Iodine in PDB 6w9d: RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Enzymatic activity of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
All present enzymatic activity of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate:
2.3.2.23;
2.3.2.24;
2.3.2.27;
Protein crystallography data
The structure of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate, PDB code: 6w9d
was solved by
A.J.Middleton,
C.L.Day,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.06 /
3.19
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.473,
135.473,
51.372,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
22.2 /
28.1
|
Other elements in 6w9d:
The structure of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
(pdb code 6w9d). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the
RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate, PDB code: 6w9d:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iodine binding site 1 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 1 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I703
b:76.1
occ:0.91
|
N
|
B:HIS595
|
4.0
|
93.6
|
1.0
|
N
|
B:LYS582
|
4.1
|
90.6
|
1.0
|
O
|
B:LYS582
|
4.1
|
90.9
|
1.0
|
CB
|
B:HIS595
|
4.1
|
0.5
|
1.0
|
N
|
B:VAL594
|
4.2
|
95.6
|
1.0
|
CD2
|
B:HIS593
|
4.3
|
0.2
|
1.0
|
CA
|
B:ASN581
|
4.4
|
87.6
|
1.0
|
CB
|
B:VAL594
|
4.5
|
89.0
|
1.0
|
ND2
|
B:ASN581
|
4.5
|
93.1
|
1.0
|
CG
|
B:ASN581
|
4.6
|
95.0
|
1.0
|
CB
|
B:HIS593
|
4.7
|
92.7
|
1.0
|
CB
|
B:ASN581
|
4.7
|
92.5
|
1.0
|
CA
|
B:HIS595
|
4.7
|
95.4
|
1.0
|
CG
|
B:HIS593
|
4.7
|
0.8
|
1.0
|
CA
|
B:VAL594
|
4.7
|
95.0
|
1.0
|
C
|
B:ASN581
|
4.8
|
91.9
|
1.0
|
C
|
B:VAL594
|
4.9
|
93.5
|
1.0
|
C
|
B:LYS582
|
4.9
|
93.9
|
1.0
|
CA
|
B:LYS582
|
5.0
|
91.4
|
1.0
|
|
Iodine binding site 2 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 2 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I101
b:0.4
occ:1.00
|
CB
|
C:LEU8
|
3.8
|
79.0
|
1.0
|
CG
|
C:LEU8
|
3.9
|
78.0
|
1.0
|
CD1
|
C:LEU8
|
3.9
|
78.8
|
1.0
|
NH1
|
B:ARG611
|
3.9
|
0.6
|
1.0
|
CG
|
C:LEU71
|
4.0
|
0.8
|
1.0
|
N
|
C:LEU8
|
4.2
|
86.3
|
1.0
|
N
|
C:LEU71
|
4.3
|
0.3
|
1.0
|
CB
|
C:LEU71
|
4.4
|
0.0
|
1.0
|
CG2
|
C:THR9
|
4.5
|
87.2
|
1.0
|
CA
|
C:LEU8
|
4.5
|
83.0
|
1.0
|
O
|
C:LEU69
|
4.6
|
96.1
|
1.0
|
N
|
C:THR9
|
4.6
|
83.3
|
1.0
|
NH2
|
B:ARG611
|
4.7
|
93.7
|
1.0
|
CZ
|
B:ARG611
|
4.8
|
96.4
|
1.0
|
CD1
|
C:LEU71
|
4.8
|
0.7
|
1.0
|
CG2
|
A:ILE88
|
4.8
|
66.3
|
1.0
|
CD2
|
C:LEU71
|
4.9
|
96.0
|
1.0
|
CA
|
C:VAL70
|
4.9
|
95.5
|
1.0
|
CA
|
C:LEU71
|
5.0
|
0.2
|
1.0
|
CB
|
C:THR7
|
5.0
|
88.6
|
1.0
|
|
Iodine binding site 3 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 3 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I201
b:0.3
occ:0.81
|
CB
|
E:CYS573
|
4.0
|
77.0
|
1.0
|
CD
|
D:PRO61
|
4.1
|
71.0
|
1.0
|
CA
|
E:CYS573
|
4.2
|
72.3
|
1.0
|
N
|
D:ALA2
|
4.2
|
74.3
|
1.0
|
CE2
|
D:PHE62
|
4.6
|
71.6
|
1.0
|
CB
|
D:ARG5
|
4.6
|
64.6
|
1.0
|
CG
|
D:PRO61
|
4.6
|
67.5
|
1.0
|
CZ
|
D:PHE62
|
4.8
|
73.9
|
1.0
|
N
|
E:CYS573
|
4.8
|
74.1
|
1.0
|
CG1
|
E:VAL572
|
4.9
|
78.8
|
1.0
|
O
|
E:VAL572
|
5.0
|
83.1
|
1.0
|
|
Iodine binding site 4 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 4 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:I703
b:83.3
occ:0.96
|
N
|
E:LYS582
|
3.8
|
83.2
|
1.0
|
ND2
|
E:ASN581
|
4.0
|
91.0
|
1.0
|
O
|
E:LYS582
|
4.0
|
76.5
|
1.0
|
N
|
E:VAL594
|
4.2
|
76.2
|
1.0
|
N
|
E:HIS595
|
4.2
|
91.8
|
1.0
|
CA
|
E:ASN581
|
4.2
|
81.4
|
1.0
|
CD2
|
E:HIS593
|
4.3
|
0.5
|
1.0
|
CG
|
E:ASN581
|
4.5
|
87.7
|
1.0
|
CB
|
E:HIS593
|
4.5
|
83.2
|
1.0
|
CB
|
E:VAL594
|
4.5
|
80.3
|
1.0
|
CB
|
E:HIS595
|
4.5
|
0.7
|
1.0
|
C
|
E:ASN581
|
4.5
|
83.3
|
1.0
|
CB
|
E:ASN581
|
4.6
|
83.9
|
1.0
|
CG
|
E:HIS593
|
4.6
|
99.5
|
1.0
|
CA
|
E:LYS582
|
4.6
|
82.0
|
1.0
|
C
|
E:LYS582
|
4.7
|
79.8
|
1.0
|
CA
|
E:VAL594
|
4.8
|
75.7
|
1.0
|
CB
|
E:LYS582
|
4.8
|
84.8
|
1.0
|
CA
|
E:HIS593
|
4.9
|
81.2
|
1.0
|
C
|
E:HIS593
|
5.0
|
75.7
|
1.0
|
|
Iodine binding site 5 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 5 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:I101
b:0.9
occ:1.00
|
NH1
|
E:ARG611
|
3.7
|
94.7
|
1.0
|
CG2
|
F:THR9
|
3.8
|
0.8
|
1.0
|
CB
|
F:LEU8
|
4.4
|
0.8
|
1.0
|
N
|
F:THR9
|
4.4
|
0.4
|
1.0
|
NH2
|
E:ARG611
|
4.4
|
98.5
|
1.0
|
N
|
F:LEU8
|
4.5
|
97.3
|
1.0
|
CZ
|
E:ARG611
|
4.6
|
96.0
|
1.0
|
CG2
|
D:ILE88
|
4.6
|
58.2
|
1.0
|
OG1
|
F:THR9
|
4.8
|
0.9
|
1.0
|
CB
|
F:THR7
|
4.8
|
89.1
|
1.0
|
CB
|
F:THR9
|
4.8
|
0.0
|
1.0
|
CG
|
F:LEU8
|
4.9
|
0.6
|
1.0
|
CA
|
F:LEU8
|
4.9
|
0.4
|
1.0
|
|
Iodine binding site 6 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 6 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:I201
b:0.7
occ:0.74
|
NZ
|
G:LYS4
|
3.5
|
0.1
|
1.0
|
CG
|
G:LYS4
|
4.1
|
92.5
|
1.0
|
ND2
|
G:ASN11
|
