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Magnesium in PDB 1sl2: Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide

Enzymatic activity of Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide

All present enzymatic activity of Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide:
2.7.7.7;

Protein crystallography data

The structure of Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide, PDB code: 1sl2 was solved by Y.Li, S.Dutta, S.Doublie, H.M.Bdour, J.S.Taylor, T.Ellenberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.983, 212.599, 51.945, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide (pdb code 1sl2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide, PDB code: 1sl2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1sl2

Go back to Magnesium Binding Sites List in 1sl2
Magnesium binding site 1 out of 3 in the Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template 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 Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4001

b:39.0
occ:1.00
 O A:ALA476 2.5 28.2 1.0
OD2 A:ASP654 2.6 40.2 1.0
O3A A:DAD4004 2.6 55.5 1.0
O1G A:DAD4004 2.6 55.2 1.0
O2B A:DAD4004 2.7 55.4 1.0
PB A:DAD4004 3.0 56.7 1.0
O1A A:DAD4004 3.0 52.9 1.0
O3B A:DAD4004 3.2 56.1 1.0
PG A:DAD4004 3.3 54.2 1.0
OD1 A:ASP475 3.4 36.6 1.0
PA A:DAD4004 3.4 53.1 1.0
N A:LEU479 3.5 31.3 1.0
C A:ALA476 3.6 27.0 1.0
N A:GLY478 3.7 28.4 1.0
CG A:ASP654 3.7 35.6 1.0
C5' A:DAD4004 3.8 53.0 1.0
CB A:LEU479 3.8 31.6 1.0
O2G A:DAD4004 3.9 54.8 1.0
O5' A:DAD4004 4.1 53.6 1.0
C A:SER477 4.1 29.6 1.0
CA A:GLY478 4.2 29.5 1.0
CA A:SER477 4.3 28.6 1.0
CA A:LEU479 4.3 31.9 1.0
N A:SER477 4.3 27.6 1.0
C A:GLY478 4.4 30.6 1.0
O1B A:DAD4004 4.4 58.6 1.0
OD1 A:ASP654 4.5 38.5 1.0
C3' A:DAD4004 4.5 52.4 1.0
CA A:ALA476 4.6 26.8 1.0
MG A:MG4002 4.6 36.8 1.0
CB A:ALA476 4.6 25.8 1.0
C4' A:DAD4004 4.6 53.0 1.0
CG A:ASP475 4.6 34.3 1.0
O3G A:DAD4004 4.7 56.5 1.0
O2A A:DAD4004 4.7 55.6 1.0
CB A:ASP654 4.7 33.9 1.0
N A:ALA476 4.7 26.6 1.0
O A:SER477 4.9 29.9 1.0
O A:HOH5173 4.9 45.0 1.0

Magnesium binding site 2 out of 3 in 1sl2

Go back to Magnesium Binding Sites List in 1sl2
Magnesium binding site 2 out of 3 in the Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template 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 Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4002

b:36.8
occ:1.00
 OD1 A:ASP654 2.4 38.5 1.0
OD2 A:ASP475 2.4 37.4 1.0
O1A A:DAD4004 2.5 52.9 1.0
O A:HOH5046 2.6 26.9 1.0
CG A:ASP654 3.0 35.6 1.0
O A:HOH5288 3.0 54.8 1.0
OD1 A:ASP475 3.0 36.6 1.0
CG A:ASP475 3.1 34.3 1.0
OD2 A:ASP654 3.1 40.2 1.0
PA A:DAD4004 3.6 53.1 1.0
O5' A:DAD4004 3.8 53.6 1.0
O A:HOH5173 3.8 45.0 1.0
C3' P:2DA22 3.8 41.2 1.0
CE1 A:HIS704 4.0 48.6 1.0
C5' A:DAD4004 4.0 53.0 1.0
CB A:GLU655 4.1 26.5 1.0
C4' P:2DA22 4.2 40.6 1.0
C A:ASP654 4.3 29.2 1.0
CB A:ASP654 4.3 33.9 1.0
O A:ASP654 4.4 29.0 1.0
OE2 A:GLU655 4.4 34.1 1.0
N A:GLU655 4.4 28.0 1.0
CB A:ASP475 4.5 30.2 1.0
O2A A:DAD4004 4.5 55.6 1.0
MG A:MG4001 4.6 39.0 1.0
O A:VAL652 4.6 26.7 1.0
N A:ASP654 4.6 29.1 1.0
CA A:ASP654 4.6 30.4 1.0
NE2 A:HIS704 4.6 49.5 1.0
C5' P:2DA22 4.6 37.8 1.0
CG A:GLU655 4.7 32.3 1.0
O1G A:DAD4004 4.8 55.2 1.0
C2' P:2DA22 4.8 42.2 1.0
O3A A:DAD4004 4.8 55.5 1.0
CD A:GLU655 4.8 30.5 1.0
CA A:GLU655 4.9 27.3 1.0

Magnesium binding site 3 out of 3 in 1sl2

Go back to Magnesium Binding Sites List in 1sl2
Magnesium binding site 3 out of 3 in the Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template 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 Ternary 5' Complex of T7 Dna Polymerase with A Dna Primer/Template Containing A Cis-Syn Thymine Dimer on the Template and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4003

b:47.3
occ:1.00
 O A:HOH5290 2.5 25.0 1.0
O A:HOH5043 2.6 29.8 1.0
O A:HOH5291 2.6 24.8 1.0
O A:HOH5289 2.7 28.0 1.0
O A:HOH5280 2.8 42.2 1.0
OD1 A:ASP5 3.3 25.8 1.0
O A:HOH5096 4.1 29.1 1.0
CG A:ASP5 4.3 22.8 1.0
CE A:MET107 4.3 28.6 1.0
OD1 A:ASP65 4.4 25.4 1.0
O A:ILE6 4.5 29.1 1.0
OD2 A:ASP5 4.5 27.6 1.0
OD2 A:ASP65 4.6 25.4 1.0
O A:HIS59 4.7 19.6 1.0
OD2 A:ASP174 4.9 37.8 1.0
CD2 A:TYR64 4.9 24.5 1.0
CG A:ASP65 5.0 23.8 1.0

Reference:

Y.Li, S.Dutta, S.Doublie, H.M.Bdour, J.S.Taylor, T.Ellenberger. Nucleotide Insertion Opposite A Cis-Syn Thymine Dimer By A Replicative Dna Polymerase From Bacteriophage T7. Nat.Struct.Mol.Biol. V. 11 784 2004.
ISSN: ISSN 1545-9993
PubMed: 15235589
DOI: 10.1038/NSMB792
Page generated: Tue Aug 13 13:46:46 2024

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