Chlorine 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:

Cobalt

(Co)

7 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl2004 b:29.8 occ:1.00 N A:TYR1930 3.3 11.7 1.0 O A:HOH2177 3.4 27.3 1.0 O A:HOH2382 3.5 50.2 1.0 N A:SER1929 3.7 13.1 1.0 CB A:TYR1930 3.7 15.0 1.0 CB A:SER1929 3.8 13.4 1.0 CB A:SER1928 3.8 15.3 1.0 CA A:SER1929 4.1 11.9 1.0 CA A:TYR1930 4.1 13.4 1.0 CB A:PHE1772 4.1 35.3 1.0 C A:SER1929 4.1 12.1 1.0 OG A:SER1928 4.1 15.3 1.0 CG A:PHE1772 4.1 31.1 1.0 O A:HOH2124 4.2 19.4 0.5 CD2 A:PHE1772 4.4 31.5 1.0 C A:SER1928 4.5 12.0 1.0 OG A:SER1929 4.6 16.5 1.0 CA A:SER1928 4.7 12.4 1.0 CD1 A:PHE1772 4.7 28.9 1.0 O A:HOH2316 5.0 41.8 1.0

Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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 B:Cl2005 b:25.8 occ:1.00 O B:HOH2155 2.9 31.4 1.0 OG1 B:THR1824 3.0 19.1 1.0 N B:ALA1837 3.2 21.9 1.0 CB B:THR1824 3.7 17.4 1.0 CG B:GLN1830 3.7 17.4 1.0 CD B:GLN1830 3.7 17.3 1.0 CA B:LEU1836 3.8 24.0 1.0 CA B:TRP1827 3.8 15.0 1.0 CG2 B:THR1824 3.9 18.4 1.0 NE2 B:GLN1830 3.9 21.0 1.0 C B:LEU1836 3.9 22.5 1.0 CB B:ALA1837 3.9 23.5 1.0 N B:TRP1827 3.9 14.3 1.0 CE B:LYS1840 4.0 28.8 1.0 CD2 B:LEU1836 4.0 21.0 1.0 CD B:LYS1840 4.0 29.0 1.0 CG2 B:VAL1826 4.1 18.0 1.0 CA B:ALA1837 4.1 23.0 1.0 CB B:TRP1827 4.2 16.2 1.0 C B:VAL1826 4.2 15.1 1.0 O B:GLN1835 4.3 31.4 1.0 OE1 B:GLN1830 4.3 20.5 1.0 CB B:LEU1836 4.4 25.0 1.0 O B:VAL1826 4.4 15.6 1.0 N B:LEU1836 4.8 25.0 1.0 CG B:LEU1836 4.9 23.2 1.0

Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl 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:Cl2006 b:33.2 occ:1.00 NZ B:LYS1840 2.9 34.4 1.0 N B:SER1825 3.1 16.9 1.0 CB B:SER1825 3.7 16.9 1.0 CE B:LYS1840 3.8 28.8 1.0 CA B:SER1825 3.9 16.3 1.0 CA B:THR1824 4.0 16.0 1.0 C B:THR1824 4.0 16.2 1.0 OG B:SER1825 4.0 20.4 1.0 CG2 B:VAL1826 4.2 18.0 1.0 N B:VAL1826 4.2 15.5 1.0 CG1 B:VAL1826 4.3 20.0 1.0 OG1 B:THR1824 4.3 19.1 1.0 C B:SER1825 4.4 16.4 1.0 CH2 B:TRP1839 4.6 33.2 1.0 O B:HIS1823 4.6 16.7 1.0 CB B:VAL1826 4.7 16.7 1.0 CB B:THR1824 4.8 17.4 1.0 CZ2 B:TRP1839 4.9 32.6 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