Magnesium in PDB 2v9p: Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form

The structure of Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form, PDB code: 2v9p was solved by C.M.Sanders, O.V.Kovalevskiy, D.Sizov, A.A.Lebedev, M.N.Isupov, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.95 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	135.111, 180.649, 187.533, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.1

The binding sites of Magnesium atom in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form (pdb code 2v9p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form, PDB code: 2v9p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form


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 Papillomavirus E1 Hexameric Helicase Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1582 b:74.4 occ:1.00 O4 A:PO41581 1.8 79.2 0.5 O2 A:PO41580 2.3 79.2 1.0 OG A:SER440 2.5 67.0 1.0 OD2 A:ASP479 3.0 89.7 1.0 NH2 B:ARG538 3.0 75.1 1.0 P A:PO41581 3.2 79.0 0.5 P A:PO41580 3.5 76.5 1.0 CB A:SER440 3.6 66.6 1.0 O2 A:PO41581 3.6 78.5 0.5 O3 A:PO41581 3.8 79.6 0.5 O4 A:PO41580 3.9 79.3 1.0 CG A:ASP479 3.9 86.0 1.0 O1 A:PO41580 4.1 76.4 1.0 O1 A:PO41581 4.2 79.5 0.5 CZ B:ARG538 4.3 76.6 1.0 OD2 B:ASP497 4.3 74.3 1.0 N A:SER440 4.6 66.4 1.0 OD1 A:ASP479 4.6 88.0 1.0 CA A:SER440 4.7 66.8 1.0 CB A:ASP479 4.7 82.9 1.0 O3 A:PO41580 4.7 78.4 1.0 NZ A:LYS439 4.8 69.0 1.0 OG1 A:THR521 4.9 70.3 1.0 NH1 B:ARG538 4.9 76.4 1.0 OD2 A:ASP478 4.9 88.6 1.0 OD1 A:ASP478 4.9 87.2 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form


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 Papillomavirus E1 Hexameric Helicase Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1581 b:54.1 occ:1.00 O4 B:PO41580 1.8 83.1 1.0 O2 B:PO41579 1.9 79.0 1.0 OG B:SER440 2.2 75.3 1.0 OD2 B:ASP479 2.7 80.7 1.0 P B:PO41580 3.2 82.7 1.0 P B:PO41579 3.3 79.8 1.0 CB B:SER440 3.3 74.3 1.0 NH2 C:ARG538 3.5 74.1 1.0 CG B:ASP479 3.6 79.3 1.0 O2 B:PO41580 3.6 80.8 1.0 O1 B:PO41579 3.7 77.9 1.0 OD1 B:ASP479 3.9 80.1 1.0 O3 B:PO41580 3.9 82.2 1.0 OD2 C:ASP497 4.0 77.2 1.0 O4 B:PO41579 4.0 78.0 1.0 N B:SER440 4.1 74.4 1.0 CA B:SER440 4.3 74.5 1.0 O1 B:PO41580 4.3 83.4 1.0 O3 B:PO41579 4.3 79.4 1.0 OG1 B:THR521 4.4 67.6 1.0 OD2 B:ASP478 4.6 80.1 1.0 OD1 B:ASP478 4.8 79.3 1.0 CZ C:ARG538 4.9 75.9 1.0 NZ B:LYS439 4.9 64.8 1.0 CB B:ASP479 4.9 76.4 1.0 CE B:LYS439 4.9 67.9 1.0 CG B:ASP478 5.0 78.2 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form


