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Bromine 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:

Magnesium (Mg) 3 atoms
Calcium (Ca) 1 atom

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine where 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:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 1jxl

Go back to Bromine Binding Sites List in 1jxl
Bromine binding site 1 out of 2 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 Bromine with other atoms in the Br 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
T:Br7

b:55.3
occ:1.00
BR T:BRU7 0.0 55.3 1.0
C5 T:BRU7 1.9 39.9 1.0
C6 T:BRU7 2.8 41.1 1.0
C4 T:BRU7 2.9 38.0 1.0
O4 T:BRU7 3.2 32.4 1.0
O T:HOH604 3.7 57.0 1.0
C8 T:DA6 3.8 32.5 1.0
C2' T:DA6 3.9 35.6 1.0
N9 T:DA6 4.0 34.0 1.0
NE A:ARG336 4.0 44.4 1.0
N7 T:DA6 4.1 33.0 1.0
N1 T:BRU7 4.2 41.2 1.0
N3 T:BRU7 4.2 36.0 1.0
OG A:SER244 4.2 34.3 1.0
N4 T:DC8 4.3 31.5 1.0
C4 T:DA6 4.3 32.8 1.0
C5 T:DA6 4.4 31.3 1.0
CD A:ARG336 4.4 40.6 1.0
C1' T:DA6 4.4 35.4 1.0
C2 T:BRU7 4.7 38.4 1.0
CZ A:ARG336 4.8 44.5 1.0
O T:HOH689 4.9 53.1 1.0
C4 T:DC8 5.0 35.9 1.0

Bromine binding site 2 out of 2 in 1jxl

Go back to Bromine Binding Sites List in 1jxl
Bromine binding site 2 out of 2 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 Bromine with other atoms in the Br binding site number 2 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
T:Br11

b:56.9
occ:1.00
BR T:BRU11 0.0 56.9 1.0
C5 T:BRU11 1.9 47.1 1.0
C6 T:BRU11 2.8 47.2 1.0
C4 T:BRU11 2.8 44.3 1.0
O4 T:BRU11 3.1 37.4 1.0
O T:HOH723 3.3 49.7 1.0
O T:HOH775 3.5 44.0 1.0
O T:HOH532 3.5 36.8 1.0
C2' T:DT10 3.6 47.9 1.0
C6 T:DT10 3.6 38.2 1.0
N1 T:DT10 3.9 40.3 1.0
C5 T:DT10 4.0 38.0 1.0
N4 T:DC12 4.0 31.9 1.0
N3 T:BRU11 4.1 42.5 1.0
N1 T:BRU11 4.1 47.4 1.0
C1' T:DT10 4.3 44.2 1.0
C7 T:DT10 4.4 38.4 1.0
C2 T:DT10 4.5 40.3 1.0
C4 T:DT10 4.7 37.3 1.0
C2 T:BRU11 4.7 45.2 1.0
C5 T:DC12 4.7 38.1 1.0
C4 T:DC12 4.7 36.3 1.0
O5' T:BRU11 4.7 58.7 1.0
N3 T:DT10 4.8 37.6 1.0
C3' T:DT10 4.9 49.7 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: Sat Dec 12 02:01:58 2020

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