Zinc in PDB 7qlb: SMYD3 in Complex with Fragment FL06268
Enzymatic activity of SMYD3 in Complex with Fragment FL06268
All present enzymatic activity of SMYD3 in Complex with Fragment FL06268:
2.1.1.354;
Protein crystallography data
The structure of SMYD3 in Complex with Fragment FL06268, PDB code: 7qlb
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)
|
29.33 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.938,
66.329,
108.165,
90,
90,
90
|
R / Rfree (%)
|
15 /
18.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the SMYD3 in Complex with Fragment FL06268
(pdb code 7qlb). 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 FL06268, PDB code: 7qlb:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 7qlb
Go back to
Zinc Binding Sites List in 7qlb
Zinc binding site 1 out
of 3 in the SMYD3 in Complex with Fragment FL06268
Mono view
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 FL06268 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:20.1
occ:1.00
|
SG
|
A:CYS208
|
2.3
|
19.0
|
1.0
|
SG
|
A:CYS261
|
2.3
|
22.6
|
1.0
|
SG
|
A:CYS263
|
2.4
|
21.1
|
1.0
|
SG
|
A:CYS266
|
2.4
|
17.6
|
1.0
|
HB2
|
A:CYS208
|
3.2
|
21.0
|
1.0
|
HB3
|
A:CYS261
|
3.2
|
23.7
|
1.0
|
HB2
|
A:CYS266
|
3.2
|
22.9
|
1.0
|
HB3
|
A:CYS263
|
3.3
|
33.6
|
1.0
|
CB
|
A:CYS261
|
3.4
|
19.8
|
1.0
|
H
|
A:CYS266
|
3.4
|
20.9
|
1.0
|
CB
|
A:CYS208
|
3.4
|
17.5
|
1.0
|
H
|
A:CYS263
|
3.4
|
31.3
|
1.0
|
CB
|
A:CYS266
|
3.4
|
19.1
|
1.0
|
CB
|
A:CYS263
|
3.5
|
28.0
|
1.0
|
H
|
A:CYS208
|
3.7
|
19.4
|
1.0
|
HH21
|
A:ARG249
|
3.7
|
18.9
|
1.0
|
HE
|
A:ARG249
|
3.8
|
19.0
|
1.0
|
HB2
|
A:CYS261
|
3.8
|
23.7
|
1.0
|
HE2
|
A:HIS206
|
3.9
|
21.3
|
1.0
|
N
|
A:CYS266
|
4.0
|
17.4
|
1.0
|
HB2
|
A:ARG265
|
4.0
|
20.5
|
1.0
|
HB3
|
A:CYS208
|
4.0
|
21.0
|
1.0
|
N
|
A:CYS263
|
4.1
|
26.1
|
1.0
|
HB3
|
A:CYS266
|
4.1
|
22.9
|
1.0
|
HB2
|
A:CYS263
|
4.2
|
33.6
|
1.0
|
CA
|
A:CYS263
|
4.3
|
26.0
|
1.0
|
N
|
A:CYS208
|
4.3
|
16.2
|
1.0
|
CA
|
A:CYS266
|
4.3
|
18.2
|
1.0
|
CA
|
A:CYS208
|
4.5
|
16.9
|
1.0
|
NH2
|
A:ARG249
|
4.5
|
15.8
|
1.0
|
NE
|
A:ARG249
|
4.6
|
15.8
|
1.0
|
CA
|
A:CYS261
|
4.6
|
20.8
|
1.0
|
C
|
A:CYS261
|
4.6
|
22.4
|
1.0
|
NE2
|
A:HIS206
|
4.7
|
17.8
|
1.0
|
HA
|
A:CYS266
