Magnesium in PDB 4jkc: Open and Closed Forms of T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkc 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)	35.29 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.195, 77.932, 93.680, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 16.4

The structure of Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jkc). 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:22.9 occ:0.51 O B:HOH2259 2.0 35.3 1.0 OD1 B:ASP1781 2.0 23.9 1.0 O B:HOH2214 2.1 27.9 0.7 O B:HOH2284 2.1 45.9 1.0 O B:HOH2205 2.1 29.6 1.0 O B:HOH2176 2.3 33.2 0.7 CG B:ASP1781 2.9 18.8 1.0 O B:HOH2214 3.1 25.9 0.3 OD2 B:ASP1781 3.1 23.3 1.0 O B:HOH2176 3.7 15.9 0.3 OE1 B:GLN1894 4.2 28.6 1.0 O B:HOH2343 4.2 21.8 0.5 OG1 B:THR1864 4.2 31.1 1.0 O B:ASP1782 4.2 17.6 1.0 CB B:ASP1781 4.3 17.2 1.0 O B:HOH2167 4.3 29.9 1.0 O B:HOH2163 4.4 24.8 1.0 O B:HOH2105 4.6 18.6 0.5 N B:ASP1782 4.7 14.1 1.0 OD1 B:ASP1782 4.8 17.6 0.3 CA B:ASP1781 4.8 14.5 1.0 O B:HOH2160 4.9 32.5 1.0 CB B:ARG1865 5.0 26.4 1.0 CD B:GLN1894 5.0 30.9 1.0

Magnesium binding site 2 out of 2 in the Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:42.4 occ:1.00 O A:HOH2422 1.7 39.3 1.0 O B:HOH2348 1.9 42.0 1.0 OE2 B:GLU1856 2.0 28.2 0.6 O A:HOH2432 2.2 39.9 1.0 O B:HOH2374 2.4 41.7 1.0 O B:HOH2249 2.5 39.2 1.0 OE1 B:GLU1856 2.9 17.6 0.4 CD B:GLU1856 3.0 24.2 0.6 OE1 B:GLU1856 3.4 24.1 0.6 OE1 A:GLU1856 3.6 28.7 1.0 O A:HOH2255 3.7 26.6 0.5 CD B:GLU1856 3.8 17.2 0.4 OE2 B:GLU1856 3.9 17.1 0.4 O A:HOH2425 3.9 45.7 1.0 O B:HOH2314 4.2 47.9 1.0 O B:HOH2305 4.2 43.4 1.0 OE2 A:GLU1856 4.2 34.5 1.0 OE2 B:GLU1855 4.2 41.6 1.0 CD A:GLU1856 4.3 33.0 1.0 CG B:GLU1856 4.3 20.0 0.6 O A:HOH2255 4.4 27.4 0.5 O B:GLU1855 4.6 19.6 1.0 O B:HOH2362 4.8 49.3 1.0 OE1 A:GLU1855 5.0 47.1 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