Atomistry » Chlorine » PDB 5rag-5rkr » 5rak
Atomistry »
  Chlorine »
    PDB 5rag-5rkr »
      5rak »

Chlorine in PDB 5rak: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B, PDB code: 5rak 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) 64.76 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.590, 93.460, 94.182, 90.00, 107.94, 90.00
R / Rfree (%) 18.2 / 21.3

Other elements in 5rak:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B 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 XS040486B (pdb code 5rak). 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 XS040486B, PDB code: 5rak:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5rak

Go back to Chlorine Binding Sites List in 5rak
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B


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 XS040486B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1802

b:24.7
occ:1.00
 O A:HOH2136 3.2 21.1 1.0
O A:HOH2246 3.3 33.3 1.0
O A:HOH2058 3.4 20.5 1.0
N A:GLU1513 3.4 20.2 1.0
CB A:GLU1513 3.5 24.2 1.0
C A:LEU1511 3.5 19.0 1.0
CA A:LEU1511 3.6 17.6 1.0
O A:HOH2195 3.7 38.1 1.0
N A:PRO1512 3.8 19.0 1.0
CG A:GLU1513 3.8 29.7 1.0
CD A:PRO1512 3.9 20.8 1.0
CD1 A:LEU1511 3.9 17.8 1.0
CA A:GLU1513 4.1 20.4 1.0
O A:LEU1511 4.1 16.4 1.0
CB A:LEU1511 4.3 16.6 1.0
CB A:TRP1402 4.3 18.6 1.0
CG A:PRO1512 4.4 24.7 1.0
CD2 A:TYR1514 4.4 17.5 1.0
C A:PRO1512 4.5 20.0 1.0
N A:TYR1514 4.6 17.9 1.0
OE2 A:GLU1513 4.6 36.4 1.0
CA A:PRO1512 4.7 21.8 1.0
CD A:GLU1513 4.7 41.3 1.0
O A:HOH2103 4.7 27.2 1.0
CG A:LEU1511 4.8 18.1 1.0
N A:LEU1511 4.8 16.5 1.0
C A:GLU1513 4.8 19.6 1.0
CE2 A:TYR1514 4.8 17.9 1.0

Chlorine binding site 2 out of 5 in 5rak

Go back to Chlorine Binding Sites List in 5rak
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B


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 XS040486B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1803

b:33.9
occ:1.00
 O A:HOH2135 3.1 40.6 1.0
NH1 A:ARG1501 3.3 32.3 1.0
CA A:MET1498 3.4 25.3 1.0
N A:THR1500 3.4 26.4 1.0
C A:MET1498 3.4 29.7 1.0
N A:ARG1501 3.5 24.9 1.0
O A:HOH2229 3.6 42.0 1.0
CB A:THR1500 3.7 36.0 1.0
N A:PRO1499 3.7 30.0 1.0
CB A:MET1498 3.8 26.7 1.0
O A:MET1498 3.8 28.5 1.0
CA A:THR1500 3.9 29.1 1.0
CD A:ARG1501 4.0 30.1 1.0
CD A:PRO1499 4.0 30.4 1.0
CG A:ARG1501 4.1 27.4 1.0
OG1 A:THR1500 4.1 39.9 1.0
C A:THR1500 4.2 26.8 1.0
CZ A:ARG1501 4.3 31.7 1.0
CB A:ARG1501 4.3 25.8 1.0
C A:PRO1499 4.4 28.5 1.0
NE A:ARG1501 4.5 31.1 1.0
CA A:ARG1501 4.6 25.3 1.0
CA A:PRO1499 4.6 29.1 1.0
CG A:MET1498 4.7 27.9 1.0
N A:MET1498 4.7 26.1 1.0
CG A:PRO1499 4.8 32.0 1.0
O A:MET1497 4.8 28.3 1.0
CG2 A:THR1500 4.9 36.7 1.0
OE1 A:GLU1437 4.9 26.3 1.0

Chlorine binding site 3 out of 5 in 5rak

Go back to Chlorine Binding Sites List in 5rak
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B


