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Chlorine in PDB 5raj: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A, PDB code: 5raj 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) 64.58 / 1.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.560, 93.330, 93.897, 90.00, 108.12, 90.00
R / Rfree (%) 19.1 / 22.3

Other elements in 5raj:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A 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 BD009815A (pdb code 5raj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A, PDB code: 5raj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5raj

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Chlorine binding site 1 out of 7 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


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 BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1801

b:34.1
occ:0.66
 CL A:W771801 0.0 34.1 0.7
C11 A:W771801 1.7 30.7 0.7
C6 A:W771801 2.7 28.3 0.7
C10 A:W771801 2.7 31.5 0.7
O A:W771801 3.0 24.7 0.7
C5 A:W771801 3.1 26.1 0.7
O A:HOH1942 3.9 49.2 1.0
C7 A:W771801 4.0 27.9 0.7
C9 A:W771801 4.0 31.2 0.7
N1 A:W771801 4.1 24.2 0.7
OE2 A:GLU1476 4.5 39.3 0.7
CD A:GLU1476 4.5 38.8 0.7
C8 A:W771801 4.6 29.1 0.7
CG A:GLU1476 4.6 36.9 0.7
OE1 A:GLU1476 4.8 40.0 0.7

Chlorine binding site 2 out of 7 in 5raj

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Chlorine binding site 2 out of 7 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


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 BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1801

b:35.4
occ:0.66
 CL1 A:W771801 0.0 35.4 0.7
C9 A:W771801 1.7 31.2 0.7
C8 A:W771801 2.7 29.1 0.7
C10 A:W771801 2.7 31.5 0.7
O A:HOH2194 3.6 33.9 0.7
C7 A:W771801 4.0 27.9 0.7
C11 A:W771801 4.0 30.7 0.7
OE1 A:GLU1476 4.1 40.0 0.7
C6 A:W771801 4.5 28.3 0.7
CB A:GLU1476 4.7 37.9 0.7

Chlorine binding site 3 out of 7 in 5raj

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Chlorine binding site 3 out of 7 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


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 BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1802

b:23.1
occ:1.00
 O A:HOH2143 3.2 22.8 1.0
O A:HOH2005 3.3 19.7 1.0
O A:HOH2243 3.3 35.9 1.0
N A:GLU1513 3.4 19.4 1.0
C A:LEU1511 3.6 17.4 1.0
CB A:GLU1513 3.6 22.9 1.0
CA A:LEU1511 3.6 15.6 1.0
N A:PRO1512 3.8 18.5 1.0
CG A:GLU1513 3.8 27.5 1.0
CD A:PRO1512 3.8 20.2 1.0
CD1 A:LEU1511 3.9 18.5 1.0
CA A:GLU1513 4.0 21.2 1.0
O A:LEU1511 4.1 16.5 1.0
CB A:TRP1402 4.2 18.4 1.0
CB A:LEU1511 4.3 16.1 1.0
CG A:PRO1512 4.4 21.8 1.0
CD2 A:TYR1514 4.4 15.9 1.0
C A:PRO1512 4.4 18.5 1.0
N A:TYR1514 4.5 17.4 1.0
CD A:GLU1513 4.6 33.9 1.0
OE2 A:GLU1513 4.6 30.7 1.0
CA A:PRO1512 4.7 20.1 1.0
O A:HOH2091 4.7 27.4 1.0
C A:GLU1513 4.8 18.1 1.0
CG A:LEU1511 4.8 18.0 1.0
CE2 A:TYR1514 4.8 17.1 1.0
N A:LEU1511 4.8 15.5 1.0
CG A:TRP1402 5.0 20.7 1.0

Chlorine binding site 4 out of 7 in 5raj

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Chlorine binding site 4 out of 7 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


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 BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1803

b:31.0
occ:1.00
 NH1 A:ARG1501 3.3 30.1 1.0
O A:HOH2069 3.3 37.0 1.0
CA A:MET1498 3.4 23.4 1.0
C A:MET1498 3.4 30.1 1.0
N A:ARG1501 3.4 24.0 1.0
N A:THR1500 3.4 23.5 1.0
CB A:THR1500 3.7 32.5 1.0
CB A:MET1498 3.7 23.9 1.0
N A:PRO1499 3.7 30.1 1.0
O A:MET1498 3.8 25.0 1.0
O A:HOH2222 3.8 40.1 1.0
CA A:THR1500 3.9 25.9 1.0
CD A:ARG1501 3.9 27.9 1.0
CG A:ARG1501 4.0 26.9 1.0
CD A:PRO1499 4.1 30.4 1.0
C A:THR1500 4.1 24.1 1.0
CB A:ARG1501 4.1 22.6 1.0
OG1 A:THR1500 4.3 35.3 1.0
CZ A:ARG1501 4.3 30.2 1.0
C A:PRO1499 4.4 27.4 1.0
CA A:ARG1501 4.4 22.6 1.0
NE A:ARG1501 4.5 29.4 1.0
CG A:MET1498 4.5 25.7 1.0
CA A:PRO1499 4.6 27.8 1.0
N A:MET1498 4.7 24.6 1.0
O A:MET1497 4.8 29.4 1.0
CG A:PRO1499 4.9 30.1 1.0
CG2 A:THR1500 4.9 35.9 1.0
OE1 A:GLU1437 4.9 27.7 1.0

Chlorine binding site 5 out of 7 in 5raj

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Chlorine binding site 5 out of 7 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


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 BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1804

b:36.0
occ:1.00
 N A:ASN1558 3.2 18.5 1.0
O A:HOH2188 3.5 44.1 1.0
O A:HOH2014 3.5 46.6 1.0
NZ A:LYS1484 3.6 25.9 1.0
OE1 A:GLN1650 3.6 39.9 1.0
CA A:THR1557 3.8 17.5 1.0
CB A:ASN1558 3.9 21.7 1.0
C A:THR1557 4.0 18.8 1.0
CG A:GLN1650 4.0 32.8 1.0
O A:HOH2265 4.1 40.7 1.0
CA A:ASN1558 4.2 19.1 1.0
CG2 A:THR1557 4.2 17.5 1.0
CD A:GLN1650 4.2 35.4 1.0
CG A:ASN1558 4.2 22.4 1.0
ND2 A:ASN1558 4.3 29.2 1.0
O A:THR1556 4.3 21.7 1.0
O A:GLN1650 4.4 28.4 1.0
CB A:THR1557 4.5 18.0 1.0
N A:THR1557 4.8 19.1 1.0
O A:ASN1558 4.8 18.4 1.0
OG1 A:THR1557 4.9 19.2 1.0
CE A:LYS1484 4.9 29.8 1.0
OD1 A:ASN1558 4.9 23.5 1.0
O A:HOH1956 5.0 29.5 1.0
C A:ASN1558 5.0 17.9 1.0
C A:THR1556 5.0 20.9 1.0

Chlorine binding site 6 out of 7 in 5raj

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Chlorine binding site 6 out of 7 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1805

b:52.0
occ:1.00
 O A:HOH2227 2.8 27.4 1.0
NE2 A:HIS1712 2.9 27.8 1.0
O A:HOH2167 2.9 21.6 1.0
O A:HOH2033 3.3 34.0 1.0
CD2 A:HIS1712 3.8 28.7 1.0
CD2 A:HIS1709 3.9 19.3 1.0
CE1 A:HIS1712 4.0 28.0 1.0
O A:HOH2174 4.1 46.5 1.0
O A:HOH2162 4.2 60.4 1.0
O A:HOH2156 4.4 18.0 1.0
NE2 A:HIS1709 4.6 19.7 1.0
CG A:HIS1709 4.6 17.1 1.0
O A:HOH2038 4.6 17.3 1.0
CB A:ALA1619 4.7 17.4 1.0
O A:HOH2207 4.7 33.1 1.0
O A:HOH2272 4.9 53.1 1.0
O A:HOH1958 4.9 45.3 1.0
CB A:HIS1709 5.0 16.9 1.0
CG A:HIS1712 5.0 26.3 1.0

Chlorine binding site 7 out of 7 in 5raj

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Chlorine binding site 7 out of 7 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1801

b:32.9
occ:1.00
 OG1 B:THR1500 3.0 51.8 1.0
NH1 B:ARG1501 3.2 28.5 1.0
CA B:MET1498 3.4 26.5 1.0
C B:MET1498 3.4 29.9 1.0
N B:THR1500 3.4 27.8 1.0
N B:ARG1501 3.4 28.1 1.0
CB B:MET1498 3.7 28.5 1.0
O B:MET1498 3.7 26.6 1.0
N B:PRO1499 3.8 31.9 1.0
CG B:ARG1501 3.8 26.7 1.0
CB B:THR1500 3.9 35.8 1.0
CA B:THR1500 4.0 28.9 1.0
CD B:ARG1501 4.0 30.3 1.0
CB B:ARG1501 4.1 25.1 1.0
CD B:PRO1499 4.1 31.3 1.0
CG2 B:THR1500 4.1 30.6 1.0
C B:THR1500 4.2 28.2 1.0
CZ B:ARG1501 4.3 29.0 1.0
C B:PRO1499 4.4 29.8 1.0
CA B:ARG1501 4.4 27.2 1.0
CG B:MET1498 4.5 29.1 1.0
NE B:ARG1501 4.5 29.2 1.0
CA B:PRO1499 4.6 30.5 1.0
N B:MET1498 4.7 30.1 1.0
O B:MET1497 4.8 28.5 1.0
OE1 B:GLU1437 4.9 28.1 1.0
CG B:PRO1499 4.9 32.5 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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