Zinc in PDB 7qnu: SMYD3 in Complex with Fragment FL08619
Enzymatic activity of SMYD3 in Complex with Fragment FL08619
All present enzymatic activity of SMYD3 in Complex with Fragment FL08619:
2.1.1.354;
Protein crystallography data
The structure of SMYD3 in Complex with Fragment FL08619, PDB code: 7qnu
was solved by
B.A.Lund,
D.Cederfelt,
D.Dobritzsch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.08 /
1.64
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.931,
65.886,
105.085,
90,
90,
90
|
R / Rfree (%)
|
18.5 /
23
|
Zinc Binding Sites:
The binding sites of Zinc atom in the SMYD3 in Complex with Fragment FL08619
(pdb code 7qnu). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
SMYD3 in Complex with Fragment FL08619, PDB code: 7qnu:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 7qnu
Go back to
Zinc Binding Sites List in 7qnu
Zinc binding site 1 out
of 3 in the SMYD3 in Complex with Fragment FL08619
![](/pictures/ZN/pdb/qn/7qnu-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/qn/7qnu-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of SMYD3 in Complex with Fragment FL08619 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:16.3
occ:1.00
|
SG
|
A:CYS263
|
2.2
|
17.4
|
1.0
|
SG
|
A:CYS208
|
2.3
|
16.8
|
1.0
|
SG
|
A:CYS261
|
2.3
|
15.8
|
1.0
|
SG
|
A:CYS266
|
2.3
|
15.7
|
1.0
|
HB2
|
A:CYS208
|
3.1
|
20.5
|
1.0
|
HB3
|
A:CYS261
|
3.2
|
21.0
|
1.0
|
HB2
|
A:CYS266
|
3.3
|
15.8
|
1.0
|
HB3
|
A:CYS263
|
3.3
|
26.4
|
1.0
|
H
|
A:CYS263
|
3.3
|
24.7
|
1.0
|
CB
|
A:CYS208
|
3.4
|
17.0
|
1.0
|
CB
|
A:CYS261
|
3.4
|
17.5
|
1.0
|
H
|
A:CYS266
|
3.4
|
18.8
|
1.0
|
CB
|
A:CYS263
|
3.4
|
22.0
|
1.0
|
H
|
A:CYS208
|
3.4
|
16.8
|
1.0
|
CB
|
A:CYS266
|
3.5
|
13.1
|
1.0
|
HE2
|
A:HIS206
|
3.7
|
14.6
|
1.0
|
HE
|
A:ARG249
|
3.7
|
17.4
|
1.0
|
HH21
|
A:ARG249
|
3.8
|
18.9
|
1.0
|
HB2
|
A:CYS261
|
3.9
|
21.0
|
1.0
|
N
|
A:CYS263
|
4.0
|
20.5
|
1.0
|
HB3
|
A:CYS208
|
4.0
|
20.5
|
1.0
|
N
|
A:CYS266
|
4.0
|
15.6
|
1.0
|
HB2
|
A:ARG265
|
4.1
|
20.7
|
1.0
|
N
|
A:CYS208
|
4.1
|
14.0
|
1.0
|
HB3
|
A:CYS266
|
4.2
|
15.8
|
1.0
|
HB2
|
A:CYS263
|
4.2
|
26.4
|
1.0
|
CA
|
A:CYS263
|
4.2
|
21.9
|
1.0
|
CA
|
A:CYS266
|
4.3
|
12.2
|
1.0
|
CA
|
A:CYS208
|
4.4
|
18.6
|
1.0
|
NE2
|
A:HIS206
|
4.5
|
12.1
|
1.0
|
NE
|
A:ARG249
|
4.6
|
14.5
|
1.0
|
CA
|
A:CYS261
|
4.6
|
16.8
|
1.0
|
C
|
A:CYS261
|
4.6
|
18.7
|
1.0
|
NH2
|
A:ARG249
|
4.6
|
15.7
|
1.0
|
O
|
A:HOH921
|
4.6
|
23.5
|
1.0
|
