Zinc in PDB 8owo: SMYD3 in Complex with Fragment FL01507
Enzymatic activity of SMYD3 in Complex with Fragment FL01507
All present enzymatic activity of SMYD3 in Complex with Fragment FL01507:
2.1.1.354;
Protein crystallography data
The structure of SMYD3 in Complex with Fragment FL01507, PDB code: 8owo
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)
|
53.08 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.08,
66.14,
107.28,
90,
90,
90
|
R / Rfree (%)
|
16.1 /
20
|
Zinc Binding Sites:
The binding sites of Zinc atom in the SMYD3 in Complex with Fragment FL01507
(pdb code 8owo). 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 FL01507, PDB code: 8owo:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 8owo
Go back to
Zinc Binding Sites List in 8owo
Zinc binding site 1 out
of 3 in the SMYD3 in Complex with Fragment FL01507
![](/pictures/ZN/pdb/ow/8owo-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ow/8owo-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 FL01507 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:22.4
occ:1.00
|
SG
|
A:CYS266
|
2.3
|
18.3
|
1.0
|
SG
|
A:CYS208
|
2.3
|
20.9
|
1.0
|
SG
|
A:CYS261
|
2.3
|
24.3
|
1.0
|
SG
|
A:CYS263
|
2.4
|
21.6
|
1.0
|
HB3
|
A:CYS261
|
3.1
|
24.2
|
1.0
|
HB2
|
A:CYS266
|
3.1
|
19.7
|
1.0
|
HB2
|
A:CYS208
|
3.2
|
23.1
|
1.0
|
CB
|
A:CYS261
|
3.3
|
20.2
|
1.0
|
CB
|
A:CYS266
|
3.4
|
16.4
|
1.0
|
HB3
|
A:CYS263
|
3.4
|
30.8
|
1.0
|
H
|
A:CYS263
|
3.4
|
31.3
|
1.0
|
CB
|
A:CYS208
|
3.4
|
19.3
|
1.0
|
H
|
A:CYS266
|
3.4
|
20.3
|
1.0
|
CB
|
A:CYS263
|
3.5
|
25.7
|
1.0
|
HH21
|
A:ARG249
|
3.7
|
18.7
|
1.0
|
H
|
A:CYS208
|
3.7
|
20.7
|
1.0
|
HB2
|
A:CYS261
|
3.7
|
24.2
|
1.0
|
HE
|
A:ARG249
|
3.8
|
20.4
|
1.0
|
HB3
|
A:CYS208
|
4.0
|
23.1
|
1.0
|
N
|
A:CYS266
|
4.0
|
16.9
|
1.0
|
HB2
|
A:ARG265
|
4.0
|
22.6
|
1.0
|
HE2
|
A:HIS206
|
4.0
|
18.8
|
1.0
|
HB3
|
A:CYS266
|
4.1
|
19.7
|
1.0
|
N
|
A:CYS263
|
4.1
|
26.1
|
1.0
|
HB2
|
A:CYS263
|
4.3
|
30.8
|
1.0
|
CA
|
A:CYS266
|
4.3
|
16.2
|
1.0
|
CA
|
A:CYS263
|
4.3
|
28.6
|
1.0
|
N
|
A:CYS208
|
4.4
|
17.2
|
1.0
|
NH2
|
A:ARG249
|
4.5
|
15.6
|
1.0
|
CA
|
A:CYS261
|
4.5
|
21.7
|
1.0
|
CA
|
A:CYS208
|
4.5
|
17.1
|
1.0
|
NE
|
A:ARG249
|
4.6
|
17.0
|
1.0
|
C
|
A:CYS261
|
4.6
|
23.2
|
1.0
|
HA
|
A:CYS266
|
4.6
|
19.5
|
1.0
|
O
|
A:CYS261
|
4.7
|
20.6
|
1.0
|
NE2
|
A:HIS206
|
4.8
|
15.7
|
1.0
|
O
|
A:HOH951
|
4.9
|
19.4
|
1.0
|
HD2
|
A:HIS206
|
4.9
|
21.4
|
1.0
|
C
|
A:CYS263
|
4.9
|
23.1
|
1.0
|
H
|
A:ARG265
|
4.9
|
20.9
|
1.0
|
HA
|
A:CYS261
|
4.9
|
26.0
|
1.0
|
CB
|
A:ARG265
|
4.9
|
18.8
|
1.0
|
N
|
A:ASP262
|
5.0
|
25.4
|
1.0
|
C
|
A:ARG265
|
5.0
|
19.5
|
1.0
|
|
Zinc binding site 2 out
of 3 in 8owo
Go back to
Zinc Binding Sites List in 8owo
Zinc binding site 2 out
of 3 in the SMYD3 in Complex with Fragment FL01507
![](/pictures/ZN/pdb/ow/8owo-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ow/8owo-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 FL01507 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:25.1
occ:1.00
|
SG
|
A:CYS75
|
2.3
|
24.7
|
1.0
|
SG
|
A:CYS71
|
2.3
|
26.2
|
1.0
|
SG
|
A:CYS52
|
2.3
|
25.5
|
1.0
|
SG
|
A:CYS49
|
2.4
|
26.2
|
1.0
|
H
|
A:CYS52
|
3.0
|
26.1
|
1.0
|
HB3
|
A:CYS52
|
3.1
|
30.1
|
1.0
|
HB3
|
A:CYS71
|
3.1
|
25.9
|
1.0
|
HB2
|
A:CYS75
|
3.1
|
33.6
|
1.0
|
CB
|
A:CYS75
|
3.1
|
28.0
|
1.0
|
HB3
|
A:CYS75
|
3.1
|
33.6
|
1.0
|
H
|
A:CYS71
|
3.2
|
32.2
|
1.0
|
HB3
|
A:CYS49
|
3.2
|
34.4
|
1.0
|
CB
|
A:CYS49
|
3.2
|
28.7
|
1.0
|
HB2
|
A:CYS49
|
3.3
|
34.4
|
1.0
|
CB
|
A:CYS52
|
3.3
|
25.1
|
1.0
|
CB
|
A:CYS71
|
3.3
|
21.6
|
1.0
|
HG
|
A:SER72
|
3.7
|
31.4
|
1.0
|
N
|
A:CYS52
|
3.8
|
21.8
|
1.0
|
O
|
A:HOH1082
|
3.8
|
30.0
|
1.0
|
HB3
|
A:ARG51
|
3.8
|
30.7
|
1.0
|
N
|
A:CYS71
|
3.9
|
26.8
|
1.0
|
HB2
|
A:CYS52
|
4.1
|
30.1
|
1.0
|
HB2
|
A:CYS71
|
4.1
|
25.9
|
1.0
|
CA
|
A:CYS52
|
4.1
|
22.7
|
1.0
|
CA
|
A:CYS71
|
4.2
|
29.0
|
1.0
|
O
|
A:HOH966
|
4.2
|
36.2
|
1.0
|
HG2
|
A:ARG51
|
4.3
|
31.6
|
1.0
|
OG
|
A:SER72
|
4.4
|
26.1
|
1.0
|
H
|
A:ARG51
|
4.5
|
24.4
|
1.0
|
CA
|
A:CYS75
|
4.6
|
20.4
|
1.0
|
HH11
|
A:ARG51
|
4.7
|
51.0
|
1.0
|
H
|
A:LEU54
|
4.7
|
35.0
|
1.0
|
CB
|
A:ARG51
|
4.7
|
25.6
|
1.0
|
CA
|
A:CYS49
|
4.7
|
23.9
|
1.0
|
HB2
|
A:LEU54
|
4.7
|
28.1
|
1.0
|
H
|
A:LEU53
|
4.7
|
24.5
|
1.0
|
HA
|
A:CYS75
|
4.8
|
24.5
|
1.0
|
H
|
A:SER72
|
4.8
|
28.5
|
1.0
|
HA
|
A:TYR70
|
4.8
|
32.1
|
1.0
|
HA
|
A:CYS52
|
4.9
|
27.2
|
1.0
|
C
|
A:CYS52
|
4.9
|
24.3
|
1.0
|
HB3
|
A:TYR70
|
4.9
|
29.6
|
1.0
|
C
|
A:CYS71
|
4.9
|
29.8
|
1.0
|
C
|
A:ARG51
|
4.9
|
26.9
|
1.0
|
H
|
A:CYS75
|
4.9
|
27.3
|
1.0
|
N
|
A:SER72
|
4.9
|
23.8
|
1.0
|
HA
|
A:CYS71
|
5.0
|
34.9
|
1.0
|
|
