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Chlorine in PDB 5ras: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B, PDB code: 5ras 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) 89.11 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.030, 93.630, 93.796, 90.00, 108.19, 90.00
R / Rfree (%) 19.2 / 21.6

Other elements in 5ras:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B 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 XS036302B (pdb code 5ras). 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 XS036302B, PDB code: 5ras:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ras

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B


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 XS036302B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1801

b:20.9
occ:1.00
 O A:HOH2149 3.3 21.2 1.0
O A:HOH2269 3.3 35.0 1.0
O A:HOH2013 3.3 19.1 1.0
N A:GLU1513 3.4 16.4 1.0
C A:LEU1511 3.5 16.9 1.0
CA A:LEU1511 3.5 16.4 1.0
CB A:GLU1513 3.7 20.5 1.0
N A:PRO1512 3.7 17.7 1.0
O A:HOH2192 3.7 44.1 1.0
CD A:PRO1512 3.8 18.3 1.0
CG A:GLU1513 3.9 24.5 1.0
CD1 A:LEU1511 3.9 17.3 1.0
O A:LEU1511 4.0 15.1 1.0
CA A:GLU1513 4.1 17.5 1.0
CB A:LEU1511 4.2 15.9 1.0
CB A:TRP1402 4.3 17.7 1.0
CD2 A:TYR1514 4.4 14.6 1.0
CG A:PRO1512 4.4 21.2 1.0
C A:PRO1512 4.4 19.0 1.0
N A:TYR1514 4.5 15.8 1.0
OE2 A:GLU1513 4.6 33.1 1.0
CA A:PRO1512 4.6 18.9 1.0
O A:HOH2004 4.7 27.9 1.0
CD A:GLU1513 4.7 33.8 1.0
CG A:LEU1511 4.7 16.5 1.0
N A:LEU1511 4.7 15.9 1.0
CE2 A:TYR1514 4.8 16.3 1.0
C A:GLU1513 4.8 16.6 1.0

Chlorine binding site 2 out of 5 in 5ras

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B


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 XS036302B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1802

b:37.0
occ:1.00
 O A:HOH2056 3.1 45.9 1.0
NH1 A:ARG1501 3.3 30.4 1.0
CA A:MET1498 3.3 29.8 1.0
C A:MET1498 3.3 32.7 1.0
N A:THR1500 3.3 26.2 1.0
CD A:ARG1501 3.5 31.6 1.0
CB A:THR1500 3.6 35.6 1.0
N A:ARG1501 3.6 26.2 1.0
N A:PRO1499 3.6 30.8 1.0
CB A:MET1498 3.7 29.7 1.0
O A:MET1498 3.8 29.4 1.0
CA A:THR1500 3.9 28.0 1.0
O A:HOH2227 3.9 41.8 1.0
CD A:PRO1499 4.0 33.1 1.0
OG1 A:THR1500 4.1 34.7 1.0
C A:THR1500 4.2 29.6 1.0
CZ A:ARG1501 4.3 31.6 1.0
C A:PRO1499 4.3 29.1 1.0
NE A:ARG1501 4.4 30.1 1.0
CB A:ARG1501 4.5 26.5 1.0
CA A:PRO1499 4.5 30.8 1.0
CG A:ARG1501 4.6 30.1 1.0
N A:MET1498 4.6 26.2 1.0
CA A:ARG1501 4.7 25.5 1.0
CG A:PRO1499 4.7 32.2 1.0
O A:MET1497 4.7 27.9 1.0
CG A:MET1498 4.7 30.5 1.0
CG2 A:THR1500 4.8 39.1 1.0
OE1 A:GLU1437 4.9 28.4 1.0

