Atomistry » Calcium » PDB 3k5m-3km5 » 3k5m
Atomistry »
  Calcium »
    PDB 3k5m-3km5 »
      3k5m »

Calcium in PDB 3k5m: Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex

Enzymatic activity of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex

All present enzymatic activity of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex, PDB code: 3k5m 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) 28.43 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.109, 95.228, 144.735, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex (pdb code 3k5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex, PDB code: 3k5m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3k5m

Go back to Calcium Binding Sites List in 3k5m
Calcium binding site 1 out of 2 in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:32.6
occ:1.00
OD2 A:ASP547 1.9 40.3 1.0
O1G A:DG3914 2.3 39.9 1.0
OD2 A:ASP419 2.4 39.2 1.0
O1B A:DG3914 2.5 42.3 1.0
O A:TYR420 2.5 30.1 1.0
O1A A:DG3914 2.5 40.2 1.0
CG A:ASP547 3.0 34.0 1.0
PA A:DG3914 3.3 36.8 1.0
PB A:DG3914 3.3 43.2 1.0
CG A:ASP419 3.4 36.7 1.0
O3A A:DG3914 3.4 40.7 1.0
PG A:DG3914 3.5 40.1 1.0
C A:TYR420 3.6 28.4 1.0
O5' A:DG3914 3.7 40.2 1.0
OD1 A:ASP419 3.7 39.7 1.0
OD1 A:ASP547 3.8 31.5 1.0
O3B A:DG3914 3.9 42.5 1.0
O A:HOH1115 4.0 39.7 1.0
CB A:ASP547 4.0 31.7 1.0
N A:SER422 4.0 27.1 1.0
O A:HOH826 4.1 35.5 1.0
O2G A:DG3914 4.2 41.6 1.0
C5' A:DG3914 4.2 34.2 1.0
CA A:LYS421 4.2 28.3 1.0
CA A:CA1002 4.3 59.1 1.0
N A:LYS421 4.3 28.9 1.0
N A:TYR420 4.4 27.4 1.0
C A:LYS421 4.5 27.4 1.0
CA A:TYR420 4.6 28.0 1.0
C A:ASP419 4.7 30.4 1.0
CB A:ASP419 4.7 35.3 1.0
O2B A:DG3914 4.8 44.7 1.0
N A:LEU423 4.8 24.4 1.0
O3G A:DG3914 4.8 43.7 1.0
O2A A:DG3914 4.8 38.6 1.0
CA A:SER422 4.9 27.8 1.0

Calcium binding site 2 out of 2 in 3k5m

Go back to Calcium Binding Sites List in 3k5m
Calcium binding site 2 out of 2 in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:59.1
occ:1.00
OD1 A:ASP419 2.8 39.7 1.0
OD1 A:ASP547 2.9 31.5 1.0
O1B A:DG3914 3.3 42.3 1.0
C3' P:DG913 3.5 27.7 1.0
OD2 A:ASP547 3.7 40.3 1.0
CG A:ASP547 3.7 34.0 1.0
O3' P:DG913 3.7 26.6 1.0
CG A:ASP419 3.9 36.7 1.0
C2' P:DG913 4.1 27.0 1.0
O A:HOH1115 4.1 39.7 1.0
O5' P:DG913 4.2 24.0 1.0
OD2 A:ASP419 4.3 39.2 1.0
CA A:CA1001 4.3 32.6 1.0
C5' A:DG3914 4.4 34.2 1.0
PB A:DG3914 4.6 43.2 1.0
C4' P:DG913 4.7 26.8 1.0
CB A:SER548 4.8 31.1 1.0
C5' P:DG913 4.8 23.4 1.0
O5' A:DG3914 4.8 40.2 1.0
O2B A:DG3914 4.8 44.7 1.0
OP2 P:DG913 4.9 21.4 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: Sat Dec 12 04:16:57 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy