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Magnesium 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
Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1jxl

Go back to Magnesium Binding Sites List in 1jxl
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg1403

b:46.0
occ:1.00
 OE2 A:GLU106 1.9 44.0 1.0
O2B A:DG3401 2.2 44.3 1.0
OD2 A:ASP7 2.6 33.4 1.0
O2A A:DG3401 2.9 64.1 1.0
CD A:GLU106 2.9 37.9 1.0
CG A:GLU106 3.1 36.7 1.0
OD2 A:ASP105 3.1 34.3 1.0
CG A:ASP7 3.2 30.2 1.0
OD1 A:ASP7 3.3 30.6 1.0
CA A:CA1402 3.5 33.1 1.0
O A:HOH670 3.5 58.1 1.0
OD1 A:ASP105 3.5 33.5 1.0
PB A:DG3401 3.5 48.3 1.0
CG A:ASP105 3.7 32.0 1.0
PA A:DG3401 3.9 64.4 1.0
O3A A:DG3401 3.9 57.3 1.0
C5' A:DG3401 4.0 64.3 1.0
OE1 A:GLU106 4.0 39.6 1.0
O5' A:DG3401 4.3 65.0 1.0
NZ A:LYS159 4.3 42.7 1.0
O3B A:DG3401 4.5 45.4 1.0
NZ A:LYS152 4.5 39.3 1.0
O A:HOH671 4.5 49.0 1.0
CB A:ASP7 4.5 25.8 1.0
O A:ASP105 4.6 28.0 1.0
CB A:GLU106 4.6 31.8 1.0
O A:HOH596 4.7 51.9 1.0
O1B A:DG3401 4.7 48.7 1.0
C A:ASP105 5.0 28.6 1.0

Magnesium binding site 2 out of 3 in 1jxl

Go back to Magnesium Binding Sites List in 1jxl
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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
A:Mg1404

b:50.1
occ:1.00
 O1G A:DG3401 1.9 39.1 1.0
O A:HOH671 2.0 49.0 1.0
O1B A:DG3401 2.4 48.7 1.0
CE1 A:TYR10 2.7 36.0 0.1
O A:HOH683 2.7 51.9 1.0
CD1 A:TYR10 2.8 34.6 0.1
PG A:DG3401 3.0 42.6 1.0
PB A:DG3401 3.3 48.3 1.0
O2G A:DG3401 3.4 36.9 1.0
O3B A:DG3401 3.6 45.4 1.0
NH1 A:ARG51 3.6 57.7 1.0
NH2 A:ARG51 3.7 54.2 1.0
CA A:CA1402 3.7 33.1 1.0
O2B A:DG3401 3.8 44.3 1.0
N A:TYR10 3.8 27.3 0.1
N A:TYR10 3.8 26.2 0.9
NZ A:LYS159 3.8 42.7 1.0
CZ A:TYR10 3.9 36.2 0.1
CD A:LYS159 4.0 45.8 1.0
OH A:TYR48 4.0 53.9 1.0
CZ A:ARG51 4.1 56.7 1.0
CG A:TYR10 4.1 33.0 0.1
O A:HOH517 4.2 42.0 1.0
O A:HOH653 4.2 45.6 1.0
CA A:TYR10 4.3 28.2 0.9
CA A:TYR10 4.3 28.3 0.1
CE A:LYS159 4.3 44.4 1.0
O3G A:DG3401 4.4 36.2 1.0
OH A:TYR10 4.5 37.2 0.1
O3A A:DG3401 4.7 57.3 1.0
O A:HOH728 4.8 58.4 1.0
C A:ASP9 4.8 27.3 1.0
OD1 A:ASP7 4.8 30.6 1.0
CB A:TYR10 4.9 30.7 0.1
O A:PHE8 4.9 26.9 1.0
CA A:ASP9 4.9 26.8 1.0
CB A:TYR10 5.0 30.0 0.9
CE2 A:TYR10 5.0 35.7 0.1

Magnesium binding site 3 out of 3 in 1jxl

Go back to Magnesium Binding Sites List in 1jxl
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg1405

b:21.2
occ:1.00
 O A:HOH600 1.8 28.5 1.0
O A:HOH688 2.0 49.9 1.0
O A:HOH685 2.1 55.1 1.0
O P:HOH674 2.3 33.5 1.0
O A:ALA181 2.3 38.3 1.0
O A:ILE186 2.4 28.4 1.0
O P:HOH519 2.5 34.9 1.0
C A:ALA181 3.5 37.4 1.0
C A:ILE186 3.6 31.8 1.0
CA A:GLY187 4.1 35.6 1.0
CA A:ALA181 4.3 37.9 1.0
N A:GLY187 4.3 32.4 1.0
OP2 P:DT12 4.4 37.5 1.0
N A:ASP182 4.4 35.6 1.0
CB A:ALA181 4.5 36.4 1.0
CA A:ASP182 4.5 33.9 1.0
C A:GLY187 4.6 37.2 1.0
OP1 P:DT12 4.6 39.1 1.0
CA A:ILE186 4.7 31.3 1.0
O A:VAL183 4.8 28.9 1.0
CB A:ILE186 4.9 32.9 1.0
O A:GLY187 5.0 37.2 1.0
C A:ASP182 5.0 32.2 1.0
N A:ILE186 5.0 29.5 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: Tue Aug 13 06:52:40 2024

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