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 Papillomavirus E1 Hexameric Helicase Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1581 b:68.7 occ:1.00 O4 C:PO41580 1.9 86.1 1.0 O2 C:PO41579 2.0 84.6 1.0 OG C:SER440 2.2 76.5 1.0 OD2 C:ASP479 2.8 80.2 1.0 CB C:SER440 3.2 74.9 1.0 P C:PO41580 3.3 85.2 1.0 P C:PO41579 3.4 84.3 1.0 CG C:ASP479 3.7 78.0 1.0 NH2 D:ARG538 3.8 75.8 1.0 O1 C:PO41580 4.0 82.2 1.0 O3 C:PO41580 4.1 85.2 1.0 OD1 C:ASP479 4.1 80.4 1.0 O1 C:PO41579 4.1 83.3 1.0 OD2 D:ASP497 4.2 76.5 1.0 N C:SER440 4.2 74.4 1.0 CA C:SER440 4.3 74.8 1.0 O4 C:PO41579 4.3 83.0 1.0 O2 C:PO41580 4.3 84.2 1.0 O3 C:PO41579 4.3 83.5 1.0 OG1 C:THR521 4.4 71.1 1.0 OD2 C:ASP478 4.5 81.6 1.0 OD1 C:ASP478 4.6 84.2 1.0 CG C:ASP478 4.8 80.0 1.0 CB C:ASP479 4.8 75.8 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1581 b:67.5 occ:1.00 OG G:SER440 1.9 73.6 1.0 O4 G:PO41580 2.0 82.0 0.5 O2 G:PO41579 2.1 79.9 1.0 OD2 G:ASP479 3.2 90.0 1.0 CB G:SER440 3.3 70.3 1.0 NH2 H:ARG538 3.3 72.1 1.0 P G:PO41580 3.4 79.9 0.5 P G:PO41579 3.4 80.9 1.0 O1 G:PO41579 3.8 79.9 1.0 O2 G:PO41580 3.8 77.7 0.5 CG G:ASP479 4.0 86.2 1.0 O4 G:PO41579 4.1 77.8 1.0 O3 G:PO41580 4.1 80.3 0.5 N G:SER440 4.2 69.2 1.0 CA G:SER440 4.2 69.8 1.0 OD2 H:ASP497 4.3 69.7 1.0 OD2 G:ASP478 4.4 89.8 1.0 O1 G:PO41580 4.4 80.8 0.5 OG1 G:THR521 4.5 70.8 1.0 NZ G:LYS439 4.5 70.8 1.0 O3 G:PO41579 4.6 82.6 1.0 CZ H:ARG538 4.6 72.7 1.0 OD1 G:ASP478 4.7 85.4 1.0 CB G:ASP479 4.7 82.6 1.0 OD1 G:ASP479 4.7 89.3 1.0 CG G:ASP478 4.9 85.8 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1581 b:64.2 occ:1.00 OG H:SER440 1.9 74.2 1.0 O2 H:PO41579 2.1 81.4 1.0 O4 H:PO41580 2.1 80.6 1.0 OD2 H:ASP479 2.9 80.4 1.0 CB H:SER440 3.0 74.0 1.0 P H:PO41580 3.5 80.5 1.0 P H:PO41579 3.5 81.7 1.0 NH2 I:ARG538 3.9 79.2 1.0 N H:SER440 3.9 73.8 1.0 CG H:ASP479 3.9 76.2 1.0 O2 H:PO41580 3.9 80.0 1.0 CA H:SER440 4.0 74.1 1.0 O1 H:PO41579 4.0 79.8 1.0 O3 H:PO41580 4.0 82.2 1.0 OG1 H:THR521 4.2 70.5 1.0 O4 H:PO41579 4.2 81.3 1.0 OD1 H:ASP478 4.3 82.5 1.0 OD2 I:ASP497 4.4 72.8 1.0 OD1 H:ASP479 4.4 73.8 1.0 OD2 H:ASP478 4.5 81.8 1.0 O3 H:PO41579 4.5 81.5 1.0 O1 H:PO41580 4.6 79.1 1.0 NZ H:LYS439 4.7 66.0 1.0 CG H:ASP478 4.7 79.4 1.0 CB H:THR521 4.9 70.6 1.0 CE2 I:TYR499 4.9 72.8 1.0 CB H:LYS439 5.0 73.0 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Papillomavirus E1 Hexameric Helicase Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg1582 b:64.3 occ:1.00 O4 I:PO41581 2.1 82.3 1.0 O2 I:PO41580 2.1 77.3 1.0 OG I:SER440 2.3 76.7 1.0 OD2 I:ASP479 2.8 83.4 1.0 CB I:SER440 3.2 74.5 1.0 P I:PO41581 3.4 79.6 1.0 P I:PO41580 3.5 78.0 1.0 NH2 J:ARG538 3.7 77.3 1.0 OD2 J:ASP497 3.8 75.6 1.0 CG I:ASP479 3.9 79.7 1.0 O2 I:PO41581 3.9 78.9 1.0 O1 I:PO41580 3.9 76.4 1.0 O3 I:PO41581 4.0 80.1 1.0 O4 I:PO41580 4.1 78.2 1.0 N I:SER440 4.3 74.2 1.0 CA I:SER440 4.3 74.7 1.0 OD1 I:ASP479 4.3 78.1 1.0 O1 I:PO41581 4.5 80.5 1.0 O3 I:PO41580 4.5 77.1 1.0 OG1 I:THR521 4.5 72.6 1.0 OD2 I:ASP478 4.7 83.5 1.0 OD1 I:ASP478 4.8 81.9 1.0 NZ I:LYS439 4.9 69.0 1.0 CG J:ASP497 4.9 74.1 1.0 CG I:ASP478 5.0 80.4 1.0

C.M.Sanders, O.V.Kovalevskiy, D.Sizov, A.A.Lebedev, M.N.Isupov, A.A.Antson. Papillomavirus E1 Helicase Assembly Maintains An Asymmetric State in the Absence of Dna and Nucleotide Cofactors. Nucleic Acids Res. V. 35 6451 2007.
ISSN: ISSN 0305-1048
PubMed: 17881379
DOI: 10.1093/NAR/GKM705