Chlorine in PDB 5l6h: UBA1 in Complex with Ub-ABPA3 Covalent Adduct
Enzymatic activity of UBA1 in Complex with Ub-ABPA3 Covalent Adduct
All present enzymatic activity of UBA1 in Complex with Ub-ABPA3 Covalent Adduct:
6.2.1.45;
Protein crystallography data
The structure of UBA1 in Complex with Ub-ABPA3 Covalent Adduct, PDB code: 5l6h
was solved by
M.Misra,
H.Schindelin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.30
|
Space group
|
P 2 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.048,
194.098,
230.172,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.3 /
21.8
|
Other elements in 5l6h:
The structure of UBA1 in Complex with Ub-ABPA3 Covalent Adduct also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
(pdb code 5l6h). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the
UBA1 in Complex with Ub-ABPA3 Covalent Adduct, PDB code: 5l6h:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Chlorine binding site 1 out
of 8 in 5l6h
Go back to
Chlorine Binding Sites List in 5l6h
Chlorine binding site 1 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1102
b:60.8
occ:1.00
|
OG1
|
A:THR571
|
3.1
|
30.5
|
1.0
|
N
|
A:THR571
|
3.5
|
31.4
|
1.0
|
CE
|
A:LYS572
|
3.7
|
51.9
|
1.0
|
O
|
A:HOH1349
|
4.0
|
41.9
|
1.0
|
CB
|
A:THR571
|
4.2
|
33.6
|
1.0
|
O
|
A:LEU569
|
4.2
|
30.0
|
1.0
|
CA
|
A:GLY570
|
4.2
|
31.9
|
1.0
|
CG2
|
A:THR571
|
4.3
|
35.2
|
1.0
|
C
|
A:GLY570
|
4.4
|
33.3
|
1.0
|
CA
|
A:THR571
|
4.4
|
32.8
|
1.0
|
NZ
|
A:LYS572
|
4.5
|
57.2
|
1.0
|
CG
|
A:LYS572
|
4.6
|
40.7
|
1.0
|
N
|
A:LYS572
|
4.7
|
34.4
|
1.0
|
O
|
A:THR177
|
4.7
|
42.6
|
1.0
|
CD
|
A:LYS572
|
4.8
|
45.9
|
1.0
|
CG1
|
A:VAL25
|
4.8
|
34.8
|
1.0
|
OE2
|
A:GLU179
|
4.9
|
51.1
|
1.0
|
OD1
|
A:ASN900
|
5.0
|
34.4
|
1.0
|
C
|
A:THR571
|
5.0
|
32.1
|
1.0
|
|
Chlorine binding site 2 out
of 8 in 5l6h
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Chlorine Binding Sites List in 5l6h
Chlorine binding site 2 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1103
b:77.8
occ:1.00
|
NH2
|
B:ARG74
|
2.9
|
49.7
|
0.5
|
NH1
|
A:ARG861
|
3.2
|
78.3
|
1.0
|
CZ
|
B:ARG74
|
3.5
|
45.2
|
0.5
|
NH1
|
B:ARG74
|
3.7
|
43.9
|
0.5
|
NE
|
A:ARG861
|
4.0
|
66.0
|
1.0
|
CZ
|
A:ARG861
|
4.1
|
73.5
|
1.0
|
O
|
B:HOH217
|
4.2
|
41.3
|
1.0
|
NE
|
B:ARG74
|
4.5
|
44.5
|
0.5
|
O
|
A:HOH1501
|
4.9
|
53.9
|
1.0
|
O
|
A:HOH1623
|
4.9
|
53.9
|
1.0
|
|
Chlorine binding site 3 out
of 8 in 5l6h
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Chlorine Binding Sites List in 5l6h
Chlorine binding site 3 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1104
b:68.9
occ:1.00
|
NH1
|
A:ARG96
|
3.2
|
60.6
|
1.0
|
O
|
A:HOH1354
|
3.6
|
53.9
|
1.0
|
CB
|
A:ALA97
|
4.0
|
55.2
|
1.0
|
CZ
|
A:ARG96
|
4.4
|
59.2
|
1.0
|
CD
|
A:ARG96
|
4.5
|
56.5
|
1.0
|
NE
|
A:ARG96
|
4.8
|
58.9
|
1.0
|
CA
|
A:ALA97
|
5.0
|
54.7
|
1.0
|
|
Chlorine binding site 4 out
of 8 in 5l6h
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Chlorine Binding Sites List in 5l6h
Chlorine binding site 4 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1105
b:91.3
occ:1.00
|
CG1
|
A:VAL117
|
3.7
|
61.4
|
1.0
|
O
|
A:LEU114
|
3.8
|
69.8
|
1.0
|
OD1
|
A:ASP136
|
