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Chlorine in PDB 5rah: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A, PDB code: 5rah 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) 89.08 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.370, 93.590, 93.580, 90.00, 107.85, 90.00
R / Rfree (%) 18 / 20.5

Other elements in 5rah:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A also contains other interesting chemical elements:

Fluorine (F) 1 atom
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 FM010032A (pdb code 5rah). 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 FM010032A, PDB code: 5rah:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5rah

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A


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 FM010032A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1802

b:22.2
occ:1.00
 O A:HOH2128 3.2 19.1 1.0
O A:HOH2253 3.2 38.8 1.0
O A:HOH2119 3.3 21.5 1.0
O A:HOH2192 3.4 41.3 1.0
N A:GLU1513 3.4 18.8 1.0
C A:LEU1511 3.6 17.6 1.0
CA A:LEU1511 3.6 16.2 1.0
CB A:GLU1513 3.7 24.6 1.0
CG A:GLU1513 3.7 27.6 1.0
N A:PRO1512 3.7 19.4 1.0
CD A:PRO1512 3.8 20.0 1.0
CD1 A:LEU1511 4.0 16.6 1.0
O A:LEU1511 4.1 16.4 1.0
CA A:GLU1513 4.1 20.2 1.0
CB A:LEU1511 4.3 15.9 1.0
CB A:TRP1402 4.3 17.0 1.0
CG A:PRO1512 4.4 22.8 1.0
CD2 A:TYR1514 4.4 16.6 1.0
C A:PRO1512 4.4 19.8 1.0
N A:TYR1514 4.6 17.6 1.0
O A:HOH1974 4.6 24.2 1.0
CA A:PRO1512 4.6 19.7 1.0
OE2 A:GLU1513 4.6 43.5 1.0
CD A:GLU1513 4.7 43.0 1.0
CG A:LEU1511 4.7 17.0 1.0
N A:LEU1511 4.8 15.1 1.0
CE2 A:TYR1514 4.8 18.5 1.0
C A:GLU1513 4.8 19.1 1.0
CD1 A:TRP1402 5.0 20.8 1.0
CG A:TRP1402 5.0 18.6 1.0

Chlorine binding site 2 out of 5 in 5rah

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A


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 FM010032A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1803

b:32.7
occ:1.00
 O A:HOH2058 3.2 38.4 1.0
NH1 A:ARG1501 3.3 31.5 1.0
N A:THR1500 3.3 24.1 1.0
CA A:MET1498 3.4 27.5 1.0
C A:MET1498 3.4 30.6 1.0
N A:ARG1501 3.6 24.3 1.0
O A:HOH2223 3.7 44.2 1.0
N A:PRO1499 3.7 31.5 1.0
CB A:THR1500 3.7 31.9 1.0
O A:MET1498 3.8 26.5 1.0
CB A:MET1498 3.8 27.5 1.0
CD A:ARG1501 3.9 30.3 1.0
CA A:THR1500 3.9 25.9 1.0
CD A:PRO1499 3.9 29.6 1.0
OG1 A:THR1500 4.1 32.4 1.0
CG A:ARG1501 4.2 27.8 1.0
C A:THR1500 4.2 26.4 1.0
C A:PRO1499 4.3 24.8 1.0
CZ A:ARG1501 4.3 31.1 1.0
CB A:ARG1501 4.4 23.6 1.0
NE A:ARG1501 4.5 30.9 1.0
CA A:PRO1499 4.6 27.8 1.0
CA A:ARG1501 4.6 24.3 1.0
N A:MET1498 4.7 27.5 1.0
CG A:PRO1499 4.7 29.2 1.0
O A:MET1497 4.7 28.6 1.0
CG A:MET1498 4.8 28.4 1.0
CG2 A:THR1500 5.0 33.8 1.0

