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Chlorine in PDB 4jk8: Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion

Protein crystallography data

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk8 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) 40.29 / 1.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.198, 78.037, 94.063, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 16

Other elements in 4jk8:

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jk8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4jk8

Go back to Chlorine Binding Sites List in 4jk8
Chlorine binding site 1 out of 6 in the Open and Closed Forms of R1865A 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2003

b:25.8
occ:1.00
 N A:TYR1930 3.3 14.6 1.0
O A:HOH2322 3.4 42.4 1.0
O A:HOH2177 3.4 33.4 1.0
N A:SER1929 3.8 14.7 1.0
CB A:TYR1930 3.8 16.3 1.0
CB A:SER1928 3.8 17.1 1.0
CB A:PHE1772 3.8 29.8 0.4
CB A:SER1929 3.9 15.5 1.0
CB A:PHE1772 4.0 31.3 0.6
CG A:PHE1772 4.0 21.7 0.4
CD2 A:PHE1772 4.1 20.9 0.6
CD2 A:PHE1772 4.1 25.0 0.4
CG A:PHE1772 4.1 25.2 0.6
CA A:SER1929 4.1 14.6 1.0
O A:HOH2124 4.1 22.3 0.5
OG A:SER1928 4.1 17.0 1.0
CA A:TYR1930 4.1 15.0 1.0
C A:SER1929 4.2 13.8 1.0
C A:SER1928 4.5 14.8 1.0
CA A:SER1928 4.7 15.8 1.0
OG A:SER1929 4.7 17.0 1.0
CD1 A:PHE1772 4.8 23.1 0.4
CE2 A:PHE1772 4.8 21.8 0.6
CE2 A:PHE1772 4.8 23.9 0.4
CD1 A:PHE1772 4.9 23.3 0.6

Chlorine binding site 2 out of 6 in 4jk8

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Chlorine binding site 2 out of 6 in the Open and Closed Forms of R1865A 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2004

b:29.2
occ:1.00
 O A:HOH2233 3.0 38.3 1.0
O A:HOH2214 3.1 29.2 1.0
NE A:ARG1941 3.2 15.8 1.0
CG A:ARG1941 3.6 15.1 1.0
CB A:ARG1941 3.7 15.3 1.0
CD2 A:HIS1944 3.8 25.6 1.0
CD A:ARG1941 4.0 15.2 1.0
NH2 A:ARG1941 4.1 17.7 1.0
CA A:ARG1941 4.1 15.4 1.0
CZ A:ARG1941 4.1 16.2 1.0
CG1 A:VAL1945 4.1 30.7 1.0
CG A:PRO1892 4.1 18.2 1.0
O A:ARG1941 4.3 17.3 1.0
CB A:GLN1890 4.4 20.0 1.0
CG A:HIS1944 4.6 22.3 1.0
CD A:PRO1892 4.6 18.1 1.0
C A:ARG1941 4.7 16.2 1.0
CB A:HIS1944 4.7 19.8 1.0
NE2 A:HIS1944 4.8 32.0 1.0
OE1 A:GLN1890 4.8 30.7 1.0
CB A:PRO1892 4.8 19.4 1.0
CG A:GLN1890 5.0 23.9 1.0

Chlorine binding site 3 out of 6 in 4jk8

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Chlorine binding site 3 out of 6 in the Open and Closed Forms of R1865A 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2005

b:22.7
occ:0.60
 O A:HOH2425 1.6 19.0 0.4
NZ A:LYS1820 2.2 18.3 0.4
CE A:LYS1820 2.4 21.4 0.4
CD A:LYS1820 2.4 20.2 0.4
O A:HOH2234 3.0 31.7 1.0
O A:HOH2225 3.1 19.0 0.5
O A:HOH2146 3.2 19.3 1.0
C A:GLN1913 3.6 14.7 1.0
N A:MET1914 3.6 14.8 1.0
CB A:MET1914 3.7 16.0 0.5
CB A:MET1914 3.7 19.0 0.5
CG A:LYS1820 3.9 18.3 0.4
O A:GLN1913 3.9 16.4 1.0
CA A:GLN1913 4.0 15.1 1.0
CE A:LYS1820 4.0 24.6 0.6
CA A:MET1914 4.1 14.7 0.5
CA A:MET1914 4.1 15.9 0.5
CG A:LYS1820 4.2 20.4 0.6
N A:GLN1913 4.2 16.1 1.0
CD A:LYS1820 4.3 22.1 0.6
O A:HOH2256 4.3 37.5 1.0
NZ A:LYS1820 4.4 17.4 0.6
OE1 A:GLU1844 4.5 22.3 1.0
O A:HOH2212 4.5 26.6 1.0
O B:HOH2105 4.5 15.5 1.0
O A:HOH2197 4.5 33.0 1.0
CG A:MET1914 4.6 19.9 0.5
O A:HOH2224 4.6 31.2 0.6
CB A:LYS1820 4.7 15.2 0.4
CB A:LYS1820 4.7 16.1 0.6
CG A:MET1914 4.8 17.4 0.5
O A:HOH2432 4.8 44.9 1.0
SD A:MET1914 4.9 21.5 0.5
C A:PRO1912 4.9 16.7 1.0