|
4.7
|
21.9
|
1.0
|
O
|
A:CYS261
|
4.7
|
22.7
|
1.0
|
HD2
|
A:HIS206
|
4.8
|
21.6
|
1.0
|
C
|
A:CYS263
|
4.8
|
25.4
|
1.0
|
O
|
A:CYS263
|
4.9
|
22.2
|
1.0
|
H
|
A:ARG265
|
4.9
|
21.1
|
1.0
|
CB
|
A:ARG265
|
4.9
|
17.1
|
1.0
|
O
|
A:HOH953
|
4.9
|
20.0
|
1.0
|
HA
|
A:CYS261
|
5.0
|
25.0
|
1.0
|
HD11
|
A:LEU253
|
5.0
|
21.8
|
1.0
|
|
Zinc binding site 2 out
of 3 in 7qlb
Go back to
Zinc Binding Sites List in 7qlb
Zinc binding site 2 out
of 3 in the SMYD3 in Complex with Fragment FL06268
Mono view
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 FL06268 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:22.7
occ:1.00
|
SG
|
A:CYS75
|
2.3
|
25.4
|
1.0
|
SG
|
A:CYS52
|
2.3
|
23.9
|
1.0
|
SG
|
A:CYS71
|
2.3
|
27.0
|
1.0
|
SG
|
A:CYS49
|
2.4
|
22.7
|
1.0
|
H
|
A:CYS52
|
3.0
|
27.5
|
1.0
|
HB3
|
A:CYS52
|
3.1
|
25.4
|
1.0
|
HB3
|
A:CYS49
|
3.1
|
28.9
|
1.0
|
CB
|
A:CYS49
|
3.2
|
24.1
|
1.0
|
CB
|
A:CYS75
|
3.2
|
24.6
|
1.0
|
HB2
|
A:CYS75
|
3.2
|
29.5
|
1.0
|
H
|
A:CYS71
|
3.2
|
29.5
|
1.0
|
HB2
|
A:CYS49
|
3.2
|
28.9
|
1.0
|
HB3
|
A:CYS75
|
3.2
|
29.5
|
1.0
|
HB3
|
A:CYS71
|
3.2
|
31.8
|
1.0
|
CB
|
A:CYS52
|
3.3
|
21.2
|
1.0
|
CB
|
A:CYS71
|
3.4
|
26.5
|
1.0
|
HG
|
A:SER72
|
3.7
|
31.5
|
1.0
|
N
|
A:CYS52
|
3.8
|
22.9
|
1.0
|
HB3
|
A:ARG51
|
3.8
|
31.7
|
1.0
|
O
|
A:HOH1108
|
3.8
|
31.1
|
1.0
|
N
|
A:CYS71
|
4.0
|
24.6
|
1.0
|
HB2
|
A:CYS52
|
4.1
|
25.4
|
1.0
|
CA
|
A:CYS52
|
4.1
|
21.6
|
1.0
|
HB2
|
A:CYS71
|
4.2
|
31.8
|
1.0
|
O
|
A:HOH980
|
4.2
|
35.8
|
1.0
|
CA
|
A:CYS71
|
4.3
|
27.1
|
1.0
|
OG
|
A:SER72
|
4.4
|
26.3
|
1.0
|
HH21
|
A:ARG51
|
4.4
|
51.3
|
1.0
|
H
|
A:ARG51
|
4.5
|
24.0
|
1.0
|
HB2
|
A:LEU54
|
4.6
|
33.7
|
1.0
|
H
|
A:LEU54
|
4.6
|
29.0
|
1.0
|
CA
|
A:CYS75
|
4.6
|
20.0
|
1.0
|
CA
|
A:CYS49
|
4.7
|
24.2
|
1.0
|
H
|
A:SER72
|
4.7
|
31.3
|
1.0
|
H
|
A:LEU53
|
4.7
|
23.9
|
1.0
|
CB
|
A:ARG51
|
4.7
|
26.4
|
1.0
|
HZ1
|
A:LYS56
|
4.7
|
93.2
|
1.0
|
HB3
|
A:TYR70
|
4.8
|
29.9
|
1.0
|
HA
|
A:TYR70
|
4.8
|
28.8
|
1.0
|
HA
|
A:CYS75
|
4.8
|
24.0
|
1.0
|
HA
|
A:CYS52
|
4.9
|
26.0
|
1.0
|
C
|
A:CYS52
|
4.9
|
24.8
|
1.0
|
C
|
A:ARG51
|
4.9
|
21.0
|
1.0
|
HD3
|
A:ARG51
|
4.9
|
44.5
|
1.0
|
C
|
A:CYS71
|
4.9
|
26.6
|
1.0
|
N
|
A:SER72
|
4.9
|
26.1
|
1.0
|
H
|
A:CYS75
|
4.9
|
27.1
|
1.0
|
|
Zinc binding site 3 out
of 3 in 7qlb
Go back to
Zinc Binding Sites List in 7qlb
Zinc binding site 3 out
of 3 in the SMYD3 in Complex with Fragment FL06268
Mono view
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 FL06268 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:22.2
occ:1.00
|
NE2
|
A:HIS83
|
2.0
|
22.3
|
1.0
|
SG
|
A:CYS62
|
2.3
|
22.2
|
1.0
|
SG
|
A:CYS87
|
2.3
|
25.4
|
1.0
|
SG
|
A:CYS65
|
2.3
|
23.2
|
1.0
|
H
|
A:CYS65
|
2.9
|
28.5
|
1.0
|
CE1
|
A:HIS83
|
2.9
|
20.7
|
1.0
|
HB3
|
A:CYS65
|
3.0
|
26.7
|
1.0
|
HE1
|
A:HIS83
|
3.0
|
24.8
|
1.0
|
HB2
|
A:CYS87
|
3.0
|
25.9
|
1.0
|
HB3
|
A:CYS62
|
3.1
|
30.5
|
1.0
|
CD2
|
A:HIS83
|
3.1
|
22.7
|
1.0
|
CB
|
A:CYS62
|
3.2
|
25.4
|
1.0
|
CB
|
A:CYS65
|
3.2
|
22.3
|
1.0
|
CB
|
A:CYS87
|
3.2
|
21.6
|
1.0
|
HD2
|
A:HIS83
|
3.4
|
27.2
|
1.0
|
HB2
|
A:CYS62
|
3.4
|
30.5
|
1.0
|
HA
|
A:CYS87
|
3.5
|
30.1
|
1.0
|
N
|
A:CYS65
|
3.6
|
23.7
|
1.0
|
HB3
|
A:GLN64
|
3.6
|
31.6
|
1.0
|
HZ3
|
A:TRP80
|
3.8
|
30.6
|
1.0
|
HB3
|
A:ALA68
|
3.9
|
27.4
|
1.0
|
CA
|
A:CYS87
|
3.9
|
25.1
|
1.0
|
CA
|
A:CYS65
|
4.0
|
28.0
|
1.0
|
HB2
|
A:CYS65
|
4.0
|
26.7
|
1.0
|
HB3
|
A:CYS87
|
4.1
|
25.9
|
1.0
|
ND1
|
A:HIS83
|
4.1
|
22.2
|
1.0
|
CG
|
A:HIS83
|
4.2
|
17.4
|
1.0
|
H
|
A:GLN64
|
4.3
|
29.6
|
1.0
|
H
|
A:ALA68
|
4.3
|
25.3
|
1.0
|
HG2
|
A:GLN64
|
4.3
|
75.9
|
1.0
|
H
|
A:ARG66
|
4.3
|
31.1
|
1.0
|
HB2
|
A:ALA68
|
4.4
|
27.4
|
1.0
|
CB
|
A:GLN64
|
4.5
|
26.3
|
1.0
|
C
|
A:GLN64
|
4.6
|
28.2
|
1.0
|
CB
|
A:ALA68
|
4.6
|
22.8
|
1.0
|
CA
|
A:CYS62
|
4.6
|
24.3
|
1.0
|
H
|
A:VAL67
|
4.7
|
32.0
|
1.0
|
O
|
A:HOH970
|
4.7
|
22.4
|
1.0
|
HA
|
A:CYS65
|
4.7
|
33.6
|
1.0
|
CZ3
|
A:TRP80
|
4.7
|
25.5
|
1.0
|
HD1
|
A:HIS83
|
4.8
|
26.7
|
1.0
|
N
|
A:ARG66
|
4.8
|
25.9
|
1.0
|
C
|
A:CYS87
|
4.8
|
29.7
|
1.0
|
N
|
A:GLN64
|
4.8
|
24.6
|
1.0
|
C
|
A:CYS65
|
4.9
|
30.8
|
1.0
|
CA
|
A:GLN64
|
4.9
|
29.1
|
1.0
|
HD12
|
A:LEU90
|
4.9
|
34.7
|
1.0
|
CG
|
A:GLN64
|
4.9
|
63.2
|
1.0
|
O
|
A:CYS87
|
4.9
|
27.4
|
1.0
|
C
|
A:CYS62
|
4.9
|
25.9
|
1.0
|
|
Reference:
B.A.Lund,
D.Cederfelt,
D.Dobritzsch.
SMYD3 in Complex with Fragment FL06268 To Be Published.
Page generated: Wed Oct 30 09:55:47 2024
|