Chlorine binding site 3 out of 5 in 5rah

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A


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 FM010032A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1804

b:34.8
occ:1.00
 O A:HOH2196 3.2 48.5 1.0
N A:ASN1558 3.2 17.6 1.0
OE1 A:GLN1650 3.4 37.2 1.0
NZ A:LYS1484 3.5 35.2 1.0
CA A:THR1557 3.7 18.5 1.0
O A:HOH1948 3.8 54.4 1.0
CB A:ASN1558 4.0 20.3 1.0
C A:THR1557 4.0 18.5 1.0
CG A:GLN1650 4.0 28.0 1.0
CD A:GLN1650 4.1 31.5 1.0
CA A:ASN1558 4.1 18.5 1.0
CG2 A:THR1557 4.2 23.9 1.0
O A:THR1556 4.2 18.4 1.0
CG A:ASN1558 4.2 23.7 1.0
ND2 A:ASN1558 4.4 25.4 1.0
CB A:THR1557 4.5 22.9 1.0
O A:GLN1650 4.5 26.2 1.0
O A:HOH2269 4.5 54.8 1.0
O A:HOH2158 4.7 34.0 1.0
N A:THR1557 4.8 18.4 1.0
OG1 A:THR1557 4.8 22.2 1.0
CE A:LYS1484 4.8 34.6 1.0
O A:ASN1558 4.8 17.1 1.0
OD1 A:ASN1558 4.9 22.3 1.0
C A:THR1556 4.9 19.4 1.0
O A:HOH2111 5.0 54.2 1.0
C A:ASN1558 5.0 17.3 1.0

Chlorine binding site 4 out of 5 in 5rah

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Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A


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 FM010032A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1805

b:54.6
occ:1.00
 NE2 A:HIS1712 2.8 23.7 1.0
O A:HOH1960 3.0 42.5 1.0
O A:HOH2073 3.0 18.0 1.0
O A:HOH2226 3.0 30.9 1.0
CD2 A:HIS1712 3.8 25.0 1.0
CD2 A:HIS1709 3.8 21.8 1.0
CE1 A:HIS1712 3.8 22.4 1.0
O A:HOH2151 4.2 52.0 1.0
O A:HOH2163 4.5 17.2 1.0
NE2 A:HIS1709 4.5 22.2 1.0
CG A:HIS1709 4.5 19.3 1.0
O A:HOH2033 4.7 17.1 1.0
O A:GLU1708 4.8 19.6 1.0
CB A:ALA1619 4.9 18.8 1.0
CB A:HIS1709 4.9 20.7 1.0
CA A:GLY1412 5.0 18.8 1.0
CG A:HIS1712 5.0 22.2 1.0
ND1 A:HIS1712 5.0 23.4 1.0

Chlorine binding site 5 out of 5 in 5rah

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Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010032A


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 FM010032A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1801

b:41.8
occ:1.00
 OG1 B:THR1500 2.9 47.2 1.0
NH1 B:ARG1501 3.3 34.9 1.0
C B:MET1498 3.3 32.1 1.0
CA B:MET1498 3.3 30.8 1.0
N B:THR1500 3.4 31.7 1.0
CD B:ARG1501 3.6 35.1 1.0
N B:PRO1499 3.6 32.6 1.0
N B:ARG1501 3.7 32.8 1.0
O B:MET1498 3.7 28.6 1.0
CD B:PRO1499 3.8 35.0 1.0
CB B:MET1498 3.8 33.5 1.0
CB B:THR1500 3.9 37.1 1.0
CA B:THR1500 4.0 33.6 1.0
CG2 B:THR1500 4.2 38.1 1.0
CZ B:ARG1501 4.3 35.1 1.0
C B:THR1500 4.3 32.8 1.0
C B:PRO1499 4.3 32.1 1.0
NE B:ARG1501 4.4 37.5 1.0
CA B:PRO1499 4.5 33.4 1.0
CB B:ARG1501 4.6 29.0 1.0
CG B:PRO1499 4.6 37.4 1.0
CG B:ARG1501 4.6 33.1 1.0
CG B:MET1498 4.6 38.5 1.0
O B:MET1497 4.7 33.6 1.0
N B:MET1498 4.7 31.0 1.0
CA B:ARG1501 4.7 28.4 1.0
OE1 B:GLU1437 4.9 30.7 1.0
CZ B:PHE1438 5.0 29.4 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: Fri Jul 26 16:20:17 2024

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