Atomistry » Chlorine » PDB 5rae-5rh4 » 5rb5
Atomistry »
  Chlorine »
    PDB 5rae-5rh4 »
      5rb5 »

Chlorine in PDB 5rb5: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A, PDB code: 5rb5 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) 55.11 / 1.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.930, 93.600, 93.810, 90.00, 107.80, 90.00
R / Rfree (%) 18.5 / 20.9

Other elements in 5rb5:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A also contains other interesting chemical elements:

Fluorine (F) 3 atoms
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 FM010010A (pdb code 5rb5). 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 FM010010A, PDB code: 5rb5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5rb5

Go back to Chlorine Binding Sites List in 5rb5
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A


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 FM010010A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1803

b:21.3
occ:1.00
 O A:HOH2125 3.2 20.1 1.0
O A:HOH2061 3.4 19.0 1.0
O A:HOH2258 3.4 34.6 1.0
N A:GLU1513 3.4 16.9 1.0
C A:LEU1511 3.6 17.1 1.0
CA A:LEU1511 3.6 16.0 1.0
O A:HOH2193 3.6 37.9 1.0
CB A:GLU1513 3.7 20.8 1.0
N A:PRO1512 3.8 17.3 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 16.9 1.0
O A:LEU1511 4.1 15.7 1.0
CA A:GLU1513 4.1 16.8 1.0
CB A:LEU1511 4.2 16.5 1.0
CB A:TRP1402 4.2 16.9 1.0
CD2 A:TYR1514 4.4 13.2 1.0
CG A:PRO1512 4.4 20.4 1.0
C A:PRO1512 4.5 17.7 1.0
O A:HOH1987 4.6 24.8 1.0
N A:TYR1514 4.6 16.2 1.0
OE2 A:GLU1513 4.6 37.5 1.0
CA A:PRO1512 4.6 17.9 1.0
CD A:GLU1513 4.7 39.1 1.0
CG A:LEU1511 4.7 16.2 1.0
N A:LEU1511 4.8 15.5 1.0
CE2 A:TYR1514 4.8 14.9 1.0
C A:GLU1513 4.9 16.7 1.0
CG A:TRP1402 5.0 16.1 1.0

Chlorine binding site 2 out of 5 in 5rb5

Go back to Chlorine Binding Sites List in 5rb5
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A


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 FM010010A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1804

b:34.5
occ:1.00
 O A:HOH2114 3.2 45.4 1.0
NH1 A:ARG1501 3.2 27.2 1.0
C A:MET1498 3.4 29.8 1.0
CA A:MET1498 3.4 25.1 1.0
N A:THR1500 3.4 24.6 1.0
CD A:ARG1501 3.5 30.9 1.0
N A:ARG1501 3.6 23.8 1.0
N A:PRO1499 3.7 25.4 1.0
CB A:THR1500 3.7 32.9 1.0
O A:MET1498 3.8 25.4 1.0
CB A:MET1498 3.9 26.4 1.0
CA A:THR1500 3.9 25.8 1.0
CD A:PRO1499 4.0 27.9 1.0
O A:HOH2232 4.1 41.2 1.0
OG1 A:THR1500 4.1 33.6 1.0
CZ A:ARG1501 4.3 28.2 1.0
C A:THR1500 4.3 26.4 1.0
C A:PRO1499 4.3 25.8 1.0
NE A:ARG1501 4.4 27.1 1.0
CB A:ARG1501 4.5 22.6 1.0
CA A:PRO1499 4.5 26.6 1.0
CG A:ARG1501 4.6 29.0 1.0
CG A:MET1498 4.6 26.8 1.0
CA A:ARG1501 4.7 23.0 1.0
N A:MET1498 4.7 24.8 1.0
O A:MET1497 4.7 24.3 1.0
CG A:PRO1499 4.8 28.4 1.0
CG2 A:THR1500 4.9 35.6 1.0
OE1 A:GLU1437 5.0 25.9 1.0

Chlorine binding site 3 out of 5 in 5rb5

Go back to Chlorine Binding Sites List in 5rb5
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A