4.6
|
63.4
|
1.0
|
O
|
A:ASP115
|
4.7
|
69.7
|
1.0
|
OH
|
C:TYR723
|
4.8
|
68.6
|
1.0
|
CG
|
A:ASP136
|
4.8
|
57.2
|
1.0
|
CG1
|
A:ILE140
|
4.9
|
46.9
|
1.0
|
C
|
A:LEU114
|
4.9
|
67.4
|
1.0
|
CG
|
A:LEU114
|
4.9
|
68.4
|
1.0
|
CB
|
A:VAL117
|
4.9
|
61.0
|
1.0
|
|
Chlorine binding site 5 out
of 8 in 5l6h
Go back to
Chlorine Binding Sites List in 5l6h
Chlorine binding site 5 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl1102
b:65.9
occ:1.00
|
O
|
C:HOH1442
|
2.1
|
74.4
|
1.0
|
OG1
|
C:THR571
|
3.1
|
36.5
|
1.0
|
O
|
C:HOH1470
|
3.1
|
43.1
|
1.0
|
N
|
C:THR571
|
3.4
|
35.1
|
1.0
|
CE
|
C:LYS572
|
3.8
|
50.5
|
1.0
|
CA
|
C:GLY570
|
4.0
|
36.2
|
1.0
|
O
|
C:LEU569
|
4.0
|
36.1
|
1.0
|
CB
|
C:THR571
|
4.0
|
35.7
|
1.0
|
C
|
C:GLY570
|
4.2
|
34.4
|
1.0
|
CG2
|
C:THR571
|
4.2
|
36.1
|
1.0
|
CA
|
C:THR571
|
4.3
|
34.8
|
1.0
|
O
|
C:HOH1261
|
4.3
|
35.8
|
1.0
|
N
|
C:LYS572
|
4.6
|
37.6
|
1.0
|
NZ
|
C:LYS572
|
4.7
|
54.2
|
1.0
|
CG1
|
C:VAL25
|
4.7
|
33.4
|
1.0
|
CG
|
C:LYS572
|
4.7
|
43.4
|
1.0
|
C
|
C:THR571
|
4.8
|
37.1
|
1.0
|
C
|
C:LEU569
|
4.8
|
36.9
|
1.0
|
CD
|
C:LYS572
|
4.9
|
46.6
|
1.0
|
N
|
C:GLY570
|
4.9
|
36.1
|
1.0
|
O
|
C:THR177
|
5.0
|
40.1
|
1.0
|
|
Chlorine binding site 6 out
of 8 in 5l6h
Go back to
Chlorine Binding Sites List in 5l6h
Chlorine binding site 6 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl1103
b:85.6
occ:1.00
|
ND2
|
C:ASN514
|
3.6
|
55.4
|
1.0
|
CB
|
C:ASN514
|
4.2
|
53.0
|
1.0
|
CG2
|
C:VAL467
|
4.2
|
45.6
|
1.0
|
CD1
|
C:TYR465
|
4.3
|
44.9
|
1.0
|
CG
|
C:ASN514
|
4.4
|
57.1
|
1.0
|
CE1
|
C:TYR465
|
4.4
|
46.8
|
1.0
|
CG
|
C:TYR465
|
4.4
|
44.5
|
1.0
|
CZ
|
C:TYR465
|
4.6
|
48.2
|
1.0
|
CD2
|
C:TYR465
|
4.6
|
46.7
|
1.0
|
CE2
|
C:TYR465
|
4.6
|
48.3
|
1.0
|
|
Chlorine binding site 7 out
of 8 in 5l6h
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Chlorine Binding Sites List in 5l6h
Chlorine binding site 7 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl1104
b:75.6
occ:1.00
|
NH1
|
C:ARG861
|
2.6
|
76.6
|
1.0
|
NH2
|
D:ARG74
|
2.6
|
54.1
|
0.6
|
CZ
|
D:ARG74
|
3.5
|
49.6
|
0.6
|
NH1
|
D:ARG74
|
3.9
|
46.2
|
0.6
|
CZ
|
C:ARG861
|
4.0
|
74.4
|
1.0
|
NE
|
D:ARG74
|
4.5
|
49.0
|
0.6
|
O
|
D:HOH223
|
4.7
|
58.6
|
1.0
|
NE
|
C:ARG861
|
4.8
|
70.7
|
1.0
|
CD
|
C:ARG861
|
4.8
|
60.9
|
1.0
|
O
|
C:HOH1413
|
4.8
|
41.9
|
1.0
|
NH2
|
C:ARG861
|
4.8
|
71.8
|
1.0
|
|
Chlorine binding site 8 out
of 8 in 5l6h
Go back to
Chlorine Binding Sites List in 5l6h
Chlorine binding site 8 out
of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl1105
b:88.9
occ:1.00
|
CA
|
C:GLY960
|
4.0
|
54.6
|
1.0
|
CZ
|
C:TYR959
|
4.2
|
59.6
|
1.0
|
CE1
|
C:TYR959
|
4.3
|
57.2
|
1.0
|
N
|
C:GLY960
|
4.3
|
52.2
|
1.0
|
OH
|
C:TYR959
|
4.4
|
60.2
|
1.0
|
CE2
|
C:TYR959
|
4.6
|
60.1
|
1.0
|
CD1
|
C:TYR959
|
4.8
|
56.5
|
1.0
|
O
|
C:HOH1404
|
4.8
|
47.8
|
1.0
|
CD2
|
C:TYR959
|
5.0
|
56.8
|
1.0
|
|
Reference:
M.Misra,
M.Kuhn,
M.Lobel,
H.An,
A.V.Statsyuk,
C.Sotriffer,
H.Schindelin.
Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme. Structure V. 25 1120 2017.
ISSN: ISSN 1878-4186
PubMed: 28578874
DOI: 10.1016/J.STR.2017.05.001
Page generated: Fri Jul 26 11:12:30 2024
|