Magnesium in PDB 4jk7: Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk7 was solved by M.J.Schellenberg, T.Wu, D.B.Ritchie, K.Atta, A.M.Macmillan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.02 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.029, 78.024, 93.805, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 17.7

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

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jk7). 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 Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Open and Closed Forms of Wild-Type 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 Wild-Type 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:0.46 O B:HOH2213 1.9 23.5 0.4 O B:HOH2321 1.9 23.1 0.5 OD1 B:ASP1781 2.0 18.0 1.0 O B:HOH2214 2.1 16.8 0.5 O B:HOH2245 2.2 23.4 0.5 CG B:ASP1781 2.9 16.8 1.0 OD2 B:ASP1781 3.1 20.7 1.0 O B:HOH2215 3.3 32.7 1.0 O B:HOH2342 3.4 29.8 1.0 O B:HOH2394 3.5 27.1 0.7 O B:HOH2245 3.7 16.9 0.5 OG1 B:THR1864 4.1 28.8 1.0 O B:HOH2299 4.2 27.0 1.0 OE1 B:GLN1894 4.2 19.1 0.5 O B:ASP1782 4.3 16.0 1.0 O B:HOH2135 4.3 32.4 1.0 CB B:ASP1781 4.3 15.9 1.0 O B:HOH2220 4.4 22.4 1.0 N B:ASP1782 4.7 13.2 1.0 O B:HOH2343 4.7 11.6 0.5 OD1 B:ASP1782 4.7 19.1 0.4 CA B:ASP1781 4.8 13.4 1.0 CD B:GLN1894 5.0 19.1 0.5 O B:HOH2282 5.0 25.0 1.0

Magnesium binding site 2 out of 2 in the Open and Closed Forms of Wild-Type 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 Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:37.8 occ:1.00 O A:HOH2468 1.7 36.3 1.0 OE2 B:GLU1856 2.1 31.4 1.0 O B:HOH2379 2.1 37.9 1.0 O A:HOH2322 2.2 33.3 1.0 O B:HOH2212 2.3 36.0 1.0 O B:HOH2247 2.7 41.4 1.0 CD B:GLU1856 3.1 23.5 1.0 OE1 B:GLU1856 3.5 30.1 1.0 O A:HOH2494 3.6 41.0 1.0 OE1 A:GLU1856 3.7 23.4 1.0 O B:HOH2314 3.7 35.2 1.0 O B:HOH2327 4.0 38.4 1.0 O B:HOH2332 4.1 40.6 1.0 O A:HOH2399 4.3 41.0 1.0 OE2 A:GLU1856 4.3 25.3 1.0 OE2 B:GLU1855 4.3 36.3 1.0 CD A:GLU1856 4.4 21.5 1.0 O A:HOH2409 4.4 35.3 1.0 CG B:GLU1856 4.5 22.7 1.0 O B:GLU1855 4.6 19.3 1.0 O3 A:GOL2002 4.9 30.7 0.8 OE1 A:GLU1855 5.0 49.8 1.0

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