Cobalt in PDB 4jk9: Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion

The structure of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion, PDB code: 4jk9 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)	34.27 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.228, 78.291, 94.090, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.5

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

Chlorine

(Cl)

3 atoms

The binding sites of Cobalt atom in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion (pdb code 4jk9). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion, PDB code: 4jk9:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2001 b:24.8 occ:1.00 O A:HOH2388 1.7 28.7 1.0 NE2 A:HIS1966 2.2 18.0 1.0 O A:HOH2269 2.2 20.8 1.0 O A:HOH2356 2.2 27.8 1.0 NE2 A:HIS1965 2.2 21.9 1.0 OD1 A:ASP1922 2.3 21.0 1.0 CG A:ASP1922 2.9 20.2 1.0 OD2 A:ASP1922 3.1 27.6 1.0 CD2 A:HIS1966 3.1 17.1 1.0 CE1 A:HIS1965 3.2 24.7 1.0 CE1 A:HIS1966 3.2 18.5 1.0 CD2 A:HIS1965 3.2 22.2 1.0 CG A:HIS1966 4.3 16.6 1.0 ND1 A:HIS1966 4.3 16.9 1.0 ND1 A:HIS1965 4.3 25.6 1.0 CB A:ASP1922 4.3 14.4 1.0 O B:HOH2170 4.3 22.4 1.0 CG A:HIS1965 4.3 21.7 1.0 O B:HOH2295 4.4 29.6 1.0 N A:ASP1922 4.6 12.9 1.0 O A:HOH2147 4.6 26.1 1.0 OE1 A:GLU1963 4.7 34.6 1.0 C A:ASP1921 4.7 13.3 1.0 CA A:ASP1922 4.8 13.1 1.0

Cobalt binding site 2 out of 7 in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2002 b:22.9 occ:0.50 O A:HOH2383 2.0 27.3 0.5 OE2 A:GLU1843 2.0 26.0 1.0 O A:HOH2347 2.1 39.0 1.0 O A:HOH2351 2.2 33.6 1.0 O A:HOH2369 2.2 36.3 1.0 CD A:GLU1843 3.0 20.7 1.0 OE1 A:GLU1843 3.4 25.4 1.0 O A:HOH2365 4.0 36.5 1.0 CG A:GLU1843 4.4 16.6 1.0

Cobalt binding site 3 out of 7 in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2001 b:14.3 occ:0.40 OD1 B:ASP1781 2.0 22.3 1.0 O B:HOH2320 2.0 18.9 0.4 O B:HOH2279 2.2 18.1 0.4 O B:HOH2153 2.3 15.6 0.4 O B:HOH2172 2.5 35.1 1.0 CG B:ASP1781 2.8 17.6 1.0 OD2 B:ASP1781 3.1 22.3 1.0 O B:ASP1782 4.2 20.0 1.0 CB B:ASP1781 4.3 16.9 1.0 OE1 B:GLN1894 4.3 27.3 1.0 OG1 B:THR1864 4.4 30.9 1.0 O B:HOH2148 4.4 30.3 1.0 O B:HOH2214 4.6 31.2 1.0 O B:HOH2142 4.6 26.2 1.0 N B:ASP1782 4.6 15.2 1.0 OD2 B:ASP1782 4.6 29.3 1.0 CA B:ASP1781 4.8 15.3 1.0

Cobalt binding site 4 out of 7 in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2002 b:19.3 occ:0.50 CO B:CO2002 0.0 19.3 0.5 CO B:CO2002 1.7 33.4 0.5 OE2 B:GLU1856 1.8 15.7 0.4 O B:HOH2280 2.0 30.8 1.0 O B:HOH2319 2.0 31.7 1.0 O B:HOH2240 2.2 15.0 0.5 O A:HOH2327 2.2 33.0 1.0 CD B:GLU1856 2.8 12.4 0.4 OE1 B:GLU1856 2.9 25.2 0.6 OE1 B:GLU1856 3.2 11.1 0.4 CD B:GLU1856 3.7 23.8 0.6 OE1 A:GLU1856 3.8 26.1 1.0 OE2 B:GLU1856 3.8 27.6 0.6 O B:HOH2169 3.8 18.8 0.6 O B:HOH2265 4.0 22.6 0.6 O A:HOH2363 4.0 44.6 1.0 O B:HOH2266 4.0 18.4 0.4 CG B:GLU1856 4.2 12.5 0.4 OE2 A:GLU1856 4.2 25.4 1.0 OE2 B:GLU1855 4.3 32.2 1.0 O B:GLU1855 4.4 18.2 1.0 CD A:GLU1856 4.4 24.1 1.0 OE2 A:GLU1855 4.5 34.6 1.0 CG B:GLU1855 5.0 23.1 1.0

