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Zinc in PDB 5kjm: SMYD2 in Complex with AZ931

Enzymatic activity of SMYD2 in Complex with AZ931

All present enzymatic activity of SMYD2 in Complex with AZ931:
2.1.1.43;

Protein crystallography data

The structure of SMYD2 in Complex with AZ931, PDB code: 5kjm was solved by A.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.02 / 2.19
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 156.033, 156.033, 52.735, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.4

Other elements in 5kjm:

The structure of SMYD2 in Complex with AZ931 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 AZ931 (pdb code 5kjm). 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 AZ931, PDB code: 5kjm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5kjm

Go back to Zinc Binding Sites List in 5kjm
Zinc binding site 1 out of 3 in the SMYD2 in Complex with AZ931


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 AZ931 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:42.8
occ:1.00
SG A:CYS78 2.3 41.2 1.0
SG A:CYS52 2.3 38.5 1.0
SG A:CYS55 2.4 41.6 1.0
SG A:CYS74 2.4 40.8 1.0
CB A:CYS52 3.0 34.4 1.0
CB A:CYS74 3.2 38.1 1.0
CB A:CYS78 3.3 38.1 1.0
CB A:CYS55 3.6 36.6 1.0
N A:CYS74 3.8 38.3 1.0
N A:CYS55 3.9 35.0 1.0
CA A:CYS74 4.1 39.0 1.0
CA A:CYS55 4.3 35.5 1.0
CA A:CYS52 4.5 34.7 1.0
CA A:CYS78 4.7 38.2 1.0
OG1 A:THR57 4.7 37.9 1.0
CB A:TYR54 4.7 33.9 1.0
CB A:THR57 4.8 38.4 1.0
C A:TYR54 4.9 38.3 1.0
C A:TYR73 4.9 42.3 1.0
CD1 A:TYR54 5.0 37.1 1.0
C A:CYS55 5.0 38.5 1.0

Zinc binding site 2 out of 3 in 5kjm

Go back to Zinc Binding Sites List in 5kjm
Zinc binding site 2 out of 3 in the SMYD2 in Complex with AZ931


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 AZ931 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:42.1
occ:1.00
SG A:CYS68 2.2 39.2 1.0
NE2 A:HIS86 2.2 36.3 1.0
SG A:CYS90 2.4 38.0 1.0
SG A:CYS65 2.5 45.4 1.0
CB A:CYS68 3.1 38.0 1.0
CD2 A:HIS86 3.1 36.5 1.0
CE1 A:HIS86 3.2 34.3 1.0
CB A:CYS90 3.3 33.8 1.0
CB A:CYS65 3.4 41.2 1.0
N A:CYS68 3.6 43.5 1.0
CA A:CYS90 3.8 33.5 1.0
CA A:CYS68 3.9 40.7 1.0
CG A:HIS86 4.3 34.4 1.0
ND1 A:HIS86 4.3 34.9 1.0
O A:HOH786 4.4 38.2 1.0
CB A:ARG67 4.4 54.0 1.0
CB A:ALA71 4.5 41.1 1.0
C A:ARG67 4.6 52.5 1.0
C A:CYS90 4.7 38.0 1.0
CA A:CYS65 4.7 42.9 1.0
C A:CYS68 4.8 46.9 1.0
N A:LYS69 4.8 44.9 1.0
CA A:ARG67 4.9 51.2 1.0
N A:CYS90 4.9 32.8 1.0
CZ3 A:TRP83 4.9 40.1 1.0
O A:CYS90 4.9 37.1 1.0
O A:CYS65 4.9 44.9 1.0
N A:ARG67 4.9 50.8 1.0
C A:CYS65 5.0 46.6 1.0

Zinc binding site 3 out of 3 in 5kjm

Go back to Zinc Binding Sites List in 5kjm
Zinc binding site 3 out of 3 in the SMYD2 in Complex with AZ931


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 AZ931 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:36.3
occ:1.00
SG A:CYS267 2.2 35.6 1.0
SG A:CYS262 2.3 34.6 1.0
SG A:CYS209 2.5 33.1 1.0
SG A:CYS264 2.5 37.1 1.0
CB A:CYS209 3.1 29.9 1.0
CB A:CYS262 3.2 30.9 1.0
CB A:CYS267 3.4 34.0 1.0
CB A:CYS264 3.5 33.5 1.0
N A:CYS209 3.6 30.0 1.0
CA A:CYS209 3.9 30.0 1.0
N A:CYS264 4.0 33.7 1.0
N A:CYS267 4.1 35.9 1.0
CA A:CYS264 4.2 33.6 1.0
CE1 A:HIS207 4.3 29.0 1.0
CA A:CYS267 4.3 35.6 1.0
CA A:CYS262 4.4 31.5 1.0
NH2 A:ARG250 4.5 31.0 1.0
C A:CYS262 4.5 37.3 1.0
C A:SER208 4.7 31.8 1.0
NE A:ARG250 4.7 33.9 1.0
ND1 A:HIS207 4.7 31.4 1.0
N A:GLU263 4.7 36.7 1.0
O A:CYS264 4.7 38.6 1.0
C A:CYS264 4.7 38.5 1.0
O A:CYS262 4.8 36.8 1.0
CB A:GLU266 5.0 34.6 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: Sun Oct 27 20:31:10 2024

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