Atomistry » Chlorine » PDB 5raf-5rke » 5ras
Atomistry »
  Chlorine »
    PDB 5raf-5rke »
      5ras »

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

Go back to Chlorine Binding Sites List in 5ras
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

Go back to Chlorine Binding Sites List in 5ras
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

Go back to Chlorine Binding Sites List in 5ras
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

Go back to Chlorine Binding Sites List in 5ras
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

Go back to Chlorine Binding Sites List in 5ras
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy