Chlorine in PDB 5rb1: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A
Protein crystallography data
The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A, PDB code: 5rb1
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)
|
54.84 /
1.76
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.650,
93.860,
93.190,
90.00,
107.84,
90.00
|
R / Rfree (%)
|
18.1 /
21.4
|
Other elements in 5rb1:
The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A
(pdb code 5rb1). 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 FM001700A, PDB code: 5rb1:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 5rb1
Go back to
Chlorine Binding Sites List in 5rb1
Chlorine binding site 1 out
of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A
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 FM001700A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1802
b:23.8
occ:1.00
|
O
|
A:HOH2265
|
3.2
|
36.9
|
1.0
|
O
|
A:HOH2042
|
3.3
|
23.1
|
1.0
|
O
|
A:HOH2132
|
3.3
|
24.1
|
1.0
|
N
|
A:GLU1513
|
3.4
|
21.2
|
1.0
|
O
|
A:HOH2177
|
3.5
|
53.2
|
1.0
|
C
|
A:LEU1511
|
3.5
|
19.7
|
1.0
|
CA
|
A:LEU1511
|
3.6
|
19.4
|
1.0
|
CB
|
A:GLU1513
|
3.6
|
25.6
|
1.0
|
N
|
A:PRO1512
|
3.7
|
21.6
|
1.0
|
CD
|
A:PRO1512
|
3.7
|
21.5
|
1.0
|
CG
|
A:GLU1513
|
3.8
|
30.2
|
1.0
|
CD1
|
A:LEU1511
|
3.9
|
20.0
|
1.0
|
O
|
A:LEU1511
|
4.0
|
17.9
|
1.0
|
CA
|
A:GLU1513
|
4.1
|
21.6
|
1.0
|
CB
|
A:LEU1511
|
4.3
|
18.9
|
1.0
|
CB
|
A:TRP1402
|
4.3
|
21.4
|
1.0
|
CD2
|
A:TYR1514
|
4.3
|
17.4
|
1.0
|
CG
|
A:PRO1512
|
4.4
|
23.1
|
1.0
|
C
|
A:PRO1512
|
4.4
|
22.4
|
1.0
|
N
|
A:TYR1514
|
4.5
|
19.4
|
1.0
|
OE2
|
A:GLU1513
|
4.6
|
35.2
|
1.0
|
CA
|
A:PRO1512
|
4.6
|
22.0
|
1.0
|
CD
|
A:GLU1513
|
4.7
|
40.9
|
1.0
|
O
|
A:HOH1980
|
4.7
|
30.5
|
1.0
|
CG
|
A:LEU1511
|
4.8
|
19.9
|
1.0
|
CE2
|
A:TYR1514
|
4.8
|
20.9
|
1.0
|
C
|
A:GLU1513
|
4.8
|
22.3
|
1.0
|
N
|
A:LEU1511
|
4.8
|
17.9
|
1.0
|
O
|
A:HOH2034
|
5.0
|
44.8
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 5rb1
Go back to
Chlorine Binding Sites List in 5rb1
Chlorine binding site 2 out
of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A
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 FM001700A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1803
b:40.1
occ:1.00
|
O
|
A:HOH2080
|
3.1
|
47.3
|
1.0
|
NH1
|
A:ARG1501
|
3.2
|
32.5
|
1.0
|
C
|
A:MET1498
|
3.3
|
35.9
|
1.0
|
CA
|
A:MET1498
|
3.3
|
31.7
|
1.0
|
N
|
A:THR1500
|
3.4
|
28.4
|
1.0
|
CD
|
A:ARG1501
|
3.5
|
37.6
|
1.0
|
O
|
A:MET1498
|
3.6
|
34.0
|
1.0
|
N
|
A:ARG1501
|
3.6
|
30.0
|
1.0
|
N
|
A:PRO1499
|
3.6
|
36.9
|
1.0
|
CB
|
A:THR1500
|
3.6
|
37.1
|
1.0
|
CB
|
A:MET1498
|
3.7
|
30.7
|
1.0
|
O
|
A:HOH2220
|
3.9
|
50.2
|
1.0
|
CA
|
A:THR1500
|
3.9
|
31.7
|
1.0
|
CD
|
A:PRO1499
|
4.0
|
36.3
|
1.0
|
OG1
|
A:THR1500
|
4.0
|
37.9
|
1.0
|
CZ
|
A:ARG1501
|
4.3
|
34.6
|
1.0
|
C
|
A:THR1500
|
4.3
|
33.2
|
1.0
|
C
|
A:PRO1499
|
4.3
|
30.1
|
1.0
|
NE
|
A:ARG1501
|
4.4
|
33.3
|
1.0
|
CB
|
A:ARG1501
|
4.4
|
30.4
|
1.0
|
CA
|
A:PRO1499
|
4.5
|
33.8
|
1.0
|
CG
|
A:ARG1501
|
4.6
|
34.9
|
1.0
|
CA
|
A:ARG1501
|
4.6
|
29.0
|
1.0
|
CG
|
A:PRO1499
|
4.6
|
34.9
|
1.0
|
N
|
A:MET1498
|
4.7
|
29.8
|
1.0
|
CG
|
A:MET1498
|
4.7
|
34.0
|
1.0
|
O
|
A:MET1497
|
4.8
|
29.5
|
1.0
|
CG2
|
A:THR1500
|
4.9
|
39.0
|
1.0
|
OE1
|
A:GLU1437
|
5.0
|
29.4
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 5rb1
Go back to
Chlorine Binding Sites List in 5rb1
Chlorine binding site 3 out
of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A
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 FM001700A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1804
b:41.5
occ:1.00
|
N
|
A:ASN1558
|
3.1
|
20.6
|
1.0
|
O
|
A:HOH2224
|
3.3
|
53.8
|
1.0
|
O
|
A:HOH1919
|
3.3
|
54.1
|
1.0
|
NZ
|
A:LYS1484
|
3.5
|
33.9
|
1.0
|
CA
|
A:THR1557
|
3.7
|
21.3
|
1.0
|
OE1
|
A:GLN1650
|
3.7
|
47.4
|
1.0
|
CB
|
A:ASN1558
|
3.8
|
21.4
|
1.0
|
C
|
A:THR1557
|
3.9
|
21.2
|
1.0
|
CG
|
A:GLN1650
|
4.1
|
35.2
|
1.0
|
CA
|
A:ASN1558
|
4.1
|
21.4
|
1.0
|
CG
|
A:ASN1558
|
4.1
|
25.3
|
1.0
|
CG2
|
A:THR1557
|
4.2
|
24.4
|
1.0
|
O
|
A:THR1556
|
4.3
|
22.5
|
1.0
|
CD
|
A:GLN1650
|
4.3
|
43.6
|
1.0
|
ND2
|
A:ASN1558
|
4.3
|
26.7
|
1.0
|
CB
|
A:THR1557
|
4.4
|
25.0
|
1.0
|
O
|
A:HOH2270
|
4.4
|
53.0
|
1.0
|
O
|
A:GLN1650
|
4.5
|
28.6
|
1.0
|
O
|
A:HOH2142
|
4.6
|
42.3
|
1.0
|
N
|
A:THR1557
|
4.7
|
20.8
|
1.0
|
OD1
|
A:ASN1558
|
4.7
|
22.5
|
1.0
|
O
|
A:ASN1558
|
4.8
|
19.1
|
1.0
|
OG1
|
A:THR1557
|
4.8
|
24.4
|
1.0
|
C
|
A:THR1556
|
4.9
|
22.5
|
1.0
|
CE
|
A:LYS1484
|
4.9
|
34.4
|
1.0
|
C
|
A:ASN1558
|
4.9
|
18.5
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 5rb1
Go back to
Chlorine Binding Sites List in 5rb1
