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Zinc in PDB 5kjn: SMYD2 in Complex with AZ506

Enzymatic activity of SMYD2 in Complex with AZ506

All present enzymatic activity of SMYD2 in Complex with AZ506:
2.1.1.43;

Protein crystallography data

The structure of SMYD2 in Complex with AZ506, PDB code: 5kjn was solved by A.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.76 / 2.72
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 154.871, 154.871, 52.286, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 22.5

Other elements in 5kjn:

The structure of SMYD2 in Complex with AZ506 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the SMYD2 in Complex with AZ506 (pdb code 5kjn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SMYD2 in Complex with AZ506, PDB code: 5kjn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5kjn

Go back to Zinc Binding Sites List in 5kjn
Zinc binding site 1 out of 3 in the SMYD2 in Complex with AZ506


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SMYD2 in Complex with AZ506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:54.0
occ:1.00
SG A:CYS52 2.3 58.0 1.0
SG A:CYS78 2.3 59.3 1.0
SG A:CYS55 2.4 47.9 1.0
SG A:CYS74 2.5 48.2 1.0
CB A:CYS74 3.2 45.7 1.0
CB A:CYS52 3.2 53.6 1.0
CB A:CYS78 3.4 55.0 1.0
CB A:CYS55 3.7 43.1 1.0
N A:CYS74 3.7 44.2 1.0
N A:CYS55 4.0 43.6 1.0
CA A:CYS74 4.1 45.4 1.0
CA A:CYS55 4.4 41.6 1.0
CA A:CYS52 4.6 53.3 1.0
CB A:TYR54 4.7 44.5 1.0
CA A:CYS78 4.8 54.4 1.0
C A:TYR73 4.8 49.8 1.0
OG1 A:THR57 4.8 42.4 1.0
CD1 A:TYR54 4.9 47.1 1.0
CB A:THR57 4.9 43.7 1.0
C A:TYR54 5.0 48.4 1.0

Zinc binding site 2 out of 3 in 5kjn

Go back to Zinc Binding Sites List in 5kjn
Zinc binding site 2 out of 3 in the SMYD2 in Complex with AZ506


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SMYD2 in Complex with AZ506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn512

b:50.3
occ:1.00
NE2 A:HIS86 2.2 48.8 1.0
SG A:CYS68 2.2 52.2 1.0
SG A:CYS90 2.3 50.2 1.0
SG A:CYS65 2.4 58.0 1.0
CE1 A:HIS86 3.1 47.5 1.0
CD2 A:HIS86 3.2 48.9 1.0
CB A:CYS68 3.3 50.1 1.0
CB A:CYS65 3.3 54.3 1.0
CB A:CYS90 3.5 45.3 1.0
N A:CYS68 3.5 54.1 1.0
CA A:CYS90 3.9 44.0 1.0
CA A:CYS68 4.0 52.6 1.0
ND1 A:HIS86 4.3 47.1 1.0
CB A:ARG67 4.3 55.0 1.0
CG A:HIS86 4.3 45.7 1.0
CB A:ALA71 4.5 45.6 1.0
C A:ARG67 4.6 59.9 1.0
CA A:CYS65 4.6 56.6 1.0
CA A:ARG67 4.7 56.5 1.0
O A:CYS65 4.8 58.3 1.0
N A:ARG67 4.8 58.1 1.0
N A:LYS69 4.8 54.5 1.0
NH1 A:ARG67 4.8 89.8 1.0
C A:CYS90 4.8 49.5 1.0
C A:CYS68 4.9 59.8 1.0
C A:CYS65 4.9 59.6 1.0
N A:CYS90 5.0 42.9 1.0

Zinc binding site 3 out of 3 in 5kjn

Go back to Zinc Binding Sites List in 5kjn
Zinc binding site 3 out of 3 in the SMYD2 in Complex with AZ506


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SMYD2 in Complex with AZ506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn513

b:52.7
occ:1.00
SG A:CYS267 2.2 40.2 1.0
SG A:CYS264 2.3 53.7 1.0
SG A:CYS262 2.5 49.8 1.0
SG A:CYS209 2.5 49.0 1.0
CB A:CYS209 3.3 45.1 1.0
CB A:CYS262 3.3 46.0 1.0
CB A:CYS267 3.4 39.5 1.0
CB A:CYS264 3.4 50.3 1.0
N A:CYS209 3.7 46.0 1.0
N A:CYS264 4.0 49.6 1.0
N A:CYS267 4.0 44.4 1.0
CA A:CYS209 4.1 44.3 1.0
CA A:CYS264 4.1 50.8 1.0
CE1 A:HIS207 4.2 40.2 1.0
CA A:CYS267 4.3 42.2 1.0
C A:CYS262 4.4 50.7 1.0
CA A:CYS262 4.4 46.3 1.0
O A:CYS262 4.6 52.0 1.0
ND1 A:HIS207 4.6 41.8 1.0
C A:SER208 4.7 48.5 1.0
C A:CYS264 4.7 57.3 1.0
NH2 A:ARG250 4.7 44.0 1.0
CB A:GLU266 4.8 47.7 1.0
O A:CYS264 4.8 58.6 1.0
N A:GLU263 4.8 47.9 1.0
NE A:ARG250 4.9 38.5 1.0
CA A:SER208 4.9 43.2 1.0
C A:GLU266 5.0 50.2 1.0

Reference:

S.D.Cowen, D.Russell, L.A.Dakin, H.Chen, N.A.Larsen, R.Godin, S.Throner, X.Zheng, A.Molina, J.Wu, T.Cheung, T.Howard, R.Garcia-Arenas, N.Keen, C.S.Pendleton, J.A.Pietenpol, A.D.Ferguson. Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. J. Med. Chem. V. 59 11079 2016.
ISSN: ISSN 1520-4804
PubMed: 28002961
Page generated: Wed Dec 16 06:27:36 2020

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