Chlorine binding site 4 out of 6 in 4jk8

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Chlorine binding site 4 out of 6 in the Open and Closed Forms of R1865A 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2003

b:19.6
occ:1.00
 OG1 B:THR1824 3.1 17.3 1.0
O B:HOH2158 3.1 21.5 1.0
N B:ALA1837 3.3 18.4 1.0
CG B:GLN1830 3.7 16.6 1.0
CD B:GLN1830 3.7 16.6 1.0
NE2 B:GLN1830 3.7 17.7 1.0
CA B:TRP1827 3.8 16.0 1.0
CB B:THR1824 3.8 15.9 1.0
CB B:ALA1837 3.8 21.6 1.0
CG2 B:THR1824 3.9 16.1 1.0
CD1 B:LEU1836 3.9 21.3 1.0
N B:TRP1827 3.9 15.1 1.0
CA B:LEU1836 4.1 17.4 1.0
CA B:ALA1837 4.1 20.0 1.0
C B:LEU1836 4.1 18.1 1.0
CG2 B:VAL1826 4.1 18.0 1.0
CD B:LYS1840 4.2 23.9 1.0
C B:VAL1826 4.2 15.4 1.0
CB B:TRP1827 4.2 17.1 1.0
CE B:LYS1840 4.2 24.8 1.0
OE1 B:GLN1830 4.3 17.8 1.0
O B:VAL1826 4.4 16.2 1.0
CG B:LEU1836 4.4 19.9 1.0
O B:GLN1835 4.7 20.9 1.0
CB B:LEU1836 4.8 18.8 1.0

Chlorine binding site 5 out of 6 in 4jk8

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Chlorine binding site 5 out of 6 in the Open and Closed Forms of R1865A 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 5 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2004

b:27.7
occ:1.00
 O B:HOH2421 2.2 34.7 0.5
NZ B:LYS1840 3.0 29.2 1.0
N B:SER1825 3.1 15.2 1.0
O B:HOH2421 3.2 34.6 0.5
O B:HOH2381 3.2 35.7 1.0
CB B:SER1825 3.7 17.7 1.0
CE B:LYS1840 3.8 24.8 1.0
CA B:SER1825 3.9 15.3 1.0
CA B:THR1824 4.1 15.3 1.0
C B:THR1824 4.1 14.6 1.0
OG B:SER1825 4.1 19.3 1.0
CG2 B:VAL1826 4.1 18.0 1.0
N B:VAL1826 4.2 15.2 1.0
CG1 B:VAL1826 4.3 19.8 1.0
OG1 B:THR1824 4.3 17.3 1.0
C B:SER1825 4.5 15.6 1.0
O B:HIS1823 4.6 16.5 1.0
O B:HOH2392 4.7 40.6 1.0
CB B:VAL1826 4.7 17.5 1.0
O B:HOH2297 4.7 39.0 1.0
CB B:THR1824 4.8 15.9 1.0

Chlorine binding site 6 out of 6 in 4jk8

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Chlorine binding site 6 out of 6 in the Open and Closed Forms of R1865A 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 6 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2005

b:26.8
occ:0.73
 CG2 B:VAL1788 3.2 23.1 0.2
O B:HOH2153 3.2 27.6 1.0
N B:THR1789 3.3 19.0 1.0
CA B:VAL1788 3.6 18.1 0.2
O B:HOH2171 3.6 27.0 1.0
CA B:VAL1788 3.7 18.7 0.8
CB B:VAL1788 3.9 18.9 0.2
C B:VAL1788 4.0 18.4 1.0
CG1 B:VAL1788 4.0 24.4 0.8
CB B:THR1789 4.1 22.7 1.0
OG1 B:THR1789 4.1 23.7 1.0
CB B:VAL1788 4.2 22.0 0.8
CA B:THR1789 4.3 20.1 1.0
CG2 B:VAL1788 4.4 20.3 0.8
O B:ARG1787 4.8 18.6 1.0
N B:VAL1788 4.8 17.8 1.0
O B:THR1789 4.9 21.1 1.0

Reference:

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
Page generated: Fri Jul 11 17:21:43 2025

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