Magnesium in PDB 1svl: Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp

The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp, PDB code: 1svl was solved by D.Gai, R.Zhao, C.V.Finkielstein, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	195.812, 86.442, 128.601, 90.00, 129.00, 90.00
R / Rfree (%)	23.6 / 26.4

The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium atom in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp (pdb code 1svl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp, PDB code: 1svl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg750 b:53.4 occ:1.00 O A:HOH227 2.0 59.0 1.0 O2B A:ADP800 2.0 42.3 1.0 O A:HOH230 2.1 43.6 1.0 O A:HOH229 2.2 36.9 1.0 O A:HOH165 2.3 46.9 1.0 OG1 A:THR433 2.3 36.1 1.0 PB A:ADP800 3.3 44.7 1.0 O3B A:ADP800 3.4 45.6 1.0 CB A:THR433 3.4 35.3 1.0 OE1 A:GLU473 3.5 52.2 1.0 O A:HOH226 3.8 46.2 1.0 O3A A:ADP800 4.2 45.7 1.0 O2A A:ADP800 4.2 47.3 1.0 O A:HOH228 4.2 51.6 1.0 N A:THR433 4.2 34.1 1.0 O1B A:ADP800 4.3 45.9 1.0 CA A:THR433 4.4 34.1 1.0 CD A:GLU473 4.4 50.5 1.0 O B:HOH113 4.4 48.9 1.0 CG2 A:THR433 4.4 35.1 1.0 O B:HOH231 4.5 59.6 1.0 OE2 A:GLU473 4.7 50.0 1.0 PA A:ADP800 4.7 47.2 1.0 CE A:LYS432 4.8 36.3 1.0 NZ B:LYS418 4.8 38.5 1.0 NZ A:LYS432 4.9 31.9 1.0 CB A:ASP474 4.9 46.4 1.0 CB A:LYS432 4.9 33.9 1.0

Magnesium binding site 2 out of 3 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg750 b:50.9 occ:1.00 O B:HOH222 2.0 34.9 1.0 OG1 B:THR433 2.0 39.2 1.0 O B:HOH224 2.0 39.1 1.0 O2B B:ADP800 2.1 36.3 1.0 O C:HOH125 2.2 42.2 1.0 O B:HOH223 2.4 50.6 1.0 CB B:THR433 3.1 38.3 1.0 O3B B:ADP800 3.2 34.4 1.0 PB B:ADP800 3.2 34.6 1.0 O2A B:ADP800 3.7 35.3 1.0 OD1 C:ASP499 3.9 44.2 1.0 NH1 C:ARG498 4.0 46.3 1.0 N B:THR433 4.0 35.8 1.0 O3A B:ADP800 4.0 37.1 1.0 CG2 B:THR433 4.1 37.0 1.0 CA B:THR433 4.1 36.7 1.0 O B:HOH196 4.2 44.3 1.0 OE1 B:GLU473 4.2 52.0 1.0 OD2 C:ASP499 4.2 43.0 1.0 NH2 C:ARG498 4.3 43.6 1.0 O1B B:ADP800 4.4 34.4 1.0 PA B:ADP800 4.4 36.3 1.0 CG C:ASP499 4.5 42.0 1.0 OE2 B:GLU473 4.6 52.6 1.0 CZ C:ARG498 4.6 45.4 1.0 CD B:GLU473 4.9 52.0 1.0

Magnesium binding site 3 out of 3 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg750 b:34.4 occ:1.00 O2B C:ADP800 2.1 29.3 1.0 OG1 C:THR433 2.1 27.8 1.0 O C:HOH218 2.1 25.3 1.0 O C:HOH216 2.2 33.2 1.0 O C:HOH217 2.3 31.3 1.0 O C:HOH48 2.4 28.9 1.0 CB C:THR433 3.1 28.0 1.0 O3B C:ADP800 3.2 32.9 1.0 PB C:ADP800 3.2 31.0 1.0 O2A C:ADP800 3.6 31.8 1.0 OE1 C:GLU473 3.9 51.5 1.0 O3A C:ADP800 4.0 30.9 1.0 N C:THR433 4.0 24.3 1.0 CG2 C:THR433 4.1 29.7 1.0 CA C:THR433 4.1 27.3 1.0 O1B C:ADP800 4.3 29.1 1.0 PA C:ADP800 4.4 28.8 1.0 O C:HOH111 4.6 33.3 1.0 OE2 C:GLU473 4.6 51.8 1.0 O C:HOH219 4.7 34.6 1.0 CD C:GLU473 4.7 49.0 1.0 OD2 C:ASP474 4.8 58.9 1.0 O1A C:ADP800 4.9 27.0 1.0

D.Gai, R.Zhao, D.Li, C.V.Finkielstein, X.S.Chen. Mechanisms of Conformational Change For A Replicative Hexameric Helicase of SV40 Large Tumor Antigen. Cell(Cambridge,Mass.) V. 119 47 2004.
ISSN: ISSN 0092-8674
PubMed: 15454080
DOI: 10.1016/J.CELL.2004.09.017