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Zinc in PDB 5kjk: SMYD2 in Complex with AZ370

Enzymatic activity of SMYD2 in Complex with AZ370

All present enzymatic activity of SMYD2 in Complex with AZ370:
2.1.1.43;

Protein crystallography data

The structure of SMYD2 in Complex with AZ370, PDB code: 5kjk was solved by A.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.21 / 1.93
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 155.865, 155.865, 52.477, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.3

Other elements in 5kjk:

The structure of SMYD2 in Complex with AZ370 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the SMYD2 in Complex with AZ370 (pdb code 5kjk). 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 AZ370, PDB code: 5kjk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5kjk

Go back to Zinc Binding Sites List in 5kjk
Zinc binding site 1 out of 3 in the SMYD2 in Complex with AZ370


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 AZ370 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:36.2
occ:1.00
SG A:CYS78 2.2 38.9 1.0
SG A:CYS52 2.3 34.4 1.0
SG A:CYS55 2.4 36.1 1.0
SG A:CYS74 2.5 39.3 1.0
CB A:CYS52 3.1 30.1 1.0
CB A:CYS74 3.2 36.9 1.0
CB A:CYS78 3.2 36.2 1.0
CB A:CYS55 3.5 31.7 1.0
N A:CYS74 3.8 38.0 1.0
N A:CYS55 3.9 31.7 1.0
CA A:CYS74 4.1 37.6 1.0
CA A:CYS55 4.3 30.9 1.0
CA A:CYS52 4.6 30.6 1.0
CA A:CYS78 4.6 36.7 1.0
CB A:TYR54 4.7 31.2 1.0
OG1 A:THR57 4.7 38.1 1.0
CB A:THR57 4.8 39.6 1.0
C A:TYR54 4.9 33.3 1.0
C A:CYS55 4.9 33.1 1.0
CD1 A:TYR54 5.0 35.6 1.0
C A:TYR73 5.0 40.7 1.0

Zinc binding site 2 out of 3 in 5kjk

Go back to Zinc Binding Sites List in 5kjk
Zinc binding site 2 out of 3 in the SMYD2 in Complex with AZ370


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 AZ370 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:35.1
occ:1.00
SG A:CYS68 2.2 35.2 1.0
NE2 A:HIS86 2.2 32.0 1.0
SG A:CYS90 2.4 37.8 1.0
SG A:CYS65 2.4 39.4 1.0
CE1 A:HIS86 3.1 29.9 1.0
CB A:CYS68 3.2 34.1 1.0
CD2 A:HIS86 3.2 32.4 1.0
CB A:CYS65 3.3 34.6 1.0
CB A:CYS90 3.3 33.3 1.0
N A:CYS68 3.6 37.3 1.0
CA A:CYS90 3.9 32.4 1.0
CA A:CYS68 4.0 36.0 1.0
ND1 A:HIS86 4.3 30.9 1.0
O A:HOH849 4.3 35.9 1.0
CG A:HIS86 4.3 31.2 1.0
CB A:ALA71 4.5 36.4 1.0
CB A:ARG67 4.6 42.1 1.0
CA A:CYS65 4.7 35.9 1.0
C A:ARG67 4.7 45.7 1.0
C A:CYS90 4.7 33.6 1.0
N A:LYS69 4.8 40.2 1.0
C A:CYS68 4.8 42.4 1.0
O A:CYS90 4.9 33.1 1.0
NH1 A:ARG67 4.9 51.2 1.0
N A:ARG67 4.9 42.4 1.0
C A:CYS65 5.0 40.5 1.0
CA A:ARG67 5.0 42.5 1.0

Zinc binding site 3 out of 3 in 5kjk

Go back to Zinc Binding Sites List in 5kjk
Zinc binding site 3 out of 3 in the SMYD2 in Complex with AZ370


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 AZ370 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:30.4
occ:1.00
SG A:CYS267 2.2 32.7 1.0
SG A:CYS262 2.3 32.0 1.0
SG A:CYS264 2.4 33.6 1.0
SG A:CYS209 2.4 29.4 1.0
CB A:CYS209 3.1 26.4 1.0
CB A:CYS262 3.2 29.2 1.0
CB A:CYS267 3.3 30.9 1.0
CB A:CYS264 3.4 30.5 1.0
N A:CYS209 3.7 27.5 1.0
N A:CYS264 3.8 33.1 1.0
N A:CYS267 4.0 32.9 1.0
CA A:CYS209 4.0 26.7 1.0
CA A:CYS264 4.1 32.2 1.0
CA A:CYS267 4.2 32.8 1.0
CE1 A:HIS207 4.3 27.8 1.0
CA A:CYS262 4.4 30.7 1.0
C A:CYS262 4.4 36.8 1.0
NH2 A:ARG250 4.4 28.9 1.0
O A:CYS262 4.6 37.0 1.0
C A:CYS264 4.7 34.7 1.0
O A:CYS264 4.7 33.8 1.0
N A:GLU263 4.7 34.8 1.0
NE A:ARG250 4.7 33.3 1.0
C A:SER208 4.7 29.7 1.0
ND1 A:HIS207 4.8 30.2 1.0
CB A:GLU266 4.9 32.2 1.0
C A:GLU263 4.9 36.6 1.0
C A:GLU266 5.0 35.5 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: Thu Aug 21 04:21:18 2025

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