4.1
|
0.5
|
1.0
|
CB
|
G:HIS7
|
4.1
|
86.5
|
1.0
|
N
|
G:LYS8
|
4.4
|
92.7
|
1.0
|
CE
|
G:LYS4
|
4.4
|
0.4
|
1.0
|
O
|
G:LYS4
|
4.4
|
82.6
|
1.0
|
C
|
G:HIS7
|
4.6
|
93.5
|
1.0
|
CA
|
G:LYS8
|
4.6
|
96.7
|
1.0
|
CB
|
G:LYS8
|
4.8
|
93.8
|
1.0
|
CD
|
G:LYS4
|
4.9
|
98.9
|
1.0
|
O
|
G:HIS7
|
4.9
|
98.3
|
1.0
|
CA
|
G:HIS7
|
5.0
|
88.2
|
1.0
|
|
Iodine binding site 7 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 7 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I703
b:64.6
occ:0.90
|
N
|
H:LYS582
|
3.7
|
64.1
|
1.0
|
O
|
H:LYS582
|
3.8
|
70.2
|
1.0
|
N
|
H:HIS595
|
4.0
|
66.7
|
1.0
|
N
|
H:VAL594
|
4.1
|
66.6
|
1.0
|
CD2
|
H:HIS593
|
4.2
|
98.4
|
1.0
|
CB
|
H:HIS595
|
4.3
|
73.7
|
1.0
|
CA
|
H:ASN581
|
4.3
|
67.7
|
1.0
|
ND2
|
H:ASN581
|
4.3
|
68.7
|
1.0
|
CB
|
H:VAL594
|
4.4
|
66.2
|
1.0
|
CB
|
H:HIS593
|
4.5
|
85.0
|
1.0
|
C
|
H:ASN581
|
4.6
|
70.7
|
1.0
|
CG
|
H:HIS593
|
4.6
|
93.5
|
1.0
|
CA
|
H:LYS582
|
4.6
|
64.3
|
1.0
|
C
|
H:LYS582
|
4.6
|
65.1
|
1.0
|
CB
|
H:ASN581
|
4.6
|
66.5
|
1.0
|
CA
|
H:VAL594
|
4.7
|
64.3
|
1.0
|
CB
|
H:LYS582
|
4.7
|
65.2
|
1.0
|
CG
|
H:ASN581
|
4.7
|
66.7
|
1.0
|
CA
|
H:HIS595
|
4.8
|
68.9
|
1.0
|
C
|
H:VAL594
|
4.9
|
64.7
|
1.0
|
C
|
H:HIS593
|
4.9
|
69.6
|
1.0
|
CA
|
H:HIS593
|
4.9
|
77.8
|
1.0
|
|
Iodine binding site 8 out
of 8 in 6w9d
Go back to
Iodine Binding Sites List in 6w9d
Iodine binding site 8 out
of 8 in the RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of RNF12 Ring Domain in Complex with A UBE2D2~Ub Conjugate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:I101
b:70.0
occ:0.57
|
NH1
|
H:ARG611
|
3.7
|
79.5
|
1.0
|
CD1
|
I:LEU71
|
3.7
|
89.5
|
1.0
|
CD1
|
I:LEU8
|
3.8
|
98.7
|
1.0
|
CB
|
I:LEU8
|
3.8
|
87.9
|
1.0
|
N
|
I:LEU8
|
4.0
|
87.9
|
1.0
|
CG
|
I:LEU8
|
4.1
|
91.8
|
1.0
|
NH2
|
H:ARG611
|
4.4
|
71.0
|
1.0
|
CA
|
I:LEU8
|
4.5
|
86.8
|
1.0
|
N
|
I:THR9
|
4.5
|
88.4
|
1.0
|
CB
|
I:THR7
|
4.5
|
81.8
|
1.0
|
CZ
|
H:ARG611
|
4.5
|
75.6
|
1.0
|
N
|
I:LEU71
|
4.6
|
89.7
|
1.0
|
CG2
|
I:THR9
|
4.7
|
88.4
|
1.0
|
O
|
I:LEU69
|
4.7
|
91.2
|
1.0
|
CB
|
I:LEU71
|
4.7
|
92.0
|
1.0
|
CG2
|
G:ILE88
|
4.7
|
73.2
|
1.0
|
CG
|
I:LEU71
|
4.7
|
91.1
|
1.0
|
|
Reference:
A.J.Middleton,
J.Zhu,
C.L.Day.
The Ring Domain of Ring Finger 12 Efficiently Builds Degradative Ubiquitin Chains J.Mol.Biol..
ISSN: ESSN 1089-8638
DOI: 10.1016/J.JMB.2020.05.001
Page generated: Mon Aug 12 00:29:00 2024
|