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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

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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

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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

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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

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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

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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: Fri Jul 26 16:20:16 2024

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