Magnesium in PDB 4jkd: Open and Closed Forms of I1790Y Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of I1790Y Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkd 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)	40.28 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.407, 77.738, 94.196, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 18.8

The structure of Open and Closed Forms of I1790Y 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 I1790Y Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jkd). 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 I1790Y Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Open and Closed Forms of I1790Y 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 I1790Y Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:34.4 occ:1.00 O A:HOH2258 1.9 25.2 0.5 O B:HOH2417 2.0 40.6 1.0 O A:HOH2279 2.2 39.4 1.0 O A:HOH2390 2.2 36.5 1.0 O B:HOH2273 2.3 32.5 1.0 OE1 B:GLU1856 2.6 28.1 1.0 OE2 A:GLU1856 2.7 32.1 0.5 CD B:GLU1856 3.6 29.5 1.0 OE1 A:GLU1856 3.7 21.7 0.5 CD A:GLU1856 3.8 26.9 0.5 OE2 B:GLU1856 3.8 33.9 1.0 O B:HOH2331 3.9 37.5 1.0 O B:HOH2334 4.1 42.6 1.0 OE1 A:GLU1856 4.1 30.9 0.5 O B:HOH2224 4.2 27.4 0.5 OE2 A:GLU1856 4.2 19.8 0.5 O A:HOH2396 4.2 40.2 1.0 OE2 B:GLU1855 4.4 39.1 1.0 CD A:GLU1856 4.4 20.1 0.5 O B:GLU1855 4.7 18.4 1.0 CG B:GLU1856 5.0 23.2 1.0

Magnesium binding site 2 out of 2 in the Open and Closed Forms of I1790Y 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 I1790Y Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:17.3 occ:0.50 O B:HOH2406 1.9 24.8 0.5 O B:HOH2404 2.0 21.6 0.5 O B:HOH2379 2.0 29.0 0.7 OD1 B:ASP1781 2.1 16.6 1.0 O B:HOH2377 2.1 27.2 1.0 CG B:ASP1781 3.0 17.0 1.0 O B:HOH2379 3.1 14.3 0.3 OD2 B:ASP1781 3.3 19.6 1.0 O B:HOH2182 3.5 27.5 1.0 OG1 B:THR1864 4.1 27.9 1.0 NE2 B:GLN1894 4.1 17.6 1.0 O B:HOH2256 4.1 16.6 0.5 O B:ASP1782 4.2 13.8 1.0 O B:HOH2169 4.3 29.0 1.0 CB B:ASP1781 4.4 14.3 1.0 O B:HOH2163 4.4 21.2 1.0 N B:ASP1782 4.7 11.3 1.0 O B:HOH2256 4.8 20.8 0.5 O B:HOH2391 4.8 45.0 1.0 OE1 B:GLN1894 4.8 38.0 1.0 O B:HOH2160 4.8 27.4 1.0 CA B:ASP1781 4.8 12.2 1.0 CD B:GLN1894 4.9 23.4 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