Zinc in PDB 6yuh: Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site

Enzymatic activity of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site

All present enzymatic activity of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site:
2.1.1.354;

Protein crystallography data

The structure of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site, PDB code: 6yuh was solved by D.Cederfelt, V.O.Talibov, D.Dobritzsch, U.H.Danielson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.30 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.142, 66.284, 105.949, 90, 90, 90
R / Rfree (%) 18.6 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site (pdb code 6yuh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site, PDB code: 6yuh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6yuh

Go back to Zinc Binding Sites List in 6yuh
Zinc binding site 1 out of 3 in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:22.0
occ:1.00
SG A:CYS208 2.3 21.7 1.0
SG A:CYS263 2.3 20.2 1.0
SG A:CYS261 2.4 21.5 1.0
SG A:CYS266 2.4 19.4 1.0
CB A:CYS263 3.3 22.1 1.0
CB A:CYS261 3.4 28.3 1.0
CB A:CYS208 3.4 17.5 1.0
CB A:CYS266 3.4 16.1 1.0
N A:CYS266 4.1 23.5 1.0
N A:CYS208 4.1 19.5 1.0
N A:CYS263 4.1 25.0 1.0
CA A:CYS263 4.2 25.5 1.0
CA A:CYS266 4.3 18.5 1.0
CA A:CYS208 4.4 18.6 1.0
NH2 A:ARG249 4.5 21.6 1.0
NE2 A:HIS206 4.5 16.1 1.0
O A:CYS263 4.6 18.8 1.0
C A:CYS263 4.6 22.6 1.0
NE A:ARG249 4.6 19.9 1.0
CA A:CYS261 4.6 24.7 1.0
O A:HOH793 4.7 26.9 1.0
C A:CYS261 4.8 26.8 1.0
O A:CYS261 4.9 24.5 1.0
CD2 A:HIS206 5.0 14.9 1.0

Zinc binding site 2 out of 3 in 6yuh

Go back to Zinc Binding Sites List in 6yuh
Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:23.6
occ:1.00
SG A:CYS49 2.2 22.0 1.0
SG A:CYS75 2.3 24.9 1.0
SG A:CYS52 2.4 23.7 1.0
SG A:CYS71 2.4 27.2 1.0
CB A:CYS49 3.1 26.2 1.0
CB A:CYS75 3.2 25.4 1.0
CB A:CYS52 3.3 23.8 1.0
CB A:CYS71 3.6 23.1 1.0
N A:CYS52 3.7 23.3 1.0
O A:HOH839 3.9 27.5 1.0
N A:CYS71 4.1 23.3 1.0
CA A:CYS52 4.1 23.7 1.0
O A:HOH824 4.2 31.4 1.0
CA A:CYS71 4.4 29.8 1.0
OG A:SER72 4.5 22.6 1.0
CB A:ARG51 4.6 24.2 1.0
CA A:CYS49 4.6 24.7 1.0
CA A:CYS75 4.7 25.2 1.0
C A:ARG51 4.8 28.7 1.0
C A:CYS52 4.9 23.6 1.0
N A:ARG51 4.9 21.6 1.0
C A:CYS71 5.0 27.4 1.0

Zinc binding site 3 out of 3 in 6yuh

Go back to Zinc Binding Sites List in 6yuh
Zinc binding site 3 out of 3 in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:33.9
occ:1.00
NE2 A:HIS83 2.1 26.8 1.0
SG A:CYS65 2.2 32.9 1.0
SG A:CYS87 2.4 33.2 1.0
SG A:CYS62 2.5 40.7 1.0
CE1 A:HIS83 3.0 26.7 1.0
CD2 A:HIS83 3.1 22.4 1.0
CB A:CYS87 3.2 35.9 1.0
CB A:CYS65 3.4 45.1 1.0
CB A:CYS62 3.4 30.6 1.0
N A:CYS65 3.7 48.8 1.0
CA A:CYS87 3.9 29.0 1.0
CA A:CYS65 4.1 45.3 1.0
ND1 A:HIS83 4.2 25.4 1.0
CG A:HIS83 4.2 26.5 1.0
CB A:GLN64 4.5 50.1 1.0
CB A:ALA68 4.6 25.8 1.0
C A:CYS87 4.7 28.2 1.0
CA A:CYS62 4.7 36.3 1.0
C A:GLN64 4.8 49.8 1.0
O A:HOH690 4.8 31.5 1.0
CZ3 A:TRP80 4.8 49.8 1.0
N A:GLN64 4.8 48.5 1.0
O A:CYS87 4.8 32.8 1.0
N A:ARG66 4.9 43.9 1.0
C A:CYS65 4.9 47.6 1.0
C A:CYS62 4.9 36.4 1.0
CA A:GLN64 5.0 50.9 1.0

Reference:

V.O.Talibov, E.Fabini, E.Fitzgerald, D.Tedesco, D.Eriksson, M.J.Talu, M.M.Rachman, F.Mihalic, E.Manoni, M.Naldi, P.Sanese, G.Forte, M.L.Signorile, X.Barril, C.Simone, M.Bartolini, D.Dobritzsch, A.Del Rio, U.H.Danielson. Discovery of An Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 33400854
DOI: 10.1002/CBIC.202000736
Page generated: Mon Jan 25 16:38:22 2021

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