Magnesium in PDB 1skr: T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp

All present enzymatic activity of T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp:
2.7.7.7;

The structure of T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp, PDB code: 1skr 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)	20.00 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.506, 214.020, 52.036, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27

The binding sites of Magnesium atom in the T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp (pdb code 1skr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp, PDB code: 1skr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:27.1 occ:1.00 O A:ALA476 2.2 24.3 1.0 OD1 A:ASP475 2.3 34.1 1.0 O1G A:DAD4004 2.3 33.2 1.0 OD2 A:ASP654 2.3 27.5 1.0 O1A A:DAD4004 2.3 28.0 1.0 O2B A:DAD4004 2.4 29.4 1.0 CG A:ASP475 3.1 31.1 1.0 CG A:ASP654 3.3 25.1 1.0 PG A:DAD4004 3.3 30.8 1.0 C A:ALA476 3.3 24.9 1.0 PB A:DAD4004 3.4 27.8 1.0 OD2 A:ASP475 3.5 34.7 1.0 O3B A:DAD4004 3.6 30.2 1.0 OD1 A:ASP654 3.6 24.4 1.0 PA A:DAD4004 3.6 28.2 1.0 MG A:MG4002 3.7 33.3 1.0 O A:HOH5168 3.8 42.8 1.0 O3A A:DAD4004 3.8 29.5 1.0 N A:ALA476 3.9 25.0 1.0 O A:HOH5055 4.0 32.0 1.0 O2G A:DAD4004 4.1 32.5 1.0 CA A:ALA476 4.1 25.6 1.0 CB A:ASP475 4.2 27.7 1.0 C A:ASP475 4.2 25.4 1.0 N A:SER477 4.3 26.6 1.0 C5' A:DAD4004 4.4 28.8 1.0 CA A:SER477 4.5 25.6 1.0 O5' A:DAD4004 4.5 28.3 1.0 O3G A:DAD4004 4.5 33.0 1.0 CB A:ALA476 4.6 21.2 1.0 CB A:ASP654 4.6 23.5 1.0 N A:GLY478 4.6 23.3 1.0 O A:ASP475 4.7 24.6 1.0 CA A:ASP475 4.7 25.2 1.0 O2A A:DAD4004 4.7 31.0 1.0 O A:ASP654 4.7 22.1 1.0 O1B A:DAD4004 4.8 29.2 1.0 C A:SER477 4.8 24.4 1.0 N A:LEU479 4.9 25.8 1.0

Magnesium binding site 2 out of 3 in the T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:33.3 occ:1.00 OD1 A:ASP654 2.4 24.4 1.0 OD2 A:ASP475 2.5 34.7 1.0 O A:HOH5017 2.5 31.5 1.0 O A:HOH5442 2.7 35.9 1.0 O1A A:DAD4004 2.7 28.0 1.0 OD1 A:ASP475 3.1 34.1 1.0 CG A:ASP475 3.1 31.1 1.0 CG A:ASP654 3.5 25.1 1.0 C3' P:2DA22 3.7 24.3 1.0 MG A:MG4001 3.7 27.1 1.0 O A:HOH5055 3.7 32.0 1.0 PA A:DAD4004 3.8 28.2 1.0 OD2 A:ASP654 3.8 27.5 1.0 CE1 A:HIS704 3.8 40.6 1.0 CB A:GLU655 4.0 22.8 1.0 OE2 A:GLU655 4.2 24.9 1.0 O2A A:DAD4004 4.2 31.0 1.0 C4' P:2DA22 4.2 24.2 1.0 O5' A:DAD4004 4.2 28.3 1.0 C5' P:2DA22 4.3 22.3 1.0 NE2 A:HIS704 4.4 41.0 1.0 C5' A:DAD4004 4.5 28.8 1.0 CB A:ASP475 4.5 27.7 1.0 O A:VAL652 4.5 22.1 1.0 C A:ASP654 4.6 22.9 1.0 O A:ASP654 4.6 22.1 1.0 N A:GLU655 4.7 23.2 1.0 O1G A:DAD4004 4.8 33.2 1.0 CB A:ASP654 4.8 23.5 1.0 CD A:GLU655 4.8 26.3 1.0 CG A:GLU655 4.8 24.1 1.0 C2' P:2DA22 4.9 23.8 1.0 CA A:GLU655 4.9 23.4 1.0 O5' P:2DA22 4.9 23.9 1.0 N A:ASP654 4.9 21.5 1.0 ND1 A:HIS704 5.0 42.7 1.0

Magnesium binding site 3 out of 3 in the T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T7 Dna Polymerase Complexed to Dna Primer/Template and Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4003 b:30.9 occ:1.00 O A:HOH5432 2.4 28.7 1.0 O A:HOH5433 2.5 27.7 1.0 O A:HOH5031 2.5 32.5 1.0 OD1 A:ASP5 2.6 25.3 1.0 O A:HOH5044 2.6 25.7 1.0 O A:HOH5020 3.5 24.3 1.0 CG A:ASP5 3.6 23.9 1.0 OD2 A:ASP5 3.8 25.8 1.0 O A:HOH5186 4.1 40.9 1.0 O A:ILE6 4.2 26.0 1.0 OD1 A:ASP65 4.3 21.8 1.0 OD2 A:ASP65 4.4 25.4 1.0 OD2 A:ASP174 4.4 35.9 1.0 O A:HIS59 4.5 21.8 1.0 O A:HOH5042 4.6 21.7 1.0 O A:HOH5066 4.6 22.2 1.0 CE A:MET107 4.7 34.8 1.0 CG A:ASP65 4.8 22.2 1.0 CB A:ASP5 4.9 23.1 1.0 CG A:ASP174 5.0 34.2 1.0

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