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Calcium in PDB 1jxl: Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide

Enzymatic activity of Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide

All present enzymatic activity of Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide, PDB code: 1jxl was solved by H.Ling, F.Boudsocq, R.Woodgate, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 500.00 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.120, 101.880, 52.450, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.8

Other elements in 1jxl:

The structure of Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Magnesium (Mg) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide (pdb code 1jxl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide, PDB code: 1jxl:

Calcium binding site 1 out of 1 in 1jxl

Go back to Calcium Binding Sites List in 1jxl
Calcium binding site 1 out of 1 in the Crystal Structure of A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide


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 A Y-Family Dna Polymerase in A Ternary Complex with Dna Substrates and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1402

b:33.1
occ:1.00
 OD2 A:ASP105 2.2 34.3 1.0
OD1 A:ASP7 2.3 30.6 1.0
O2G A:DG3401 2.3 36.9 1.0
O A:HOH671 2.4 49.0 1.0
O A:PHE8 2.4 26.9 1.0
O2B A:DG3401 2.5 44.3 1.0
PG A:DG3401 3.3 42.6 1.0
PB A:DG3401 3.4 48.3 1.0
CG A:ASP7 3.4 30.2 1.0
MG A:MG1403 3.5 46.0 1.0
CG A:ASP105 3.5 32.0 1.0
C A:PHE8 3.5 26.7 1.0
O3B A:DG3401 3.6 45.4 1.0
O A:HOH517 3.7 42.0 1.0
MG A:MG1404 3.7 50.1 1.0
O1G A:DG3401 3.9 39.1 1.0
OD2 A:ASP7 3.9 33.4 1.0
N A:TYR10 4.1 27.3 0.1
N A:PHE8 4.1 26.4 1.0
O1B A:DG3401 4.1 48.7 1.0
N A:TYR10 4.3 26.2 0.9
CB A:ASP105 4.3 32.5 1.0
OD1 A:ASP105 4.3 33.5 1.0
CA A:PHE8 4.4 25.6 1.0
C A:ASP7 4.4 27.4 1.0
N A:ASP9 4.4 28.0 1.0
NZ A:LYS159 4.4 42.7 1.0
CA A:ASP9 4.4 26.8 1.0
C A:ASP9 4.5 27.3 1.0
N A:PHE11 4.6 27.0 1.0
O A:ASP105 4.6 28.0 1.0
CB A:ASP7 4.7 25.8 1.0
O A:ASP7 4.7 28.4 1.0
O3G A:DG3401 4.7 36.2 1.0
O3A A:DG3401 4.8 57.3 1.0
CA A:ASP7 4.9 25.8 1.0
CA A:TYR10 4.9 28.3 0.1
CB A:PHE8 5.0 24.4 1.0

Reference:

H.Ling, F.Boudsocq, R.Woodgate, W.Yang. Crystal Structure of A Y-Family Dna Polymerase in Action: A Mechanism For Error-Prone and Lesion-Bypass Replication. Cell(Cambridge,Mass.) V. 107 91 2001.
ISSN: ISSN 0092-8674
PubMed: 11595188
DOI: 10.1016/S0092-8674(01)00515-3
Page generated: Thu Jul 11 11:05:33 2024

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