Magnesium in PDB 4jkb: Open and Closed Forms of V1788D Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of V1788D Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkb 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)	40.04 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.355, 78.159, 93.766, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 14.5

The structure of Open and Closed Forms of V1788D 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 V1788D Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jkb). 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 V1788D Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Open and Closed Forms of V1788D 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 V1788D Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:20.8 occ:0.48 O B:HOH2305 2.0 22.5 0.5 O B:HOH2219 2.0 32.6 1.0 O B:HOH2220 2.1 21.0 0.6 OD1 B:ASP1781 2.1 23.0 1.0 O B:HOH2249 2.1 21.3 0.5 O B:HOH2370 2.2 24.1 0.4 CG B:ASP1781 2.9 20.1 1.0 OD2 B:ASP1781 3.0 23.1 1.0 O B:HOH2249 3.4 22.0 0.5 OG1 B:THR1864 4.1 26.9 1.0 O B:HOH2287 4.1 36.2 1.0 O B:HOH2398 4.2 48.2 1.0 O B:ASP1782 4.2 14.9 1.0 OE1 B:GLN1894 4.3 27.0 1.0 CB B:ASP1781 4.3 17.4 1.0 O B:HOH2136 4.4 33.1 1.0 O B:HOH2224 4.4 22.5 1.0 O B:HOH2149 4.5 14.3 0.3 OD1 B:ASP1782 4.7 18.3 0.3 N B:ASP1782 4.7 13.5 1.0 CA B:ASP1781 4.9 14.2 1.0 O B:HOH2190 4.9 29.5 1.0

Magnesium binding site 2 out of 2 in the Open and Closed Forms of V1788D 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 V1788D Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:39.1 occ:1.00 O A:HOH2413 1.9 33.3 1.0 OE2 B:GLU1856 2.0 23.6 0.5 O B:HOH2342 2.3 48.2 1.0 O A:HOH2302 2.3 40.6 1.0 O B:HOH2218 2.3 38.0 1.0 OE1 B:GLU1856 2.7 22.6 0.5 CD B:GLU1856 3.0 18.7 0.5 OE1 B:GLU1856 3.3 19.4 0.5 OE1 A:GLU1856 3.6 26.9 1.0 CD B:GLU1856 3.6 20.4 0.5 O B:HOH2300 3.7 22.2 0.4 OE2 B:GLU1856 3.8 19.8 0.5 O B:HOH2310 3.9 43.8 1.0 O A:HOH2369 4.2 46.5 1.0 OE2 A:GLU1856 4.2 30.9 1.0 O B:HOH2313 4.2 47.5 1.0 CD A:GLU1856 4.3 27.3 1.0 CG B:GLU1856 4.3 16.2 0.5 OE2 B:GLU1855 4.3 36.9 1.0 O B:HOH2318 4.4 43.0 1.0 O B:GLU1855 4.6 18.2 1.0 OE1 A:GLU1855 5.0 43.4 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