Magnesium in PDB 4jkh: Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkh was solved by M.J.Schellenberg, T.Wu, D.B.Ritchie, K.A.Atta, A.M.Macmillan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.29 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.473, 77.739, 94.234, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.9

The structure of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jkh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:26.6 occ:0.64 OE1 B:GLU1781 2.0 29.3 1.0 O B:HOH2242 2.1 37.2 1.0 O B:HOH2240 2.1 30.9 1.0 O B:HOH2241 2.2 31.0 1.0 O B:HOH2239 2.2 28.0 0.8 O B:HOH2195 2.2 29.6 1.0 CD B:GLU1781 3.2 26.9 1.0 CB B:GLU1781 3.9 22.3 1.0 OG1 B:THR1864 4.0 27.8 1.0 OE2 B:GLU1781 4.0 30.6 1.0 CG B:GLU1781 4.0 23.9 1.0 O B:HOH2217 4.2 30.9 1.0 O B:HOH2193 4.2 39.6 1.0 O B:ASP1782 4.2 18.1 1.0 O B:HOH2136 4.2 33.9 1.0 O B:HOH2189 4.3 39.9 1.0 O B:HOH2243 4.3 25.0 1.0 CA B:GLU1781 4.4 17.4 1.0 OE1 B:GLN1894 4.4 33.2 1.0 N B:ASP1782 4.4 19.2 1.0 O B:LEU1891 4.8 24.7 1.0 O B:HOH2262 4.8 35.8 1.0 CB B:ARG1865 4.9 29.6 0.6 C B:GLU1781 4.9 17.9 1.0

Magnesium binding site 2 out of 2 in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:47.1 occ:1.00 O A:HOH2343 1.9 46.1 1.0 O B:HOH2322 2.1 52.4 1.0 O A:HOH2254 2.2 39.9 1.0 O B:HOH2212 2.2 38.6 1.0 OE2 B:GLU1856 2.3 40.8 1.0 CD B:GLU1856 3.2 33.9 1.0 OE1 B:GLU1856 3.5 33.5 1.0 OE1 A:GLU1856 3.8 34.8 1.0 OE2 A:GLU1856 4.1 35.2 1.0 O A:HOH2253 4.3 50.5 1.0 CD A:GLU1856 4.4 33.4 1.0 OE2 B:GLU1855 4.4 47.7 1.0 O B:GLU1855 4.6 24.1 1.0 CG B:GLU1856 4.6 30.9 1.0 OE1 A:GLU1855 4.7 39.0 0.6

M.J.Schellenberg, T.Wu, D.B.Ritchie, S.Fica, J.P.Staley, K.A.Atta, P.Lapointe, A.M.Macmillan. A Conformational Switch in PRP8 Mediates Metal Ion Coordination That Promotes Pre-Mrna Exon Ligation. Nat.Struct.Mol.Biol. V. 20 728 2013.
ISSN: ISSN 1545-9993
PubMed: 23686287
DOI: 10.1038/NSMB.2556