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 FM010010A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1805

b:36.2
occ:1.00
 N A:ASN1558 3.1 17.9 1.0
O A:HOH2223 3.3 49.8 1.0
O A:HOH1916 3.4 57.2 1.0
OE1 A:GLN1650 3.5 40.9 1.0
NZ A:LYS1484 3.6 28.5 1.0
CA A:THR1557 3.7 18.4 1.0
CB A:ASN1558 3.9 18.9 1.0
C A:THR1557 3.9 17.6 1.0
CG A:GLN1650 4.0 28.8 1.0
CA A:ASN1558 4.1 17.7 1.0
CD A:GLN1650 4.1 35.3 1.0
CG A:ASN1558 4.2 20.6 1.0
CG2 A:THR1557 4.2 21.7 1.0
O A:THR1556 4.3 20.0 1.0
ND2 A:ASN1558 4.3 25.2 1.0
CB A:THR1557 4.4 21.7 1.0
O A:GLN1650 4.5 22.8 1.0
O A:HOH2273 4.5 50.9 1.0
O A:HOH2126 4.7 34.1 1.0
N A:THR1557 4.8 18.2 1.0
O A:ASN1558 4.8 17.6 1.0
OD1 A:ASN1558 4.8 20.2 1.0
OG1 A:THR1557 4.8 22.9 1.0
CE A:LYS1484 4.9 31.9 1.0
C A:THR1556 4.9 19.5 1.0
C A:ASN1558 4.9 16.4 1.0

Chlorine binding site 4 out of 5 in 5rb5

Go back to Chlorine Binding Sites List in 5rb5
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A


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 FM010010A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1806

b:48.2
occ:1.00
 NE2 A:HIS1712 2.9 21.8 1.0
O A:HOH2231 3.0 30.5 1.0
O A:HOH2096 3.0 19.3 1.0
O A:HOH1951 3.1 35.1 1.0
CE1 A:HIS1712 3.8 20.4 1.0
CD2 A:HIS1709 3.8 18.4 1.0
CD2 A:HIS1712 3.8 23.2 1.0
O A:HOH2183 4.2 54.7 1.0
NE2 A:HIS1709 4.5 21.7 1.0
O A:HOH2164 4.5 19.1 1.0
CG A:HIS1709 4.6 16.5 1.0
O A:HOH2062 4.6 16.9 1.0
CB A:ALA1619 4.7 17.0 1.0
O A:ALA1685 4.9 15.4 1.0
ND1 A:HIS1712 5.0 21.9 1.0
CG A:HIS1712 5.0 20.9 1.0
O A:GLU1708 5.0 19.0 1.0

Chlorine binding site 5 out of 5 in 5rb5

Go back to Chlorine Binding Sites List in 5rb5
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010010A


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 FM010010A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1802

b:41.5
occ:1.00
 OG1 B:THR1500 2.7 38.1 1.0
C B:MET1498 3.3 31.6 1.0
NH1 B:ARG1501 3.3 35.9 1.0
CA B:MET1498 3.3 33.5 1.0
N B:THR1500 3.3 29.3 1.0
CD B:ARG1501 3.4 33.0 1.0
N B:PRO1499 3.6 31.6 1.0
N B:ARG1501 3.7 32.2 1.0
CB B:THR1500 3.7 33.5 1.0
O B:MET1498 3.8 28.2 1.0
CD B:PRO1499 3.8 33.9 1.0
CB B:MET1498 3.9 31.3 1.0
CA B:THR1500 3.9 30.2 1.0
CG2 B:THR1500 4.1 33.5 1.0
C B:PRO1499 4.3 29.6 1.0
CZ B:ARG1501 4.3 33.5 1.0
C B:THR1500 4.3 31.3 1.0
NE B:ARG1501 4.3 33.6 1.0
CA B:PRO1499 4.5 32.7 1.0
CB B:ARG1501 4.5 27.3 1.0
CG B:PRO1499 4.5 35.7 1.0
CG B:ARG1501 4.5 29.9 1.0
N B:MET1498 4.6 29.6 1.0
CG B:MET1498 4.6 35.4 1.0
O B:MET1497 4.6 30.3 1.0
CA B:ARG1501 4.7 28.3 1.0
OE1 B:GLU1437 4.8 30.0 1.0
O B:HOH1941 5.0 47.0 1.0
CZ B:PHE1438 5.0 29.3 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 16:27:39 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy