' T:G2P101 4.0 72.7 1.0
O3' T:G2P101 4.1 75.4 1.0
PA T:G2P101 4.2 94.3 1.0
C3' T:G2P101 4.2 72.2 1.0
O2G T:G2P101 4.5 0.0 1.0
ND2 A:ASN479 4.5 67.8 1.0
C3A T:G2P101 4.6 0.6 1.0
OD1 A:ASN479 4.6 56.4 1.0
O1G T:G2P101 4.8 0.6 1.0

Reference:

L.Wang, Y.Zhou, L.Xu, R.Xiao, X.Lu, L.Chen, J.Chong, H.Li, C.He, X.D.Fu, D.Wang. Molecular Basis For 5-Carboxycytosine Recognition By Rna Polymerase II Elongation Complex. Nature V. 523 621 2015.
ISSN: ESSN 1476-4687
PubMed: 26123024
DOI: 10.1038/NATURE14482
Page generated: Sat Sep 28 22:51:46 2024

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