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

Protein crystallography data

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

Other elements in 4jkb:

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:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4jkb

Go back to Chlorine Binding Sites List in 4jkb
Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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
A:Cl2003

b:22.5
occ:1.00
 O A:HOH2446 2.9 32.9 0.3
O A:HOH2316 3.2 20.7 1.0
N A:GLY1867 3.3 14.3 1.0
CA A:GLY1867 3.7 15.6 1.0
CB A:ARG1865 3.7 14.8 1.0
O A:HOH2432 3.7 47.6 1.0
NZ A:LYS1838 4.0 23.8 1.0
N A:LYS1866 4.1 14.7 1.0
NE A:ARG1865 4.2 16.2 1.0
CD A:ARG1865 4.2 17.1 1.0
CZ A:ARG1865 4.3 18.3 1.0
C A:ARG1865 4.4 13.4 1.0
CL A:CL2004 4.4 45.3 1.0
C A:LYS1866 4.4 14.5 1.0
O A:HOH2446 4.5 48.0 0.7
CA A:ARG1865 4.5 14.1 1.0
NH2 A:ARG1865 4.6 20.9 1.0
CG A:ARG1865 4.6 16.3 1.0
CE A:LYS1838 4.7 27.8 1.0
CA A:LYS1866 4.7 16.6 0.3
CA A:LYS1866 4.8 16.4 0.7
C A:GLY1867 4.8 13.9 1.0
NH1 A:ARG1865 4.8 18.5 1.0
O A:ARG1865 4.9 13.7 1.0

Chlorine binding site 2 out of 5 in 4jkb

Go back to Chlorine Binding Sites List in 4jkb
Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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
A:Cl2004

b:45.3
occ:1.00
 O A:HOH2291 2.9 38.9 1.0
O A:HOH2446 2.9 48.0 0.7
N A:LYS1866 3.1 14.7 1.0
O A:HOH2446 3.2 32.9 0.3
CG A:LYS1866 3.4 29.7 0.7
CA A:ARG1865 3.6 14.1 1.0
CG A:LYS1866 3.7 25.8 0.3
CB A:LYS1866 3.7 21.1 0.3
CB A:LYS1866 3.8 20.9 0.7
C A:ARG1865 3.8 13.4 1.0
CA A:LYS1866 4.0 16.6 0.3
CA A:LYS1866 4.0 16.4 0.7
CB A:ARG1865 4.1 14.8 1.0
CD A:LYS1866 4.2 25.6 0.3
O A:THR1864 4.4 17.7 1.0
CL A:CL2003 4.4 22.5 1.0
O A:HOH2172 4.6 19.7 1.0
CE A:LYS1866 4.6 33.5 0.3
CD A:LYS1866 4.7 29.0 0.7
CG A:ARG1865 4.7 16.3 1.0
N A:ARG1865 4.8 14.0 1.0
CE A:LYS1866 5.0 34.8 0.7

Chlorine binding site 3 out of 5 in 4jkb

Go back to Chlorine Binding Sites List in 4jkb
Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl binding site number 3 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
A:Cl2005

b:25.9
occ:1.00
 O A:HOH2248 2.9 33.4 1.0
O A:HOH2260 3.0 27.0 1.0
NE A:ARG1941 3.2 13.2 1.0
CG A:ARG1941 3.6 12.5 1.0
CB A:ARG1941 3.7 12.2 1.0
CD2 A:HIS1944 3.7 22.1 1.0
CD A:ARG1941 4.0 12.6 1.0
NH2 A:ARG1941 4.0 15.5 1.0
CZ A:ARG1941 4.0 13.8 1.0
CA A:ARG1941 4.1 12.6 1.0
CG A:PRO1892 4.1 14.7 1.0
CG1 A:VAL1945 4.2 22.2 0.4
CB A:GLN1890 4.2 15.7 1.0
O A:ARG1941 4.3 14.5 1.0
CG2 A:VAL1945 4.4 24.5 0.6
O A:HOH2436 4.5 42.8 0.5
CD A:PRO1892 4.5 14.9 1.0
CG A:HIS1944 4.6 19.2 1.0
C A:ARG1941 4.7 13.1 1.0
CB A:HIS1944 4.7 16.6 1.0
OE1 A:GLN1890 4.7 25.9 1.0
NE2 A:HIS1944 4.7 27.5 1.0
CG A:GLN1890 4.9 20.6 1.0
CB A:PRO1892 4.9 14.0 1.0

Chlorine binding site 4 out of 5 in 4jkb

Go back to Chlorine Binding Sites List in 4jkb
Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl2004

b:21.4
occ:0.80
 OG1 B:THR1824 3.0 18.4 1.0
N B:ALA1837 3.2 17.6 1.0
CA B:LEU1836 3.6 17.0 1.0
CB B:THR1824 3.7 17.5 1.0
CD B:LYS1840 3.7 23.4 0.4
CG B:GLN1830 3.8 16.9 1.0
NE2 B:GLN1830 3.8 21.7 1.0
CD B:GLN1830 3.8 17.4 1.0
CA B:TRP1827 3.8 12.8 1.0
C B:LEU1836 3.8 17.6 1.0
CE B:LYS1840 3.9 24.5 0.4
CG2 B:THR1824 3.9 19.4 1.0
O B:HOH2222 4.0 40.3 0.6
N B:TRP1827 4.0 12.5 1.0
CB B:ALA1837 4.0 20.5 1.0
CG2 B:VAL1826 4.1 16.4 1.0
CD2 B:LEU1836 4.1 16.7 1.0
CA B:ALA1837 4.1 17.9 1.0
O B:GLN1835 4.2 25.5 1.0
CB B:LEU1836 4.2 17.0 1.0
CB B:TRP1827 4.2 13.9 1.0
C B:VAL1826 4.3 13.0 1.0
OE1 B:GLN1830 4.4 18.2 1.0
O B:VAL1826 4.5 13.4 1.0
N B:LEU1836 4.7 18.7 1.0
CG B:LEU1836 4.8 17.5 1.0
C B:GLN1835 4.9 20.2 1.0
CG B:LYS1840 4.9 21.8 0.4
O B:LEU1836 5.0 20.4 1.0

Chlorine binding site 5 out of 5 in 4jkb

Go back to Chlorine Binding Sites List in 4jkb
Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl2005

b:31.2
occ:1.00
 O B:HOH2323 2.2 43.5 1.0
NZ B:LYS1840 3.1 25.7 0.4
N B:SER1825 3.1 13.4 1.0
O B:HOH2362 3.6 49.3 1.0
O B:HOH2222 3.7 40.3 0.6
CB B:SER1825 3.8 16.7 1.0
CE B:LYS1840 3.8 24.5 0.4
CA B:SER1825 3.9 13.5 1.0
CA B:THR1824 4.0 14.5 1.0
C B:THR1824 4.0 13.3 1.0
CG2 B:VAL1826 4.1 16.4 1.0
OG B:SER1825 4.2 19.9 1.0
O B:HOH2285 4.2 29.3 1.0
N B:VAL1826 4.2 12.2 1.0
OG1 B:THR1824 4.3 18.4 1.0
CG1 B:VAL1826 4.4 17.6 1.0
O B:HOH2296 4.5 39.4 0.8
C B:SER1825 4.5 12.9 1.0
O B:HIS1823 4.6 16.1 1.0
CH2 B:TRP1839 4.6 37.9 1.0
CB B:THR1824 4.7 17.5 1.0
CB B:VAL1826 4.7 15.3 1.0
CZ2 B:TRP1839 4.9 37.6 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 17:22:40 2025

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