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 XS040486B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1804

b:33.4
occ:1.00
 N A:ASN1558 3.2 20.2 1.0
OE1 A:GLN1650 3.5 40.5 1.0
O A:HOH1912 3.6 55.3 1.0
O A:HOH2204 3.7 42.1 1.0
NZ A:LYS1484 3.8 30.5 1.0
CA A:THR1557 3.8 19.2 1.0
CB A:ASN1558 3.9 20.2 1.0
CG A:GLN1650 4.0 30.8 1.0
C A:THR1557 4.0 19.8 1.0
CG2 A:THR1557 4.1 19.1 1.0
CD A:GLN1650 4.1 33.9 1.0
CA A:ASN1558 4.2 18.9 1.0
CG A:ASN1558 4.3 21.6 1.0
O A:GLN1650 4.4 27.5 1.0
O A:HOH2274 4.4 51.5 1.0
ND2 A:ASN1558 4.4 26.1 1.0
O A:THR1556 4.4 21.2 1.0
CB A:THR1557 4.4 21.4 1.0
O A:ASN1558 4.8 18.6 1.0
OG1 A:THR1557 4.9 19.9 1.0
N A:THR1557 4.9 19.4 1.0
O A:HOH1987 4.9 31.4 1.0
OD1 A:ASN1558 4.9 24.9 1.0
C A:ASN1558 5.0 18.3 1.0

Chlorine binding site 4 out of 5 in 5rak

Go back to Chlorine Binding Sites List in 5rak
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B


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 XS040486B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1805

b:52.9
occ:1.00
 NE2 A:HIS1712 2.9 27.7 1.0
O A:HOH2137 3.0 21.5 1.0
O A:HOH1972 3.1 38.5 1.0
O A:HOH2227 3.1 30.4 1.0
CD2 A:HIS1709 3.7 21.5 1.0
CD2 A:HIS1712 3.8 29.0 1.0
O A:HOH2185 3.8 51.8 1.0
CE1 A:HIS1712 3.9 27.5 1.0
NE2 A:HIS1709 4.4 22.8 1.0
CG A:HIS1709 4.4 19.9 1.0
O A:HOH2175 4.6 17.9 1.0
O A:HOH2046 4.8 18.0 1.0
O A:GLU1708 4.8 19.1 1.0
CB A:HIS1709 4.8 19.7 1.0
O A:HOH2062 4.9 49.6 1.0
O A:HOH2280 4.9 61.2 1.0
CA A:HIS1709 4.9 19.4 1.0
CB A:ALA1619 4.9 18.6 1.0
CG A:HIS1712 5.0 27.5 1.0

Chlorine binding site 5 out of 5 in 5rak

Go back to Chlorine Binding Sites List in 5rak
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B


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 XS040486B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1801

b:36.5
occ:1.00
 OG1 B:THR1500 2.9 50.0 1.0
NH1 B:ARG1501 3.2 33.6 1.0
CA B:MET1498 3.3 31.2 1.0
C B:MET1498 3.3 32.4 1.0
N B:THR1500 3.4 30.5 1.0
N B:ARG1501 3.5 31.9 1.0
N B:PRO1499 3.7 32.9 1.0
O B:MET1498 3.7 29.8 1.0
CB B:MET1498 3.8 31.2 1.0
CB B:THR1500 3.8 38.6 1.0
CA B:THR1500 4.0 33.6 1.0
CD B:PRO1499 4.0 33.9 1.0
CD B:ARG1501 4.1 33.7 1.0
CG B:ARG1501 4.1 33.0 1.0
CG2 B:THR1500 4.1 36.8 1.0
C B:THR1500 4.2 30.4 1.0
CB B:ARG1501 4.2 30.6 1.0
CZ B:ARG1501 4.3 34.8 1.0
C B:PRO1499 4.4 30.6 1.0
CA B:ARG1501 4.5 31.6 1.0
CG B:MET1498 4.5 35.3 1.0
CA B:PRO1499 4.6 31.8 1.0
NE B:ARG1501 4.6 34.4 1.0
N B:MET1498 4.7 32.8 1.0
O B:MET1497 4.8 31.8 1.0
OE1 B:GLU1437 4.9 30.5 1.0
CG B:PRO1499 5.0 34.4 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: Sat Jul 12 08:06:27 2025

Last articles

Mg in 1W5N
Mg in 1W5O
Mg in 1W56
Mg in 1W5F
Mg in 1W5A
Mg in 1W58
Mg in 1W2B
Mg in 1VQP
Mg in 1VQO
Mg in 1W55
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy