Zinc in PDB 8uq8: Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker
Enzymatic activity of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker
All present enzymatic activity of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker:
2.3.2.23;
2.3.2.24;
Protein crystallography data
The structure of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker, PDB code: 8uq8
was solved by
Q.Hu,
M.V.Botuyan,
G.Mer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
36.06 /
2.34
|
|
Space group
|
P 31
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.539,
107.539,
113.985,
90,
90,
120
|
|
R / Rfree (%)
|
19.6 /
23.6
|
Other elements in 8uq8:
The structure of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker
(pdb code 8uq8). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker, PDB code: 8uq8:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8uq8
Go back to
Zinc Binding Sites List in 8uq8
Zinc binding site 1 out
of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn4007
b:33.0
occ:1.00
|
ND1
|
A:HIS33
|
2.0
|
39.1
|
1.0
|
|
SG
|
A:CYS31
|
2.2
|
31.6
|
1.0
|
|
SG
|
A:CYS51
|
2.3
|
30.8
|
1.0
|
|
SG
|
A:CYS54
|
2.4
|
37.7
|
1.0
|
|
HB2
|
A:HIS33
|
2.7
|
32.3
|
1.0
|
|
CE1
|
A:HIS33
|
3.0
|
45.3
|
1.0
|
|
CG
|
A:HIS33
|
3.0
|
36.2
|
1.0
|
|
HB2
|
A:CYS31
|
3.1
|
41.9
|
1.0
|
|
HB3
|
A:CYS51
|
3.1
|
41.5
|
1.0
|
|
CB
|
A:CYS51
|
3.1
|
34.5
|
1.0
|
|
HE1
|
A:HIS33
|
3.2
|
54.3
|
1.0
|
|
HB2
|
A:CYS51
|
3.2
|
41.5
|
1.0
|
|
H
|
A:CYS54
|
3.3
|
48.3
|
1.0
|
|
CB
|
A:CYS31
|
3.3
|
34.9
|
1.0
|
|
HB3
|
A:CYS54
|
3.3
|
41.7
|
1.0
|
|
CB
|
A:HIS33
|
3.3
|
26.9
|
1.0
|
|
CB
|
A:CYS54
|
3.4
|
34.7
|
1.0
|
|
HB2
|
A:PHE53
|
3.6
|
36.5
|
1.0
|
|
HB3
|
A:CYS31
|
3.7
|
41.9
|
1.0
|
|
N
|
A:CYS54
|
3.8
|
40.2
|
1.0
|
|
HB3
|
A:HIS33
|
3.9
|
32.3
|
1.0
|
|
H
|
A:HIS33
|
3.9
|
39.1
|
1.0
|
|
NE2
|
A:HIS33
|
4.1
|
43.1
|
1.0
|
|
CD2
|
A:HIS33
|
4.1
|
34.0
|
1.0
|
|
HD12
|
A:LEU29
|
4.1
|
34.8
|
1.0
|
|
CA
|
A:CYS54
|
4.2
|
37.9
|
1.0
|
|
HB3
|
A:ARG56
|
4.2
|
49.1
|
1.0
|
|
HB2
|
A:CYS54
|
4.2
|
41.7
|
1.0
|
|
H
|
A:PHE53
|
4.3
|
40.0
|
1.0
|
|
HB2
|
A:LEU29
|
4.4
|
34.7
|
1.0
|
|
H
|
A:ARG56
|
4.4
|
43.8
|
1.0
|
|
N
|
A:HIS33
|
4.5
|
32.6
|
1.0
|
|
CA
|
A:HIS33
|
4.5
|
29.0
|
1.0
|
|
CB
|
A:PHE53
|
4.6
|
30.4
|
1.0
|
|
CA
|
A:CYS31
|
4.6
|
32.4
|
1.0
|
|
CA
|
A:CYS51
|
4.6
|
35.4
|
1.0
|
|
HD2
|
A:PHE53
|
4.6
|
39.7
|
1.0
|
|
C
|
A:PHE53
|
4.7
|
41.6
|
1.0
|
|
O
|
A:CYS31
|
4.8
|
33.8
|
1.0
|
|
H
|
A:CYS31
|
4.8
|
37.6
|
1.0
|
|
C
|
A:CYS31
|
4.8
|
35.3
|
1.0
|
|
HD13
|
A:LEU29
|
4.8
|
34.8
|
1.0
|
|
H
|
A:ARG55
|
4.8
|
46.6
|
1.0
|
|
C
|
A:CYS54
|
4.8
|
37.8
|
1.0
|
|
HE2
|
A:HIS33
|
4.9
|
51.7
|
1.0
|
|
HD3
|
A:ARG56
|
4.9
|
50.4
|
1.0
|
|
CD1
|
A:LEU29
|
4.9
|
29.0
|
1.0
|
|
HA
|
A:CYS51
|
4.9
|
42.5
|
1.0
|
|
HB3
|
A:PHE53
|
4.9
|
36.5
|
1.0
|
|
N
|
A:PHE53
|
5.0
|
33.3
|
1.0
|
|
HD2
|
A:HIS33
|
5.0
|
40.8
|
1.0
|
|
HB2
|
A:ARG56
|
5.0
|
49.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8uq8
Go back to
Zinc Binding Sites List in 8uq8
Zinc binding site 2 out
of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn4008
b:30.1
occ:1.00
|
SG
|
A:CYS39
|
2.3
|
35.2
|
1.0
|
|
SG
|
A:CYS36
|
2.3
|
29.3
|
1.0
|
|
SG
|
A:CYS19
|
2.3
|
32.0
|
1.0
|
|
SG
|
A:CYS16
|
2.3
|
32.1
|
1.0
|
|
HB2
|
A:CYS39
|
2.8
|
38.5
|
1.0
|
|
H
|
A:CYS19
|
2.9
|
39.2
|
1.0
|
|
HB3
|
A:CYS16
|
3.0
|
39.1
|
1.0
|
|
HB3
|
A:CYS19
|
3.1
|
36.2
|
1.0
|
|
CB
|
A:CYS16
|
3.1
|
32.6
|
1.0
|
|
CB
|
A:CYS39
|
3.1
|
32.1
|
1.0
|
|
HH22
|
A:ARG91
|
3.1
|
70.6
|
1.0
|
|
HB2
|
A:CYS16
|
3.3
|
39.1
|
1.0
|
|
CB
|
A:CYS19
|
3.3
|
30.2
|
1.0
|
|
H
|
A:CYS36
|
3.3
|
33.5
|
1.0
|
|
HB3
|
A:CYS36
|
3.4
|
37.2
|
1.0
|
|
CB
|
A:CYS36
|
3.5
|
31.0
|
1.0
|
|
HB
|
A:ILE18
|
3.6
|
32.7
|
1.0
|
|
N
|
A:CYS19
|
3.6
|
32.7
|
1.0
|
|
HB3
|
A:CYS39
|
3.7
|
38.5
|
1.0
|
|
NH2
|
A:ARG91
|
3.7
|
58.8
|
1.0
|
|
HH21
|
A:ARG91
|
3.7
|
70.6
|
1.0
|
|
H
|
A:CYS39
|
3.8
|
44.4
|
1.0
|
|
HB3
|
A:SER99
|
4.0
|
82.3
|
1.0
|
|
N
|
A:CYS36
|
4.0
|
27.9
|
1.0
|
|
CA
|
A:CYS19
|
4.1
|
32.1
|
1.0
|
|
HB2
|
A:CYS19
|
4.1
|
36.2
|
1.0
|
|
H
|
A:ILE18
|
4.2
|
28.9
|
1.0
|
|
HB2
|
A:CYS36
|
4.3
|
37.2
|
1.0
|
|
CA
|
A:CYS36
|
4.3
|
30.6
|
1.0
|
|
CA
|
A:CYS39
|
4.3
|
35.9
|
1.0
|
|
N
|
A:CYS39
|
4.3
|
37.0
|
1.0
|
|
HG
|
A:SER99
|
4.4
|
91.5
|
1.0
|
|
HB2
|
A:LEU35
|
4.4
|
35.9
|
1.0
|
|
CB
|
A:ILE18
|
4.5
|
27.2
|
1.0
|
|
CA
|
A:CYS16
|
4.6
|
28.3
|
1.0
|
|
H
|
A:GLU21
|
4.6
|
38.0
|
1.0
|
|
HA
|
A:CYS39
|
4.6
|
43.0
|
1.0
|
|
O
|
A:CYS36
|
4.7
|
26.2
|
1.0
|
|
HG22
|
A:ILE18
|
4.7
|
41.1
|
1.0
|
|
C
|
A:ILE18
|
4.7
|
33.8
|
1.0
|
|
HB2
|
A:GLU21
|
4.7
|
37.2
|
1.0
|
|
H
|
A:MET20
|
4.8
|
37.3
|
1.0
|
|
HA
|
A:CYS19
|
4.8
|
38.5
|
1.0
|
|
C
|
A:CYS36
|
4.8
|
27.0
|
1.0
|
|
HD23
|
A:LEU23
|
4.8
|
33.7
|
1.0
|
|
CB
|
A:SER99
|
4.9
|
68.6
|
1.0
|
|
CZ
|
A:ARG91
|
4.9
|
78.9
|
1.0
|
|
HH12
|
A:ARG91
|
4.9
|
164.3
|
1.0
|
|
HB2
|
A:PRO38
|
4.9
|
37.6
|
1.0
|
|
N
|
A:ILE18
|
4.9
|
24.1
|
1.0
|
|
C
|
A:CYS19
|
4.9
|
30.6
|
1.0
|
|
CA
|
A:ILE18
|
5.0
|
32.6
|
1.0
|
|
HA
|
A:CYS16
|
5.0
|
34.0
|
1.0
|
|
C
|
A:CYS16
|
5.0
|
30.5
|
1.0
|
|
HD2
|
A:PRO38
|
5.0
|
40.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8uq8
Go back to
Zinc Binding Sites List in 8uq8
Zinc binding site 3 out
of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Zn4010
b:32.9
occ:1.00
|
ND1
|
a:HIS33
|
2.0
|
38.2
|
1.0
|
|
SG
|
a:CYS31
|
2.2
|
31.8
|
1.0
|
|
SG
|
a:CYS51
|
2.3
|
32.7
|
1.0
|
|
SG
|
a:CYS54
|
2.4
|
38.2
|
1.0
|
|
HB2
|
a:HIS33
|
2.7
|
33.0
|
1.0
|
|
CG
|
a:HIS33
|
3.0
|
34.5
|
1.0
|
|
CE1
|
a:HIS33
|
3.0
|
43.1
|
1.0
|
|
HB3
|
a:CYS51
|
3.1
|
42.1
|
1.0
|
|
CB
|
a:CYS51
|
3.1
|
35.1
|
1.0
|
|
HB2
|
a:CYS31
|
3.1
|
35.5
|
1.0
|
|
HB2
|
a:CYS51
|
3.2
|
42.1
|
1.0
|
|
H
|
a:CYS54
|
3.2
|
48.5
|
1.0
|
|
HE1
|
a:HIS33
|
3.2
|
51.7
|
1.0
|
|
CB
|
a:CYS31
|
3.3
|
29.6
|
1.0
|
|
CB
|
a:HIS33
|
3.3
|
27.4
|
1.0
|
|
HB3
|
a:CYS54
|
3.3
|
39.6
|
1.0
|
|
CB
|
a:CYS54
|
3.5
|
33.0
|
1.0
|
|
HB2
|
a:PHE53
|
3.6
|
38.5
|
1.0
|
|
HB3
|
a:CYS31
|
3.7
|
35.5
|
1.0
|
|
N
|
a:CYS54
|
3.8
|
40.4
|
1.0
|
|
HB3
|
a:HIS33
|
3.8
|
33.0
|
1.0
|
|
H
|
a:HIS33
|
4.0
|
40.1
|
1.0
|
|
NE2
|
a:HIS33
|
4.1
|
42.1
|
1.0
|
|
CD2
|
a:HIS33
|
4.1
|
34.4
|
1.0
|
|
HD12
|
a:LEU29
|
4.1
|
37.8
|
1.0
|
|
CA
|
a:CYS54
|
4.2
|
39.5
|
1.0
|
|
HB3
|
a:ARG56
|
4.2
|
48.7
|
1.0
|
|
HB2
|
a:CYS54
|
4.2
|
39.6
|
1.0
|
|
H
|
a:PHE53
|
4.3
|
37.6
|
1.0
|
|
HB2
|
a:LEU29
|
4.4
|
34.7
|
1.0
|
|
H
|
a:ARG56
|
4.4
|
48.0
|
1.0
|
|
CB
|
a:PHE53
|
4.5
|
32.1
|
1.0
|
|
CA
|
a:HIS33
|
4.5
|
29.0
|
1.0
|
|
N
|
a:HIS33
|
4.5
|
33.4
|
1.0
|
|
HD2
|
a:PHE53
|
4.6
|
39.0
|
1.0
|
|
CA
|
a:CYS51
|
4.6
|
36.3
|
1.0
|
|
CA
|
a:CYS31
|
4.6
|
33.0
|
1.0
|
|
C
|
a:PHE53
|
4.7
|
39.1
|
1.0
|
|
H
|
a:CYS31
|
4.7
|
39.6
|
1.0
|
|
O
|
a:CYS31
|
4.8
|
32.9
|
1.0
|
|
C
|
a:CYS31
|
4.8
|
34.2
|
1.0
|
|
C
|
a:CYS54
|
4.8
|
36.1
|
1.0
|
|
H
|
a:ARG55
|
4.8
|
49.7
|
1.0
|
|
HD13
|
a:LEU29
|
4.9
|
37.8
|
1.0
|
|
HB3
|
a:PHE53
|
4.9
|
38.5
|
1.0
|
|
HE2
|
a:HIS33
|
4.9
|
50.5
|
1.0
|
|
HD3
|
a:ARG56
|
4.9
|
52.5
|
1.0
|
|
N
|
a:PHE53
|
4.9
|
31.4
|
1.0
|
|
HA
|
a:CYS51
|
4.9
|
43.5
|
1.0
|
|
CD1
|
a:LEU29
|
4.9
|
31.5
|
1.0
|
|
CA
|
a:PHE53
|
5.0
|
33.0
|
1.0
|
|
HD2
|
a:HIS33
|
5.0
|
41.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8uq8
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Zinc Binding Sites List in 8uq8
Zinc binding site 4 out
of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker
 Mono view
 Stereo pair view
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A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Zn4011
b:32.6
occ:1.00
|
SG
|
a:CYS16
|
2.3
|
32.2
|
1.0
|
|
SG
|
a:CYS36
|
2.3
|
29.4
|
1.0
|
|
SG
|
a:CYS19
|
2.3
|
31.1
|
1.0
|
|
SG
|
a:CYS39
|
2.3
|
36.0
|
1.0
|
|
HB2
|
a:CYS39
|
2.9
|
41.4
|
1.0
|
|
H
|
a:CYS19
|
2.9
|
37.1
|
1.0
|
|
HB3
|
a:CYS16
|
3.0
|
