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: Tue Apr 11 18:13:47 2023

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