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Chlorine in PDB 5rac: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A, PDB code: 5rac was solved by M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.54 / 1.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.890, 93.950, 93.270, 90.00, 108.05, 90.00
R / Rfree (%) 18.7 / 22

Other elements in 5rac:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A (pdb code 5rac). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A, PDB code: 5rac:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5rac

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1802

b:27.6
occ:1.00
 O A:HOH2144 3.2 27.2 1.0
O A:HOH2120 3.3 26.7 1.0
O A:HOH2152 3.3 47.4 1.0
O A:HOH2261 3.4 44.4 1.0
N A:GLU1513 3.4 24.2 1.0
C A:LEU1511 3.5 22.5 1.0
CA A:LEU1511 3.6 22.0 1.0
CB A:GLU1513 3.6 29.0 1.0
CD A:PRO1512 3.7 25.6 1.0
N A:PRO1512 3.7 24.9 1.0
CG A:GLU1513 3.7 35.5 1.0
CD1 A:LEU1511 4.0 22.1 1.0
O A:LEU1511 4.0 18.7 1.0
CA A:GLU1513 4.1 24.6 1.0
CB A:TRP1402 4.2 22.1 0.4
CB A:LEU1511 4.3 20.1 1.0
CD2 A:TYR1514 4.4 19.5 1.0
CG A:PRO1512 4.4 26.3 1.0
C A:PRO1512 4.4 24.7 1.0
N A:TYR1514 4.5 20.4 1.0
CA A:PRO1512 4.6 26.0 1.0
OE2 A:GLU1513 4.7 49.9 1.0
O A:HOH1998 4.7 31.9 1.0
CD A:GLU1513 4.7 51.3 1.0
CE2 A:TYR1514 4.8 22.3 1.0
N A:LEU1511 4.8 20.1 1.0
CG A:LEU1511 4.8 21.1 1.0
C A:GLU1513 4.8 24.8 1.0
O A:HOH2008 4.9 49.1 1.0
CG A:TRP1402 4.9 22.9 0.4

Chlorine binding site 2 out of 5 in 5rac

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1803

b:42.4
occ:1.00
 O A:HOH1985 3.0 49.7 1.0
NH1 A:ARG1501 3.3 36.2 1.0
C A:MET1498 3.4 39.8 1.0
CA A:MET1498 3.4 34.4 1.0
N A:THR1500 3.4 33.5 1.0
CB A:THR1500 3.6 43.3 1.0
CD A:ARG1501 3.6 40.5 1.0
N A:ARG1501 3.6 34.9 1.0
N A:PRO1499 3.7 41.6 1.0
O A:MET1498 3.7 36.6 1.0
CB A:MET1498 3.8 34.7 1.0
CA A:THR1500 3.9 36.9 1.0
CD A:PRO1499 3.9 41.4 1.0
O A:HOH2217 4.0 46.5 1.0
OG1 A:THR1500 4.1 42.8 1.0
C A:THR1500 4.3 38.5 1.0
CZ A:ARG1501 4.3 36.1 1.0
C A:PRO1499 4.4 33.6 1.0
NE A:ARG1501 4.5 35.9 1.0
CB A:ARG1501 4.5 33.6 1.0
CG A:PRO1499 4.6 39.9 1.0
CA A:PRO1499 4.6 35.4 1.0
CG A:ARG1501 4.7 38.1 1.0
CA A:ARG1501 4.7 34.2 1.0
N A:MET1498 4.7 32.8 1.0
O A:MET1497 4.7 32.1 1.0
CG2 A:THR1500 4.7 43.9 1.0
CG A:MET1498 4.8 36.1 1.0

Chlorine binding site 3 out of 5 in 5rac

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1804

b:36.1
occ:1.00
 N A:ASN1558 3.2 22.4 1.0
OE1 A:GLN1650 3.4 39.9 1.0
NZ A:LYS1484 3.6 33.0 1.0
O A:HOH2209 3.6 39.9 1.0
CA A:THR1557 3.8 21.8 1.0
CG A:GLN1650 3.9 30.0 1.0
CB A:ASN1558 3.9 22.8 1.0
C A:THR1557 4.0 22.2 1.0
O A:HOH2132 4.1 57.1 1.0
CD A:GLN1650 4.1 33.8 1.0
CA A:ASN1558 4.1 22.8 1.0
CG2 A:THR1557 4.2 27.1 1.0
O A:HOH2265 4.3 68.6 1.0
CG A:ASN1558 4.3 26.5 1.0
O A:THR1556 4.4 23.9 1.0
ND2 A:ASN1558 4.4 25.2 1.0
O A:GLN1650 4.4 29.3 1.0
CB A:THR1557 4.5 25.9 1.0
O A:HOH2099 4.6 39.5 1.0
O A:ASN1558 4.8 20.8 1.0
N A:THR1557 4.8 21.7 1.0
OG1 A:THR1557 4.8 25.5 1.0
CE A:LYS1484 4.8 35.1 1.0
OD1 A:ASN1558 4.9 24.6 1.0
C A:ASN1558 5.0 20.1 1.0
C A:THR1556 5.0 22.9 1.0

Chlorine binding site 4 out of 5 in 5rac

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Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1805

b:61.7
occ:1.00
 NE2 A:HIS1712 2.9 23.5 1.0
O A:HOH2069 3.1 21.2 1.0
O A:HOH1913 3.2 59.6 1.0
O A:HOH2228 3.3 37.0 1.0
CD2 A:HIS1709 3.4 22.6 1.0
CD2 A:HIS1712 3.8 27.1 1.0
CE1 A:HIS1712 3.9 25.4 1.0
NE2 A:HIS1709 4.1 23.7 1.0
O A:HOH2176 4.2 67.2 1.0
CG A:HIS1709 4.4 22.5 1.0
O A:HOH2160 4.6 23.2 1.0
O A:HOH1999 4.8 20.6 1.0
O A:HOH2231 4.8 75.3 1.0
O A:HOH2054 4.8 47.2 1.0
O A:GLU1708 4.8 22.4 1.0
CA A:GLY1412 4.9 24.8 1.0
CB A:HIS1709 4.9 23.6 1.0
CB A:ALA1619 4.9 23.3 1.0
O A:ALA1685 5.0 19.5 1.0
O A:HOH2222 5.0 50.6 1.0

Chlorine binding site 5 out of 5 in 5rac

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Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001810A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1802

b:44.8
occ:1.00
 OG1 B:THR1500 2.6 53.4 1.0
C B:MET1498 3.3 38.8 1.0
NH1 B:ARG1501 3.3 38.7 1.0
CA B:MET1498 3.3 36.9 1.0
N B:THR1500 3.4 36.8 1.0
CD B:ARG1501 3.5 41.7 1.0
N B:PRO1499 3.6 41.0 1.0
O B:MET1498 3.7 36.9 1.0
N B:ARG1501 3.8 37.3 1.0
CB B:THR1500 3.8 44.2 1.0
CD B:PRO1499 3.9 43.3 1.0
CB B:MET1498 3.9 37.1 1.0
CA B:THR1500 4.0 39.8 1.0
CZ B:ARG1501 4.3 38.6 1.0
CG2 B:THR1500 4.3 42.0 1.0
C B:PRO1499 4.3 39.3 1.0
C B:THR1500 4.4 36.8 1.0
NE B:ARG1501 4.4 41.2 1.0
CA B:PRO1499 4.5 41.8 1.0
CG B:PRO1499 4.5 44.5 1.0
O B:MET1497 4.6 37.1 1.0
N B:MET1498 4.6 33.0 1.0
CB B:ARG1501 4.6 35.3 1.0
CG B:ARG1501 4.6 39.1 1.0
CG B:MET1498 4.7 43.1 1.0
OE1 B:GLU1437 4.8 33.1 1.0
CA B:ARG1501 4.8 36.6 1.0
O B:HOH1912 4.9 56.6 1.0
CZ B:PHE1438 4.9 40.1 1.0

Reference:

M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Pandda Analysis Group Deposition of Human JMJD1B Screened Against the Dspl Fragment Library To Be Published.
Page generated: Sat Jul 12 08:03:59 2025

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