41.1
|
1.0
|
|
HB3
|
a:CYS19
|
3.0
|
35.0
|
1.0
|
|
CB
|
a:CYS16
|
3.1
|
34.2
|
1.0
|
|
CB
|
a:CYS39
|
3.2
|
34.5
|
1.0
|
|
CB
|
a:CYS19
|
3.3
|
29.2
|
1.0
|
|
H
|
a:CYS36
|
3.3
|
34.0
|
1.0
|
|
HB2
|
a:CYS16
|
3.3
|
41.1
|
1.0
|
|
HH12
|
a:ARG91
|
3.4
|
46.5
|
1.0
|
|
HB3
|
a:CYS36
|
3.4
|
38.1
|
1.0
|
|
CB
|
a:CYS36
|
3.5
|
31.8
|
1.0
|
|
HB
|
a:ILE18
|
3.6
|
32.9
|
1.0
|
|
HG
|
a:SER99
|
3.6
|
58.0
|
1.0
|
|
N
|
a:CYS19
|
3.7
|
30.9
|
1.0
|
|
H
|
a:CYS39
|
3.8
|
46.9
|
1.0
|
|
HB3
|
a:CYS39
|
3.8
|
41.4
|
1.0
|
|
HH22
|
a:ARG91
|
3.8
|
56.5
|
1.0
|
|
OG
|
a:SER99
|
4.0
|
48.4
|
1.0
|
|
N
|
a:CYS36
|
4.0
|
28.4
|
1.0
|
|
HB2
|
a:CYS19
|
4.0
|
35.0
|
1.0
|
|
CA
|
a:CYS19
|
4.1
|
29.3
|
1.0
|
|
H
|
a:ILE18
|
4.2
|
33.4
|
1.0
|
|
NH1
|
a:ARG91
|
4.2
|
38.7
|
1.0
|
|
HB2
|
a:CYS36
|
4.3
|
38.1
|
1.0
|
|
CA
|
a:CYS36
|
4.3
|
30.5
|
1.0
|
|
N
|
a:CYS39
|
4.3
|
39.1
|
1.0
|
|
CA
|
a:CYS39
|
4.4
|
38.1
|
1.0
|
|
HB2
|
a:LEU35
|
4.4
|
35.2
|
1.0
|
|
NH2
|
a:ARG91
|
4.5
|
47.0
|
1.0
|
|
CB
|
a:ILE18
|
4.5
|
27.4
|
1.0
|
|
HG22
|
a:ILE18
|
4.5
|
41.5
|
1.0
|
|
CA
|
a:CYS16
|
4.6
|
29.2
|
1.0
|
|
HB2
|
a:GLU21
|
4.6
|
37.8
|
1.0
|
|
H
|
a:MET20
|
4.7
|
37.7
|
1.0
|
|
H
|
a:GLU21
|
4.7
|
38.4
|
1.0
|
|
O
|
a:CYS36
|
4.7
|
28.7
|
1.0
|
|
HA
|
a:CYS39
|
4.7
|
45.7
|
1.0
|
|
C
|
a:ILE18
|
4.7
|
34.1
|
1.0
|
|
HH11
|
a:ARG91
|
4.8
|
46.5
|
1.0
|
|
HA
|
a:CYS19
|
4.8
|
35.2
|
1.0
|
|
HD23
|
a:LEU23
|
4.8
|
34.8
|
1.0
|
|
HB2
|
a:PRO38
|
4.8
|
37.0
|
1.0
|
|
CZ
|
a:ARG91
|
4.8
|
44.5
|
1.0
|
|
C
|
a:CYS36
|
4.9
|
26.6
|
1.0
|
|
N
|
a:ILE18
|
4.9
|
27.9
|
1.0
|
|
C
|
a:CYS19
|
4.9
|
31.5
|
1.0
|
|
CA
|
a:ILE18
|
5.0
|
32.3
|
1.0
|
|
C
|
a:CYS16
|
5.0
|
33.8
|
1.0
|
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Reference:
Q.Hu,
M.V.Botuyan,
G.Mer.
Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2-Residue Linker To Be Published.
Page generated: Thu Oct 31 12:25:30 2024
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