Atomistry » Chlorine » PDB 5rad-5rh3 » 5rak
Atomistry »
  Chlorine »
    PDB 5rad-5rh3 »
      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 Dec 12 12:25:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy