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Chlorine in PDB 5rb1: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A, PDB code: 5rb1 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) 54.84 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.650, 93.860, 93.190, 90.00, 107.84, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 5rb1:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A 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 FM001700A (pdb code 5rb1). 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 FM001700A, PDB code: 5rb1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5rb1

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A


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 FM001700A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1802

b:23.8
occ:1.00
 O A:HOH2265 3.2 36.9 1.0
O A:HOH2042 3.3 23.1 1.0
O A:HOH2132 3.3 24.1 1.0
N A:GLU1513 3.4 21.2 1.0
O A:HOH2177 3.5 53.2 1.0
C A:LEU1511 3.5 19.7 1.0
CA A:LEU1511 3.6 19.4 1.0
CB A:GLU1513 3.6 25.6 1.0
N A:PRO1512 3.7 21.6 1.0
CD A:PRO1512 3.7 21.5 1.0
CG A:GLU1513 3.8 30.2 1.0
CD1 A:LEU1511 3.9 20.0 1.0
O A:LEU1511 4.0 17.9 1.0
CA A:GLU1513 4.1 21.6 1.0
CB A:LEU1511 4.3 18.9 1.0
CB A:TRP1402 4.3 21.4 1.0
CD2 A:TYR1514 4.3 17.4 1.0
CG A:PRO1512 4.4 23.1 1.0
C A:PRO1512 4.4 22.4 1.0
N A:TYR1514 4.5 19.4 1.0
OE2 A:GLU1513 4.6 35.2 1.0
CA A:PRO1512 4.6 22.0 1.0
CD A:GLU1513 4.7 40.9 1.0
O A:HOH1980 4.7 30.5 1.0
CG A:LEU1511 4.8 19.9 1.0
CE2 A:TYR1514 4.8 20.9 1.0
C A:GLU1513 4.8 22.3 1.0
N A:LEU1511 4.8 17.9 1.0
O A:HOH2034 5.0 44.8 1.0

Chlorine binding site 2 out of 5 in 5rb1

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A


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 FM001700A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1803

b:40.1
occ:1.00
 O A:HOH2080 3.1 47.3 1.0
NH1 A:ARG1501 3.2 32.5 1.0
C A:MET1498 3.3 35.9 1.0
CA A:MET1498 3.3 31.7 1.0
N A:THR1500 3.4 28.4 1.0
CD A:ARG1501 3.5 37.6 1.0
O A:MET1498 3.6 34.0 1.0
N A:ARG1501 3.6 30.0 1.0
N A:PRO1499 3.6 36.9 1.0
CB A:THR1500 3.6 37.1 1.0
CB A:MET1498 3.7 30.7 1.0
O A:HOH2220 3.9 50.2 1.0
CA A:THR1500 3.9 31.7 1.0
CD A:PRO1499 4.0 36.3 1.0
OG1 A:THR1500 4.0 37.9 1.0
CZ A:ARG1501 4.3 34.6 1.0
C A:THR1500 4.3 33.2 1.0
C A:PRO1499 4.3 30.1 1.0
NE A:ARG1501 4.4 33.3 1.0
CB A:ARG1501 4.4 30.4 1.0
CA A:PRO1499 4.5 33.8 1.0
CG A:ARG1501 4.6 34.9 1.0
CA A:ARG1501 4.6 29.0 1.0
CG A:PRO1499 4.6 34.9 1.0
N A:MET1498 4.7 29.8 1.0
CG A:MET1498 4.7 34.0 1.0
O A:MET1497 4.8 29.5 1.0
CG2 A:THR1500 4.9 39.0 1.0
OE1 A:GLU1437 5.0 29.4 1.0

Chlorine binding site 3 out of 5 in 5rb1

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A


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 FM001700A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1804

b:41.5
occ:1.00
 N A:ASN1558 3.1 20.6 1.0
O A:HOH2224 3.3 53.8 1.0
O A:HOH1919 3.3 54.1 1.0
NZ A:LYS1484 3.5 33.9 1.0
CA A:THR1557 3.7 21.3 1.0
OE1 A:GLN1650 3.7 47.4 1.0
CB A:ASN1558 3.8 21.4 1.0
C A:THR1557 3.9 21.2 1.0
CG A:GLN1650 4.1 35.2 1.0
CA A:ASN1558 4.1 21.4 1.0
CG A:ASN1558 4.1 25.3 1.0
CG2 A:THR1557 4.2 24.4 1.0
O A:THR1556 4.3 22.5 1.0
CD A:GLN1650 4.3 43.6 1.0
ND2 A:ASN1558 4.3 26.7 1.0
CB A:THR1557 4.4 25.0 1.0
O A:HOH2270 4.4 53.0 1.0
O A:GLN1650 4.5 28.6 1.0
O A:HOH2142 4.6 42.3 1.0
N A:THR1557 4.7 20.8 1.0
OD1 A:ASN1558 4.7 22.5 1.0
O A:ASN1558 4.8 19.1 1.0
OG1 A:THR1557 4.8 24.4 1.0
C A:THR1556 4.9 22.5 1.0
CE A:LYS1484 4.9 34.4 1.0
C A:ASN1558 4.9 18.5 1.0

Chlorine binding site 4 out of 5 in 5rb1

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Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A


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 FM001700A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1805

b:55.1
occ:1.00
 NE2 A:HIS1712 2.8 21.6 1.0
O A:HOH2057 3.0 20.6 1.0
O A:HOH1941 3.1 45.8 1.0
O A:HOH2231 3.2 32.8 1.0
O A:HOH2253 3.4 64.5 1.0
CD2 A:HIS1709 3.7 21.9 1.0
CD2 A:HIS1712 3.7 24.3 1.0
CE1 A:HIS1712 3.8 22.2 1.0
NE2 A:HIS1709 4.3 22.8 1.0
O A:HOH2175 4.3 55.7 1.0
CG A:HIS1709 4.5 20.3 1.0
O A:HOH2168 4.6 20.0 1.0
O A:HOH2025 4.7 18.5 1.0
CB A:ALA1619 4.8 22.9 1.0
O A:GLU1708 4.9 18.9 1.0
CG A:HIS1712 4.9 23.4 1.0
ND1 A:HIS1712 4.9 22.8 1.0
CA A:GLY1412 4.9 24.8 1.0
O A:ALA1685 5.0 17.5 1.0

Chlorine binding site 5 out of 5 in 5rb1

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Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A


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 FM001700A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1801

b:44.3
occ:1.00
 OG1 B:THR1500 2.9 47.4 1.0
C B:MET1498 3.3 37.9 1.0
CA B:MET1498 3.3 35.3 1.0
NH1 B:ARG1501 3.3 37.5 1.0
N B:THR1500 3.4 34.8 1.0
CD B:ARG1501 3.6 39.3 1.0
N B:PRO1499 3.6 36.1 1.0
O B:MET1498 3.7 33.9 1.0
N B:ARG1501 3.7 36.5 1.0
CD B:PRO1499 3.8 40.0 1.0
CB B:THR1500 3.8 40.2 1.0
CB B:MET1498 3.9 34.8 1.0
CA B:THR1500 4.0 37.7 1.0
CG2 B:THR1500 4.1 40.0 1.0
C B:PRO1499 4.3 35.0 1.0
CZ B:ARG1501 4.3 38.5 1.0
C B:THR1500 4.4 34.6 1.0
NE B:ARG1501 4.4 38.9 1.0
CA B:PRO1499 4.5 39.5 1.0
CG B:PRO1499 4.5 41.0 1.0
O B:MET1497 4.6 33.4 1.0
N B:MET1498 4.6 33.4 1.0
CG B:MET1498 4.6 41.0 1.0
CB B:ARG1501 4.6 33.3 1.0
CG B:ARG1501 4.7 35.6 1.0
OE1 B:GLU1437 4.8 32.3 1.0
CA B:ARG1501 4.8 33.2 1.0
CZ B:PHE1438 4.9 38.7 1.0
O B:HOH1962 4.9 51.8 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 08:10:54 2025

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