Magnesium in PDB 4jk8: Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk8 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 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.198, 78.037, 94.063, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 16

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Magnesium atom in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jk8). 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Open and Closed Forms of R1865A 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:18.3 occ:1.00 O B:HOH2160 2.0 21.9 1.0 O B:HOH2375 2.0 20.7 1.0 OD1 B:ASP1781 2.1 16.7 1.0 O B:HOH2412 2.1 22.3 1.0 O B:HOH2177 2.1 19.8 1.0 O B:HOH2156 2.1 19.6 1.0 CG B:ASP1781 3.0 16.7 1.0 OD2 B:ASP1781 3.3 18.8 1.0 O B:ASP1782 4.0 17.9 1.0 O B:HOH2261 4.1 40.7 1.0 O B:HOH2241 4.1 39.9 1.0 O B:HOH2255 4.1 29.6 1.0 O B:HOH2233 4.2 29.4 0.8 OE1 B:GLN1894 4.3 21.1 1.0 CB B:ASP1781 4.4 15.9 1.0 O B:HOH2121 4.4 21.4 1.0 N B:ASP1782 4.5 14.8 1.0 OD1 B:ASP1782 4.5 18.6 1.0 O B:HOH2151 4.5 31.7 1.0 OG1 B:THR1864 4.6 28.7 1.0 O B:HOH2145 4.7 23.8 1.0 CA B:ASP1781 4.8 15.4 1.0 O B:HOH2234 4.9 23.1 0.3 CE B:MET1868 4.9 27.0 0.8 CB B:ALA1865 5.0 29.6 1.0

Magnesium binding site 2 out of 2 in the Open and Closed Forms of R1865A 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:39.3 occ:1.00 O A:HOH2449 1.8 37.0 1.0 O B:HOH2394 2.0 44.4 1.0 OE2 B:GLU1856 2.0 23.1 0.5 O B:HOH2376 2.1 35.4 1.0 O A:HOH2448 2.2 36.8 1.0 O B:HOH2291 2.2 29.2 0.6 CD B:GLU1856 3.0 21.3 0.5 OE1 B:GLU1856 3.1 23.3 0.5 OE1 B:GLU1856 3.4 24.8 0.5 O A:HOH2342 3.8 45.3 1.0 CD B:GLU1856 3.8 19.9 0.5 O B:HOH2174 3.8 25.5 0.6 OE1 A:GLU1856 3.9 24.7 1.0 O B:HOH2348 3.9 25.6 0.4 OE2 B:GLU1856 3.9 21.8 0.5 O B:HOH2347 3.9 32.9 0.5 O A:HOH2481 4.2 44.1 1.0 OE2 B:GLU1855 4.3 38.8 1.0 OE2 A:GLU1856 4.3 25.4 1.0 CG B:GLU1856 4.4 18.6 0.5 O B:GLU1855 4.5 21.9 1.0 CD A:GLU1856 4.5 23.0 1.0 O A:HOH2335 4.5 41.7 1.0 OE1 A:GLU1855 5.0 30.0 0.2

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