Chlorine binding site 4 out
of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A
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 FM001700A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1805
b:55.1
occ:1.00
|
NE2
|
A:HIS1712
|
2.8
|
21.6
|
1.0
|
O
|
A:HOH2057
|
3.0
|
20.6
|
1.0
|
O
|
A:HOH1941
|
3.1
|
45.8
|
1.0
|
O
|
A:HOH2231
|
3.2
|
32.8
|
1.0
|
O
|
A:HOH2253
|
3.4
|
64.5
|
1.0
|
CD2
|
A:HIS1709
|
3.7
|
21.9
|
1.0
|
CD2
|
A:HIS1712
|
3.7
|
24.3
|
1.0
|
CE1
|
A:HIS1712
|
3.8
|
22.2
|
1.0
|
NE2
|
A:HIS1709
|
4.3
|
22.8
|
1.0
|
O
|
A:HOH2175
|
4.3
|
55.7
|
1.0
|
CG
|
A:HIS1709
|
4.5
|
20.3
|
1.0
|
O
|
A:HOH2168
|
4.6
|
20.0
|
1.0
|
O
|
A:HOH2025
|
4.7
|
18.5
|
1.0
|
CB
|
A:ALA1619
|
4.8
|
22.9
|
1.0
|
O
|
A:GLU1708
|
4.9
|
18.9
|
1.0
|
CG
|
A:HIS1712
|
4.9
|
23.4
|
1.0
|
ND1
|
A:HIS1712
|
4.9
|
22.8
|
1.0
|
CA
|
A:GLY1412
|
4.9
|
24.8
|
1.0
|
O
|
A:ALA1685
|
5.0
|
17.5
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 5rb1
Go back to
Chlorine Binding Sites List in 5rb1
Chlorine binding site 5 out
of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001700A
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 FM001700A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl1801
b:44.3
occ:1.00
|
OG1
|
B:THR1500
|
2.9
|
47.4
|
1.0
|
C
|
B:MET1498
|
3.3
|
37.9
|
1.0
|
CA
|
B:MET1498
|
3.3
|
35.3
|
1.0
|
NH1
|
B:ARG1501
|
3.3
|
37.5
|
1.0
|
N
|
B:THR1500
|
3.4
|
34.8
|
1.0
|
CD
|
B:ARG1501
|
3.6
|
39.3
|
1.0
|
N
|
B:PRO1499
|
3.6
|
36.1
|
1.0
|
O
|
B:MET1498
|
3.7
|
33.9
|
1.0
|
N
|
B:ARG1501
|
3.7
|
36.5
|
1.0
|
CD
|
B:PRO1499
|
3.8
|
40.0
|
1.0
|
CB
|
B:THR1500
|
3.8
|
40.2
|
1.0
|
CB
|
B:MET1498
|
3.9
|
34.8
|
1.0
|
CA
|
B:THR1500
|
4.0
|
37.7
|
1.0
|
CG2
|
B:THR1500
|
4.1
|
40.0
|
1.0
|
C
|
B:PRO1499
|
4.3
|
35.0
|
1.0
|
CZ
|
B:ARG1501
|
4.3
|
38.5
|
1.0
|
C
|
B:THR1500
|
4.4
|
34.6
|
1.0
|
NE
|
B:ARG1501
|
4.4
|
38.9
|
1.0
|
CA
|
B:PRO1499
|
4.5
|
39.5
|
1.0
|
CG
|
B:PRO1499
|
4.5
|
41.0
|
1.0
|
O
|
B:MET1497
|
4.6
|
33.4
|
1.0
|
N
|
B:MET1498
|
4.6
|
33.4
|
1.0
|
CG
|
B:MET1498
|
4.6
|
41.0
|
1.0
|
CB
|
B:ARG1501
|
4.6
|
33.3
|
1.0
|
CG
|
B:ARG1501
|
4.7
|
35.6
|
1.0
|
OE1
|
B:GLU1437
|
4.8
|
32.3
|
1.0
|
CA
|
B:ARG1501
|
4.8
|
33.2
|
1.0
|
CZ
|
B:PHE1438
|
4.9
|
38.7
|
1.0
|
O
|
B:HOH1962
|
4.9
|
51.8
|
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 16:27:22 2024
|