Magnesium in PDB 1zyq: T7 Dna Polymerase in Complex with 8OG and Incoming Ddatp

All present enzymatic activity of T7 Dna Polymerase in Complex with 8OG and Incoming Ddatp:
2.7.7.7;

The structure of T7 Dna Polymerase in Complex with 8OG and Incoming Ddatp, PDB code: 1zyq was solved by L.G.Brieba, R.J.Kokoska, K.Bebenek, T.A.Kunkel, T.Ellenberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.60 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.148, 213.007, 52.990, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.2

The binding sites of Magnesium atom in the T7 Dna Polymerase in Complex with 8OG and Incoming Ddatp (pdb code 1zyq). 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 in Complex with 8OG and Incoming Ddatp, PDB code: 1zyq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the T7 Dna Polymerase in Complex with 8OG and Incoming 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 in Complex with 8OG and Incoming Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:30.1 occ:1.00 O A:ALA476 2.2 28.7 1.0 OD2 A:ASP654 2.3 37.3 1.0 O1G A:DAD1024 2.4 34.1 1.0 OD2 A:ASP475 2.5 39.3 1.0 O1A A:DAD1024 2.6 28.9 1.0 OD1 A:ASP475 2.6 43.7 1.0 O2B A:DAD1024 2.6 30.3 1.0 CG A:ASP475 2.8 39.5 1.0 C A:ALA476 3.2 27.8 1.0 PG A:DAD1024 3.3 31.7 1.0 CG A:ASP654 3.4 35.6 1.0 PB A:DAD1024 3.6 28.6 1.0 N A:ALA476 3.6 25.4 1.0 O2G A:DAD1024 3.7 33.4 1.0 O3B A:DAD1024 3.7 31.1 1.0 PA A:DAD1024 3.8 29.1 1.0 CA A:ALA476 3.9 27.4 1.0 OD1 A:ASP654 4.0 36.9 1.0 O3A A:DAD1024 4.0 30.4 1.0 N A:SER477 4.1 27.8 1.0 C A:ASP475 4.2 25.9 1.0 CB A:ASP475 4.2 31.7 1.0 CA A:SER477 4.4 26.7 1.0 MG A:MG4002 4.4 49.0 1.0 CB A:ALA476 4.4 26.4 1.0 O A:ASP654 4.4 28.4 1.0 CB A:ASP654 4.5 31.5 1.0 N A:GLY478 4.6 25.2 1.0 O5' A:DAD1024 4.7 29.2 1.0 O3G A:DAD1024 4.7 33.9 1.0 CA A:ASP475 4.7 26.4 1.0 C A:SER477 4.7 25.4 1.0 O A:ASP475 4.8 24.3 1.0 C5' A:DAD1024 4.9 29.7 1.0 N A:LEU479 5.0 26.5 1.0 O2A A:DAD1024 5.0 31.9 1.0

Magnesium binding site 2 out of 3 in the T7 Dna Polymerase in Complex with 8OG and Incoming 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 in Complex with 8OG and Incoming Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:49.0 occ:1.00 OD1 A:ASP654 2.9 36.9 1.0 OD2 A:ASP475 2.9 39.3 1.0 O1A A:DAD1024 3.3 28.9 1.0 OE2 A:GLU655 3.5 36.8 1.0 CE1 A:HIS704 3.5 56.0 1.0 CB A:GLU655 3.6 27.4 1.0 C3' P:DDG1022 3.7 31.0 1.0 CG A:ASP654 3.8 35.6 1.0 C5' P:DDG1022 4.0 28.1 1.0 NE2 A:HIS704 4.1 56.5 1.0 CG A:ASP475 4.1 39.5 1.0 OD2 A:ASP654 4.2 37.3 1.0 O2A A:DAD1024 4.2 31.9 1.0 PA A:DAD1024 4.2 29.1 1.0 C4' P:DDG1022 4.3 30.9 1.0 O A:VAL652 4.3 19.8 1.0 CD A:GLU655 4.4 35.4 1.0 O5' P:DDG1022 4.4 24.5 1.0 MG A:MG4001 4.4 30.1 1.0 CG A:GLU655 4.5 32.3 1.0 N A:GLU655 4.5 26.6 1.0 OP1 P:DDG1022 4.6 27.1 1.0 C A:ASP654 4.6 28.4 1.0 CA A:GLU655 4.6 26.4 1.0 ND1 A:HIS704 4.7 55.8 1.0 O A:ASP654 4.7 28.4 1.0 CB A:ASP475 4.8 31.7 1.0 O A:HOH5076 4.8 40.9 1.0 O1G A:DAD1024 4.9 34.1 1.0 N A:ASP654 5.0 27.3 1.0

Magnesium binding site 3 out of 3 in the T7 Dna Polymerase in Complex with 8OG and Incoming 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 in Complex with 8OG and Incoming Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4003 b:29.4 occ:1.00 OD1 A:ASP5 2.5 28.8 1.0 OD2 A:ASP5 3.1 31.1 1.0 CG A:ASP5 3.1 27.2 1.0 OD1 A:ASP174 3.6 41.1 1.0 O A:ILE6 3.7 25.5 1.0 CE A:MET135 3.9 48.9 1.0 O A:HOH5072 4.6 27.8 1.0 CB A:ASP5 4.6 22.7 1.0 OE2 A:GLU7 4.6 35.2 1.0 OD2 A:ASP65 4.7 24.6 1.0 CG A:ASP174 4.7 36.9 1.0 N A:ILE6 4.7 21.2 1.0 C A:ILE6 4.8 24.7 1.0 OE1 A:GLU7 4.8 34.8 1.0 O A:HOH5016 4.9 70.5 1.0 CD A:GLU7 5.0 32.1 1.0

L.G.Brieba, R.J.Kokoska, K.Bebenek, T.A.Kunkel, T.Ellenberger. A Lysine Residue in the Fingers Subdomain of T7 Dna Polymerase Modulates the Miscoding Potential of 8-Oxo-7,8-Dihydroguanosine. Structure V. 13 1653 2005.
ISSN: ISSN 0969-2126
PubMed: 16271888
DOI: 10.1016/J.STR.2005.07.020