HD11
|
A:LEU253
|
4.6
|
27.3
|
1.0
|
O
|
A:CYS263
|
4.6
|
15.6
|
1.0
|
HD2
|
A:HIS206
|
4.6
|
12.4
|
1.0
|
C
|
A:CYS263
|
4.7
|
22.0
|
1.0
|
HA
|
A:CYS266
|
4.7
|
14.2
|
1.0
|
O
|
A:CYS261
|
4.7
|
18.3
|
1.0
|
HD12
|
A:LEU253
|
4.8
|
27.3
|
1.0
|
H
|
A:ARG265
|
4.9
|
17.2
|
1.0
|
HA
|
A:SER207
|
4.9
|
16.8
|
1.0
|
HA
|
A:CYS208
|
4.9
|
22.4
|
1.0
|
HA
|
A:CYS261
|
4.9
|
20.3
|
1.0
|
CD2
|
A:HIS206
|
5.0
|
10.3
|
1.0
|
|
Zinc binding site 2 out
of 3 in 7qnu
Go back to
Zinc Binding Sites List in 7qnu
Zinc binding site 2 out
of 3 in the SMYD3 in Complex with Fragment FL08619
![](/pictures/ZN/pdb/qn/7qnu-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/qn/7qnu-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of SMYD3 in Complex with Fragment FL08619 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:16.8
occ:1.00
|
SG
|
A:CYS75
|
2.2
|
17.6
|
1.0
|
SG
|
A:CYS71
|
2.3
|
18.5
|
1.0
|
SG
|
A:CYS49
|
2.3
|
16.8
|
1.0
|
SG
|
A:CYS52
|
2.3
|
18.4
|
1.0
|
H
|
A:CYS52
|
3.0
|
20.5
|
1.0
|
HB3
|
A:CYS49
|
3.1
|
23.3
|
1.0
|
HB3
|
A:CYS52
|
3.1
|
25.0
|
1.0
|
CB
|
A:CYS75
|
3.1
|
21.8
|
1.0
|
CB
|
A:CYS49
|
3.1
|
19.3
|
1.0
|
HB2
|
A:CYS75
|
3.2
|
26.2
|
1.0
|
HB3
|
A:CYS75
|
3.2
|
26.2
|
1.0
|
H
|
A:CYS71
|
3.2
|
24.6
|
1.0
|
HB2
|
A:CYS49
|
3.3
|
23.3
|
1.0
|
CB
|
A:CYS52
|
3.3
|
20.8
|
1.0
|
HB3
|
A:CYS71
|
3.3
|
25.0
|
1.0
|
CB
|
A:CYS71
|
3.4
|
20.8
|
1.0
|
HG
|
A:SER72
|
3.7
|
19.2
|
1.0
|
N
|
A:CYS52
|
3.7
|
17.1
|
1.0
|
HB3
|
A:ARG51
|
3.8
|
17.9
|
1.0
|
N
|
A:CYS71
|
4.0
|
20.4
|
1.0
|
HB2
|
A:CYS52
|
4.1
|
25.0
|
1.0
|
CA
|
A:CYS52
|
4.1
|
17.2
|
1.0
|
HD3
|
A:ARG51
|
4.1
|
46.8
|
1.0
|
HH21
|
A:ARG51
|
4.1
|
46.5
|
1.0
|
HB2
|
A:CYS71
|
4.2
|
25.0
|
1.0
|
O
|
A:HOH1034
|
4.2
|
38.4
|
1.0
|
O
|
A:HOH948
|
4.2
|
26.6
|
1.0
|
CA
|
A:CYS71
|
4.3
|
25.8
|
1.0
|
H
|
A:ARG51
|
4.4
|
20.9
|
1.0
|
OG
|
A:SER72
|
4.4
|
15.9
|
1.0
|
CA
|
A:CYS75
|
4.6
|
17.0
|
1.0
|
CA
|
A:CYS49
|
4.6
|
18.9
|
1.0
|
H
|
A:LEU54
|
4.7
|
23.5
|
1.0
|
H
|
A:SER72
|
4.7
|
18.9
|
1.0
|
HA
|
A:TYR70
|
4.7
|
24.1
|
1.0
|
HB2
|
A:LEU54
|
4.7
|
24.9
|
1.0
|
CB
|
A:ARG51
|
4.7
|
14.9
|
1.0
|
H
|
A:LEU53
|
4.7
|
22.0
|
1.0
|
HA
|
A:CYS75
|
4.7
|
20.5
|
1.0
|
NH2
|
A:ARG51
|
4.9
|
38.7
|
1.0
|
C
|
A:ARG51
|
4.9
|
17.4
|
1.0
|
HD1
|
A:TYR70
|
4.9
|
19.0
|
1.0
|
HA
|
A:CYS52
|
4.9
|
20.7
|
1.0
|
C
|
A:CYS71
|
4.9
|
16.1
|
1.0
|
N
|
A:SER72
|
4.9
|
15.7
|
1.0
|
H
|
A:CYS75
|
5.0
|
20.3
|
1.0
|
C
|
A:CYS52
|
5.0
