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Magnesium in PDB 3k5l: Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex

Enzymatic activity of Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex

All present enzymatic activity of Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex, PDB code: 3k5l was solved by W.Yang, F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.42 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.974, 101.198, 121.717, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex (pdb code 3k5l). 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 E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex, PDB code: 3k5l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3k5l

Go back to Magnesium Binding Sites List in 3k5l
Magnesium binding site 1 out of 2 in the Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex


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 E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:23.5
occ:1.00
O A:TYR420 1.9 19.8 1.0
OD1 A:ASP419 2.0 17.3 1.0
OD2 A:ASP547 2.1 18.7 1.0
O1A A:DTP914 2.1 15.4 1.0
O1G A:DTP914 2.2 11.1 1.0
O1B A:DTP914 2.3 13.2 1.0
C A:TYR420 3.1 18.4 1.0
CG A:ASP547 3.1 17.8 1.0
CG A:ASP419 3.2 17.3 1.0
PB A:DTP914 3.3 14.7 1.0
PG A:DTP914 3.4 9.6 1.0
PA A:DTP914 3.4 16.1 1.0
OD1 A:ASP547 3.5 19.5 1.0
N A:TYR420 3.8 17.6 1.0
O3B A:DTP914 3.8 13.4 1.0
OD2 A:ASP419 3.9 17.1 1.0
O3A A:DTP914 3.9 14.7 1.0
CA A:TYR420 3.9 18.1 1.0
C5' A:DTP914 4.0 19.1 1.0
O2G A:DTP914 4.0 10.8 1.0
N A:LYS421 4.1 18.1 1.0
N A:SER422 4.2 16.5 1.0
CB A:ASP419 4.3 16.1 1.0
CB A:ASP547 4.3 15.4 1.0
CA A:LYS421 4.3 17.5 1.0
C A:ASP419 4.3 17.3 1.0
O5' A:DTP914 4.3 18.1 1.0
CB A:TYR420 4.5 17.9 1.0
MG A:MG1002 4.5 17.9 1.0
O2A A:DTP914 4.5 16.0 1.0
C A:LYS421 4.5 16.4 1.0
N A:LEU423 4.6 15.9 1.0
O3G A:DTP914 4.7 11.3 1.0
O2B A:DTP914 4.7 15.5 1.0
CA A:ASP419 4.8 15.9 1.0
O A:ASP419 4.9 17.4 1.0
CB A:LEU423 5.0 14.0 1.0

Magnesium binding site 2 out of 2 in 3k5l

Go back to Magnesium Binding Sites List in 3k5l
Magnesium binding site 2 out of 2 in the Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex


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 E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:17.9
occ:1.00
OD1 A:ASP547 2.5 19.5 1.0
OD2 A:ASP419 2.8 17.1 1.0
O1A A:DTP914 3.2 15.4 1.0
C3' P:DOC913 3.3 16.8 1.0
O A:HOH804 3.6 3.8 1.0
CG A:ASP547 3.7 17.8 1.0
CG A:ASP419 3.8 17.3 1.0
O2A A:DTP914 3.8 16.0 1.0
PA A:DTP914 3.9 16.1 1.0
O5' A:DTP914 3.9 18.1 1.0
O A:ASP545 3.9 19.1 1.0
C5' P:DOC913 4.0 15.8 1.0
OD1 A:ASP419 4.0 17.3 1.0
O5' P:DOC913 4.1 17.1 1.0
C4' P:DOC913 4.1 16.8 1.0
CB A:SER548 4.2 9.1 1.0
C2' P:DOC913 4.2 17.1 1.0
OD2 A:ASP547 4.2 18.7 1.0
OG A:SER548 4.3 7.1 1.0
C5' A:DTP914 4.5 19.1 1.0
N A:SER548 4.5 11.7 1.0
N A:ASP547 4.5 14.4 1.0
MG A:MG1001 4.5 23.5 1.0
C A:ASP547 4.7 13.0 1.0
CB A:ASP547 4.9 15.4 1.0
CA A:ASP547 4.9 13.5 1.0
CA A:SER548 5.0 10.3 1.0

Reference:

F.Wang, W.Yang. Structural Insight Into Translesion Synthesis By Dna Pol II. Cell(Cambridge,Mass.) V. 139 1279 2009.
ISSN: ISSN 0092-8674
PubMed: 20064374
DOI: 10.1016/J.CELL.2009.11.043
Page generated: Mon Dec 14 08:21:31 2020

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