Zinc binding site 3 out
of 3 in 8owo
Go back to
Zinc Binding Sites List in 8owo
Zinc binding site 3 out
of 3 in the SMYD3 in Complex with Fragment FL01507
![](/pictures/ZN/pdb/ow/8owo-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ow/8owo-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 FL01507 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn504
b:30.0
occ:1.00
|
NE2
|
A:HIS83
|
2.0
|
27.0
|
1.0
|
SG
|
A:CYS62
|
2.3
|
25.3
|
1.0
|
SG
|
A:CYS87
|
2.3
|
28.7
|
1.0
|
SG
|
A:CYS65
|
2.3
|
29.7
|
1.0
|
H
|
A:CYS65
|
2.9
|
32.1
|
1.0
|
CE1
|
A:HIS83
|
2.9
|
25.6
|
1.0
|
HB3
|
A:CYS65
|
2.9
|
36.7
|
1.0
|
HE1
|
A:HIS83
|
3.0
|
30.8
|
1.0
|
HB3
|
A:CYS62
|
3.0
|
38.4
|
1.0
|
HB2
|
A:CYS87
|
3.1
|
35.4
|
1.0
|
CD2
|
A:HIS83
|
3.1
|
27.6
|
1.0
|
CB
|
A:CYS65
|
3.2
|
30.6
|
1.0
|
CB
|
A:CYS62
|
3.2
|
32.0
|
1.0
|
CB
|
A:CYS87
|
3.2
|
29.5
|
1.0
|
HD2
|
A:HIS83
|
3.4
|
33.1
|
1.0
|
HB2
|
A:CYS62
|
3.4
|
38.4
|
1.0
|
HA
|
A:CYS87
|
3.5
|
34.7
|
1.0
|
N
|
A:CYS65
|
3.5
|
26.7
|
1.0
|
HZ3
|
A:TRP80
|
3.8
|
39.5
|
1.0
|
HB3
|
A:GLN64
|
3.8
|
38.7
|
1.0
|
CA
|
A:CYS87
|
3.9
|
28.9
|
1.0
|
HB3
|
A:ALA68
|
3.9
|
33.7
|
1.0
|
CA
|
A:CYS65
|
3.9
|
34.7
|
1.0
|
HB2
|
A:CYS65
|
4.0
|
36.7
|
1.0
|
HB3
|
A:CYS87
|
4.1
|
35.4
|
1.0
|
ND1
|
A:HIS83
|
4.1
|
24.6
|
1.0
|
HG2
|
A:GLN64
|
4.1
|
60.8
|
1.0
|
CG
|
A:HIS83
|
4.2
|
26.6
|
1.0
|
H
|
A:ARG66
|
4.2
|
39.0
|
1.0
|
H
|
A:ALA68
|
4.4
|
34.9
|
1.0
|
H
|
A:GLN64
|
4.4
|
37.7
|
1.0
|
HB2
|
A:ALA68
|
4.6
|
33.7
|
1.0
|
C
|
A:GLN64
|
4.6
|
41.1
|
1.0
|
CB
|
A:GLN64
|
4.6
|
32.2
|
1.0
|
CA
|
A:CYS62
|
4.6
|
28.0
|
1.0
|
HA
|
A:CYS65
|
4.7
|
41.7
|
1.0
|
H
|
A:VAL67
|
4.7
|
38.1
|
1.0
|
CB
|
A:ALA68
|
4.7
|
28.1
|
1.0
|
CZ3
|
A:TRP80
|
4.7
|
32.9
|
1.0
|
N
|
A:ARG66
|
4.7
|
32.5
|
1.0
|
O
|
A:HOH958
|
4.8
|
25.2
|
1.0
|
CG
|
A:GLN64
|
4.8
|
50.6
|
1.0
|
C
|
A:CYS65
|
4.8
|
35.9
|
1.0
|
C
|
A:CYS87
|
4.8
|
31.4
|
1.0
|
HD1
|
A:HIS83
|
4.8
|
29.5
|
1.0
|
N
|
A:GLN64
|
4.9
|
31.4
|
1.0
|
CA
|
A:GLN64
|
4.9
|
33.8
|
1.0
|
OE1
|
A:GLN64
|
4.9
|
50.1
|
1.0
|
O
|
A:CYS87
|
4.9
|
31.6
|
1.0
|
C
|
A:CYS62
|
4.9
|
29.7
|
1.0
|
HH
|
A:TYR70
|
5.0
|
30.4
|
1.0
|
N
|
A:CYS87
|
5.0
|
28.1
|
1.0
|
|
Reference:
B.A.Lund,
D.Cederfelt,
D.Dobritzsch.
SMYD3 in Complex with Fragments To Be Published.
Page generated: Thu Dec 28 13:31:58 2023
|