Chlorine binding site 3 out of 5 in 5ras

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B


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 XS036302B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1803

b:40.9
occ:1.00
 N A:ASN1558 3.1 19.0 1.0
O A:HOH2199 3.2 50.5 1.0
O A:HOH1974 3.3 53.8 1.0
NZ A:LYS1484 3.5 28.9 1.0
OE1 A:GLN1650 3.6 45.1 1.0
CA A:THR1557 3.7 17.7 1.0
C A:THR1557 3.8 17.3 1.0
CB A:ASN1558 3.8 19.4 1.0
CG A:GLN1650 4.0 30.9 1.0
CA A:ASN1558 4.0 18.4 1.0
CG A:ASN1558 4.2 23.1 1.0
O A:THR1556 4.2 20.5 1.0
CD A:GLN1650 4.2 36.5 1.0
CG2 A:THR1557 4.2 23.1 1.0
O A:HOH2273 4.3 41.7 1.0
ND2 A:ASN1558 4.3 27.2 1.0
O A:GLN1650 4.4 23.7 1.0
CB A:THR1557 4.4 22.5 1.0
N A:THR1557 4.7 18.7 1.0
OD1 A:ASN1558 4.7 20.3 1.0
O A:ASN1558 4.8 16.9 1.0
O A:HOH2104 4.8 36.4 1.0
OG1 A:THR1557 4.8 22.2 1.0
C A:THR1556 4.8 19.8 1.0
C A:ASN1558 4.9 16.4 1.0
CE A:LYS1484 4.9 31.0 1.0

Chlorine binding site 4 out of 5 in 5ras

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Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B


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 XS036302B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1804

b:47.3
occ:1.00
 NE2 A:HIS1712 2.9 22.1 1.0
O A:HOH2237 2.9 28.4 1.0
O A:HOH2050 3.0 33.4 1.0
O A:HOH2092 3.0 19.2 1.0
CE1 A:HIS1712 3.8 19.6 1.0
CD2 A:HIS1709 3.8 18.3 1.0
CD2 A:HIS1712 3.9 22.7 1.0
O A:HOH2180 4.2 55.4 1.0
O A:HOH2164 4.4 18.9 1.0
NE2 A:HIS1709 4.5 20.4 1.0
O A:HOH2062 4.6 16.9 1.0
CG A:HIS1709 4.6 15.9 1.0
CB A:ALA1619 4.8 16.6 1.0
O A:HOH2040 4.9 40.7 1.0
ND1 A:HIS1712 4.9 22.1 1.0
CA A:GLY1412 5.0 20.1 1.0
O A:HOH2224 5.0 30.5 1.0
O A:GLU1708 5.0 17.4 1.0
O A:ALA1685 5.0 14.9 1.0

Chlorine binding site 5 out of 5 in 5ras

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Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS036302B


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 XS036302B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1802

b:40.3
occ:1.00
 OG1 B:THR1500 2.6 36.1 1.0
C B:MET1498 3.3 29.8 1.0
CA B:MET1498 3.3 30.1 1.0
NH1 B:ARG1501 3.3 32.2 1.0
N B:THR1500 3.4 29.3 1.0
CD B:ARG1501 3.4 30.8 1.0
N B:PRO1499 3.5 29.3 1.0
O B:MET1498 3.7 30.9 1.0
CB B:THR1500 3.7 32.8 1.0
N B:ARG1501 3.8 30.3 1.0
CD B:PRO1499 3.8 33.3 1.0
CB B:MET1498 3.9 28.3 1.0
CA B:THR1500 4.0 30.9 1.0
CG2 B:THR1500 4.2 35.5 1.0
C B:PRO1499 4.3 29.9 1.0
CZ B:ARG1501 4.3 32.5 1.0
NE B:ARG1501 4.3 30.7 1.0
C B:THR1500 4.4 30.0 1.0
CA B:PRO1499 4.4 31.7 1.0
O B:MET1497 4.5 28.7 1.0
CG B:ARG1501 4.6 28.4 1.0
CG B:PRO1499 4.6 34.2 1.0
N B:MET1498 4.6 29.7 1.0
CB B:ARG1501 4.6 24.9 1.0
CG B:MET1498 4.7 34.0 1.0
CA B:ARG1501 4.8 28.0 1.0
OE1 B:GLU1437 4.8 30.2 1.0
O B:HOH1938 5.0 37.2 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 08:08:40 2025

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