Magnesium in PDB 4d2i: Crystal Structure of the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp

The structure of Crystal Structure of the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp, PDB code: 4d2i was solved by N.J.Rzechorzek, J.K.Blackwood, S.M.Bray, J.D.Maman, L.Pellegrini, N.P.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.733 / 2.84
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	150.210, 150.210, 140.540, 90.00, 90.00, 120.00
R / Rfree (%)	21.12 / 25.41

The binding sites of Magnesium atom in the Crystal Structure of the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp (pdb code 4d2i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp, PDB code: 4d2i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp


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 the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1478 b:40.7 occ:1.00 O A:HOH2030 2.0 40.3 1.0 O A:HOH2031 2.0 45.6 1.0 OG A:SER155 2.1 41.8 1.0 O A:HOH2029 2.1 40.9 1.0 O2G A:ANP1477 2.1 41.1 1.0 O2B A:ANP1477 2.2 43.5 1.0 CB A:SER155 3.3 42.9 1.0 PG A:ANP1477 3.6 37.2 1.0 PB A:ANP1477 3.6 41.1 1.0 OE1 A:GLU180 3.6 49.1 1.0 O1A A:ANP1477 3.8 67.0 1.0 OE2 A:GLU180 3.8 51.9 1.0 N3B A:ANP1477 4.0 44.9 1.0 N A:SER155 4.0 36.2 1.0 OE2 A:GLU355 4.1 47.8 1.0 OE1 A:GLU355 4.1 43.2 1.0 CD A:GLU180 4.1 49.6 1.0 CA A:SER155 4.2 39.5 1.0 O1B A:ANP1477 4.3 36.7 1.0 O3G A:ANP1477 4.4 42.8 1.0 CD A:GLU355 4.5 48.4 1.0 O A:HOH2052 4.6 44.7 1.0 O1G A:ANP1477 4.6 39.7 1.0 O3A A:ANP1477 4.7 49.2 1.0 CB A:LYS154 4.7 35.5 1.0 CE A:LYS154 4.8 34.6 1.0 PA A:ANP1477 4.9 45.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp


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 the Hera Hexameric Dna Translocase From Sulfolobus Solfataricus Bound to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1479 b:40.8 occ:1.00 O2G B:ANP1478 2.0 37.5 1.0 O B:HOH2013 2.1 38.1 1.0 O B:HOH2014 2.2 36.2 1.0 O B:HOH2012 2.2 35.4 1.0 OG B:SER155 2.2 35.4 1.0 O2B B:ANP1478 2.4 31.8 1.0 CB B:SER155 3.3 35.6 1.0 PG B:ANP1478 3.3 52.6 1.0 PB B:ANP1478 3.6 32.3 1.0 N3B B:ANP1478 3.7 45.0 1.0 O1A B:ANP1478 3.8 44.5 1.0 OE2 B:GLU180 3.8 46.3 1.0 OE1 B:GLU180 3.9 43.5 1.0 N B:SER155 4.0 37.1 1.0 O3G B:ANP1478 4.0 39.5 1.0 OE1 B:GLU355 4.1 43.7 1.0 OE2 B:GLU355 4.1 38.1 1.0 CA B:SER155 4.2 34.1 1.0 CD B:GLU180 4.3 44.9 1.0 O1B B:ANP1478 4.4 38.6 1.0 CD B:GLU355 4.5 38.1 1.0 O1G B:ANP1478 4.5 35.6 1.0 O B:HOH2018 4.7 38.1 1.0 O3A B:ANP1478 4.7 56.4 1.0 CB B:LYS154 4.8 32.4 1.0 PA B:ANP1478 4.9 43.0 1.0

N.J.Rzechorzek, J.K.Blackwood, S.M.Bray, J.D.Maman, L.Pellegrini, N.P.Robinson. Structure of the Hexameric Hera Atpase Reveals A Mechanism of Translocation-Coupled Dna-End Processing in Archaea Nat.Commun. V. 5 5506 2014.
ISSN: ISSN 2041-1723
PubMed: 25420454
DOI: 10.1038/NCOMMS6506