Chlorine 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:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl2002 b:21.6 occ:1.00 O A:HOH2167 3.2 15.6 1.0 N A:GLY1867 3.3 12.1 1.0 O A:HOH2384 3.6 44.1 1.0 CA A:GLY1867 3.6 12.3 1.0 CB A:ARG1865 3.7 11.9 1.0 NZ A:LYS1838 3.8 20.4 1.0 N A:LYS1866 4.1 12.9 1.0 NE A:ARG1865 4.2 14.0 1.0 CD A:ARG1865 4.2 13.2 1.0 CZ A:ARG1865 4.3 15.7 1.0 C A:ARG1865 4.4 11.5 1.0 O A:HOH2469 4.4 54.3 1.0 C A:LYS1866 4.4 12.2 1.0 CE A:LYS1838 4.5 17.6 1.0 O A:HOH2146 4.5 26.5 1.0 CA A:ARG1865 4.5 12.4 1.0 NH2 A:ARG1865 4.6 17.7 1.0 CG A:ARG1865 4.6 13.1 1.0 CA A:LYS1866 4.8 13.1 1.0 C A:GLY1867 4.8 11.6 1.0 NH1 A:ARG1865 4.9 16.3 1.0 O A:ARG1865 4.9 12.0 1.0

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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 A:Cl2003 b:22.2 occ:1.00 O A:HOH2203 3.0 25.4 1.0 O A:HOH2285 3.0 18.2 1.0 O B:HOH2115 3.2 14.3 1.0 C A:GLN1913 3.5 9.1 1.0 N A:MET1914 3.6 9.6 1.0 CA A:GLN1913 3.8 9.8 1.0 O A:GLN1913 3.8 10.7 1.0 CB A:MET1914 3.8 11.7 1.0 CE A:LYS1820 3.9 27.2 1.0 N A:GLN1913 4.1 10.6 1.0 CA A:MET1914 4.2 9.9 1.0 NZ A:LYS1820 4.3 25.6 1.0 CG A:LYS1820 4.3 16.3 1.0 O A:HOH2296 4.3 32.4 1.0 CD A:LYS1820 4.3 23.3 1.0 O A:HOH2217 4.4 27.4 1.0 O A:HOH2339 4.5 41.0 1.0 O B:HOH2204 4.5 26.8 1.0 OE1 A:GLU1844 4.5 17.6 1.0 O B:HOH2103 4.6 10.2 1.0 O A:HOH2179 4.7 22.0 1.0 C A:PRO1912 4.7 12.6 1.0 CB A:LYS1820 4.9 12.3 1.0 O A:HOH2398 4.9 34.5 1.0 CG A:MET1914 4.9 17.2 1.0 CB A:PRO1912 5.0 13.9 1.0 O B:HOH2216 5.0 24.7 1.0

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl2002 b:19.9 occ:1.00 OG1 B:THR1824 3.0 14.4 1.0 N B:ALA1837 3.1 14.6 1.0 O B:HOH2386 3.2 40.2 1.0 O B:HOH2281 3.3 28.9 1.0 CA B:LEU1836 3.7 16.2 1.0 CG B:GLN1830 3.7 13.0 1.0 CB B:THR1824 3.7 13.2 1.0 CD B:GLN1830 3.7 16.7 1.0 NE2 B:GLN1830 3.8 18.9 1.0 C B:LEU1836 3.9 14.7 1.0 CA B:TRP1827 3.9 9.7 1.0 CB B:ALA1837 3.9 16.8 1.0 N B:TRP1827 4.0 9.8 1.0 CG2 B:THR1824 4.0 14.5 1.0 CG2 B:VAL1826 4.1 12.4 1.0 CD2 B:LEU1836 4.1 13.6 1.0 CA B:ALA1837 4.1 15.1 1.0 CB B:TRP1827 4.3 11.1 1.0 C B:VAL1826 4.3 9.9 1.0 CB B:LEU1836 4.3 16.7 1.0 OE1 B:GLN1830 4.3 15.9 1.0 O B:HOH2350 4.3 39.7 1.0 O B:GLN1835 4.4 26.6 1.0 O B:VAL1826 4.5 11.6 1.0 N B:LEU1836 4.8 15.9 1.0 CG B:LEU1836 4.9 15.9 1.0

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl2003 b:18.7 occ:1.00 N B:THR1789 3.1 11.9 1.0 O B:HOH2258 3.3 32.6 1.0 CA B:VAL1788 3.5 13.1 1.0 OG1 B:THR1789 3.7 16.8 1.0 O B:HOH2227 3.8 13.7 1.0 C B:VAL1788 3.8 13.5 1.0 CB B:THR1789 3.9 13.8 1.0 CB B:VAL1788 3.9 15.1 1.0 CA B:THR1789 4.1 12.7 1.0 O B:HOH2202 4.4 34.4 1.0 CG1 B:VAL1788 4.5 15.5 1.0 O B:ARG1787 4.7 13.2 1.0 N B:VAL1788 4.8 12.2 1.0 O B:THR1789 4.9 15.5 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