Cobalt binding site 5 out of 7 in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2002 b:33.4 occ:0.50 CO B:CO2002 0.0 33.4 0.5 CO B:CO2002 1.7 19.3 0.5 OE1 A:GLU1856 2.3 26.1 1.0 OE2 B:GLU1856 2.4 15.7 0.4 O B:HOH2240 2.5 15.0 0.5 O A:HOH2327 2.6 33.0 1.0 O A:HOH2363 2.9 44.6 1.0 O B:HOH2319 2.9 31.7 1.0 CD A:GLU1856 3.1 24.1 1.0 OE2 A:GLU1856 3.3 25.4 1.0 CD B:GLU1856 3.4 12.4 0.4 OE1 B:GLU1856 3.4 25.2 0.6 O B:HOH2169 3.6 18.8 0.6 O B:HOH2280 3.7 30.8 1.0 OE1 B:GLU1856 3.8 11.1 0.4 OE2 B:GLU1856 4.0 27.6 0.6 CD B:GLU1856 4.1 23.8 0.6 OE2 A:GLU1855 4.1 34.6 1.0 CG A:GLU1856 4.5 21.6 1.0 O A:GLU1855 4.6 20.0 1.0 CG B:GLU1856 4.7 12.5 0.4 O B:HOH2266 4.7 18.4 0.4 CA A:GLU1856 4.9 16.7 1.0 O A:HOH2172 4.9 24.6 1.0 CB A:GLU1856 4.9 17.7 1.0

Cobalt binding site 6 out of 7 in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2003 b:26.7 occ:1.00 O B:HOH2317 1.8 41.6 1.0 O B:HOH2330 2.1 25.1 1.0 OD1 B:ASP1922 2.2 23.6 1.0 NE2 B:HIS1966 2.2 20.4 1.0 NE2 B:HIS1965 2.2 26.0 1.0 O B:HOH2283 2.2 33.1 1.0 CG B:ASP1922 3.0 21.9 1.0 CE1 B:HIS1965 3.1 27.5 1.0 CD2 B:HIS1966 3.1 19.8 1.0 CE1 B:HIS1966 3.1 21.8 1.0 OD2 B:ASP1922 3.2 27.3 1.0 CD2 B:HIS1965 3.3 26.1 1.0 ND1 B:HIS1965 4.2 27.8 1.0 ND1 B:HIS1966 4.3 19.1 1.0 CG B:HIS1966 4.3 19.8 1.0 O A:HOH2153 4.3 21.7 1.0 CG B:HIS1965 4.3 25.5 1.0 O A:HOH2345 4.4 34.0 1.0 O A:HOH2368 4.4 46.7 1.0 CB B:ASP1922 4.4 18.0 1.0 O B:HOH2217 4.4 29.9 1.0 OE1 B:GLU1963 4.5 42.9 1.0 N B:ASP1922 4.6 15.2 1.0 C B:ASP1921 4.7 14.7 1.0 CA B:ASP1922 4.8 15.9 1.0 O B:ASP1921 5.0 14.9 1.0

Cobalt binding site 7 out of 7 in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2004 b:17.7 occ:0.40 O B:HOH2292 1.8 16.9 0.4 OE2 B:GLU1888 2.0 31.7 1.0 O B:HOH2226 2.2 21.0 0.4 CD B:GLU1888 3.1 31.9 1.0 OE1 B:GLU1888 3.6 40.9 1.0 N B:GLU1888 4.2 19.9 1.0 CG B:GLU1888 4.4 28.2 1.0 CA B:SER1887 4.6 17.7 1.0 CB B:GLU1888 4.6 23.2 1.0 OG B:SER1887 4.7 19.1 1.0 C B:SER1887 4.9 17.7 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