Magnesium in PDB 3c6h: Crystal Structure of the RB49 GP17 Nuclease Domain

The structure of Crystal Structure of the RB49 GP17 Nuclease Domain, PDB code: 3c6h was solved by S.Sun, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.436, 126.724, 52.391, 90.00, 106.03, 90.00
R / Rfree (%)	24.2 / 29

The binding sites of Magnesium atom in the Crystal Structure of the RB49 GP17 Nuclease Domain (pdb code 3c6h). 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 RB49 GP17 Nuclease Domain, PDB code: 3c6h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the RB49 GP17 Nuclease Domain


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 RB49 GP17 Nuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:44.9 occ:1.00 O A:HOH606 2.3 59.0 1.0 O A:HOH565 2.4 30.2 1.0 OD1 A:ASP539 2.4 51.3 1.0 OD2 A:ASP398 2.9 50.0 1.0 OD2 A:ASP406 3.1 52.9 1.0 CG A:ASP539 3.1 51.5 1.0 O A:CYS399 3.2 44.9 1.0 CG A:ASP406 3.4 55.3 1.0 CG A:ASP398 3.4 48.2 1.0 OD1 A:ASP398 3.4 51.7 1.0 OD2 A:ASP539 3.4 52.7 1.0 O A:TYR407 3.6 49.0 1.0 CB A:ASP406 3.9 53.3 1.0 OD1 A:ASP406 4.0 55.7 1.0 CB A:ASP539 4.1 48.8 1.0 C A:CYS399 4.1 44.6 1.0 O A:HOH611 4.2 60.5 1.0 O A:ASP398 4.6 40.9 1.0 C A:SER400 4.6 44.3 1.0 N A:TYR407 4.7 51.7 1.0 CA A:ASP539 4.7 48.5 1.0 C A:ASP398 4.7 41.3 1.0 CA A:ASP406 4.7 52.4 1.0 CB A:ASP398 4.7 42.9 1.0 C A:TYR407 4.8 48.3 1.0 O A:HOH571 4.8 57.6 1.0 N A:CYS399 4.9 42.7 1.0 N A:SER400 4.9 44.7 1.0 C A:ASP406 5.0 52.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the RB49 GP17 Nuclease Domain


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 RB49 GP17 Nuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:55.1 occ:1.00 OD1 B:ASP539 2.6 51.2 1.0 OD2 B:ASP398 3.0 60.6 1.0 O B:HOH4 3.4 47.8 1.0 OD1 B:ASP398 3.5 60.5 1.0 CG B:ASP398 3.7 57.7 1.0 CG B:ASP539 3.8 50.0 1.0 OD1 B:ASP538 4.1 55.0 1.0 CA B:ASP539 4.4 44.1 1.0 OD1 B:ASP406 4.6 67.4 1.0 CB B:ASP539 4.6 46.1 1.0 CG B:MET542 4.6 48.8 1.0 OD2 B:ASP539 4.6 52.0 1.0 N B:ASP539 4.8 44.6 1.0 CB B:MET542 5.0 44.9 1.0

S.Sun, K.Kondabagil, B.Draper, T.I.Alam, V.D.Bowman, Z.Zhang, S.Hegde, A.Fokine, M.G.Rossmann, V.B.Rao. The Structure of the Phage T4 Dna Packaging Motor Suggests A Mechanism Dependent on Electrostatic Forces. Cell(Cambridge,Mass.) V. 135 1251 2008.
ISSN: ISSN 0092-8674
PubMed: 19109896
DOI: 10.1016/J.CELL.2008.11.015