|
18.2
|
1.0
|
HB3
|
A:TYR70
|
5.0
|
19.4
|
1.0
|
|
Zinc binding site 3 out
of 3 in 7qnu
Go back to
Zinc Binding Sites List in 7qnu
Zinc binding site 3 out
of 3 in the SMYD3 in Complex with Fragment FL08619
![](/pictures/ZN/pdb/qn/7qnu-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/qn/7qnu-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of SMYD3 in Complex with Fragment FL08619 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn504
b:20.4
occ:1.00
|
NE2
|
A:HIS83
|
2.0
|
16.7
|
1.0
|
SG
|
A:CYS65
|
2.2
|
20.5
|
1.0
|
SG
|
A:CYS87
|
2.2
|
23.4
|
1.0
|
SG
|
A:CYS62
|
2.4
|
19.5
|
1.0
|
HB3
|
A:CYS62
|
2.9
|
25.0
|
1.0
|
CE1
|
A:HIS83
|
2.9
|
13.2
|
1.0
|
H
|
A:CYS65
|
2.9
|
35.6
|
1.0
|
HB2
|
A:CYS87
|
2.9
|
18.9
|
1.0
|
HE1
|
A:HIS83
|
3.0
|
15.9
|
1.0
|
CD2
|
A:HIS83
|
3.1
|
17.7
|
1.0
|
CB
|
A:CYS87
|
3.1
|
16.0
|
1.0
|
CB
|
A:CYS62
|
3.1
|
20.8
|
1.0
|
HB3
|
A:CYS65
|
3.1
|
30.3
|
1.0
|
CB
|
A:CYS65
|
3.3
|
25.2
|
1.0
|
HB2
|
A:CYS62
|
3.3
|
25.0
|
1.0
|
HD2
|
A:HIS83
|
3.3
|
21.2
|
1.0
|
HA
|
A:CYS87
|
3.4
|
21.1
|
1.0
|
N
|
A:CYS65
|
3.7
|
29.6
|
1.0
|
HB3
|
A:GLN64
|
3.7
|
37.6
|
1.0
|
HB3
|
A:ALA68
|
3.8
|
24.8
|
1.0
|
CA
|
A:CYS87
|
3.8
|
17.6
|
1.0
|
HZ3
|
A:TRP80
|
3.9
|
41.8
|
1.0
|
HB3
|
A:CYS87
|
3.9
|
18.9
|
1.0
|
ND1
|
A:HIS83
|
4.0
|
16.4
|
1.0
|
HB2
|
A:CYS65
|
4.1
|
30.3
|
1.0
|
CA
|
A:CYS65
|
4.1
|
31.4
|
1.0
|
HG2
|
A:GLN64
|
4.1
|
52.2
|
1.0
|
CG
|
A:HIS83
|
4.2
|
13.3
|
1.0
|
H
|
A:GLN64
|
4.2
|
30.9
|
1.0
|
H
|
A:ALA68
|
4.3
|
22.3
|
1.0
|
H
|
A:ARG66
|
4.4
|
32.4
|
1.0
|
O
|
A:HOH917
|
4.5
|
31.9
|
1.0
|
CB
|
A:GLN64
|
4.5
|
31.2
|
1.0
|
CA
|
A:CYS62
|
4.5
|
21.9
|
1.0
|
HB2
|
A:ALA68
|
4.5
|
24.8
|
1.0
|
CB
|
A:ALA68
|
4.6
|
20.6
|
1.0
|
C
|
A:CYS87
|
4.7
|
24.2
|
1.0
|
H
|
A:VAL67
|
4.7
|
23.4
|
1.0
|
C
|
A:GLN64
|
4.7
|
32.3
|
1.0
|
CZ3
|
A:TRP80
|
4.7
|
34.8
|
1.0
|
HD1
|
A:HIS83
|
4.8
|
19.8
|
1.0
|
N
|
A:GLN64
|
4.8
|
25.7
|
1.0
|
O
|
A:CYS87
|
4.8
|
23.5
|
1.0
|
CG
|
A:GLN64
|
4.8
|
43.5
|
1.0
|
HA
|
A:CYS65
|
4.8
|
37.8
|
1.0
|
N
|
A:ARG66
|
4.9
|
27.0
|
1.0
|
C
|
A:CYS62
|
4.9
|
20.4
|
1.0
|
C
|
A:CYS65
|
4.9
|
35.0
|
1.0
|
N
|
A:CYS87
|
4.9
|
18.5
|
1.0
|
CA
|
A:GLN64
|
4.9
|
30.4
|
1.0
|
HD12
|
A:LEU90
|
5.0
|
24.8
|
1.0
|
HA
|
A:CYS62
|
5.0
|
26.4
|
1.0
|
H
|
A:CYS87
|
5.0
|
22.2
|
1.0
|
|
Reference:
B.A.Lund,
D.Cederfelt,
D.Dobritzsch.
SMYD3 in Complex with Fragments To Be Published.
Page generated: Tue Apr 11 18:13:47 2023
|