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Zinc in PDB 4wuy: Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor

Enzymatic activity of Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor

All present enzymatic activity of Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor, PDB code: 4wuy was solved by H.Nguyen, A.Allali-Hassani, S.Antonysamy, S.Chang, L.H.Chen, C.Curtis, S.Emtage, L.Fan, T.Gheyi, F.Li, S.Liu, J.R.Martin, D.Mendel, J.B.Olsen, L.Pelletier, T.Shatseva, S.Wu, F.F.Zhang, C.H.Arrowsmith, P.J.Brown, R.M.Campbell, B.A.Garcia, D.Barsyte-Lovejoy, M.Mader, M.Vedadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.70 / 1.63
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.025, 99.920, 60.297, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor (pdb code 4wuy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor, PDB code: 4wuy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4wuy

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Zinc binding site 1 out of 4 in the Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor


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 Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:13.1
occ:1.00
 NE2 A:HIS86 2.1 10.4 1.0
SG A:CYS68 2.3 13.7 1.0
SG A:CYS65 2.3 13.5 1.0
SG A:CYS90 2.3 14.6 1.0
CE1 A:HIS86 3.0 11.6 1.0
CD2 A:HIS86 3.1 10.6 1.0
CB A:CYS68 3.2 13.2 1.0
CB A:CYS65 3.3 14.0 1.0
CB A:CYS90 3.3 8.6 1.0
N A:CYS68 3.6 16.0 1.0
CA A:CYS90 3.9 10.8 1.0
CA A:CYS68 4.0 13.6 1.0
ND1 A:HIS86 4.1 9.4 1.0
CG A:HIS86 4.2 10.4 1.0
CB A:ARG67 4.3 13.3 1.0
O A:HOH639 4.4 15.5 1.0
C A:ARG67 4.6 17.6 1.0
CA A:CYS65 4.7 11.4 1.0
CZ3 A:TRP83 4.7 17.5 1.0
CB A:ALA71 4.7 13.2 1.0
C A:CYS90 4.8 12.3 1.0
CA A:ARG67 4.8 14.6 1.0
C A:CYS68 4.8 12.4 1.0
N A:ARG67 4.9 14.1 1.0
N A:LYS69 4.9 14.3 1.0
O A:CYS90 4.9 13.2 1.0
N A:CYS90 5.0 10.3 1.0
C A:CYS65 5.0 14.0 1.0

Zinc binding site 2 out of 4 in 4wuy

Go back to Zinc Binding Sites List in 4wuy
Zinc binding site 2 out of 4 in the Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor


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 Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:14.4
occ:1.00
 SG A:CYS267 2.3 15.5 1.0
SG A:CYS262 2.3 13.5 1.0
SG A:CYS264 2.3 15.0 1.0
SG A:CYS209 2.4 14.1 1.0
CB A:CYS209 3.1 13.4 1.0
CB A:CYS262 3.2 11.1 1.0
CB A:CYS267 3.4 16.7 1.0
CB A:CYS264 3.4 15.8 1.0
N A:CYS209 3.7 10.7 1.0
N A:CYS264 3.9 15.7 1.0
CA A:CYS209 4.0 11.2 1.0
N A:CYS267 4.0 18.1 1.0
CA A:CYS264 4.2 16.5 1.0
CA A:CYS267 4.3 18.1 1.0
NE2 A:HIS207 4.3 7.9 1.0
NH1 A:ARG250 4.4 15.4 1.0
C A:CYS262 4.4 14.2 1.0
CA A:CYS262 4.4 12.0 1.0
O A:CYS262 4.6 15.4 1.0
C A:CYS264 4.7 18.5 1.0
NE A:ARG250 4.7 16.8 1.0
CD2 A:HIS207 4.7 9.2 1.0
N A:GLU263 4.7 15.7 1.0
C A:SER208 4.7 10.4 1.0
O A:CYS264 4.8 18.5 1.0
CB A:GLU266 4.9 22.5 1.0
C A:GLU266 5.0 20.6 1.0

Zinc binding site 3 out of 4 in 4wuy

Go back to Zinc Binding Sites List in 4wuy
Zinc binding site 3 out of 4 in the Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor


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 Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:13.9
occ:1.00
 SG A:CYS55 2.3 12.6 1.0
SG A:CYS78 2.3 14.7 1.0
SG A:CYS74 2.3 14.2 1.0
SG A:CYS52 2.4 11.8 1.0
CB A:CYS52 3.1 12.3 1.0
CB A:CYS74 3.2 14.9 1.0
CB A:CYS78 3.3 9.7 1.0
CB A:CYS55 3.5 12.0 1.0
N A:CYS74 3.8 10.9 1.0
N A:CYS55 3.9 8.8 1.0
CA A:CYS74 4.1 13.6 1.0
CA A:CYS55 4.3 10.4 1.0
O A:HOH994 4.5 35.4 1.0
CA A:CYS52 4.6 10.2 1.0
CB A:TYR54 4.7 9.9 1.0
OG1 A:THR57 4.7 15.1 1.0
CA A:CYS78 4.7 10.2 1.0
CB A:THR57 4.7 15.4 1.0
O A:HOH649 4.9 36.1 1.0
C A:CYS55 4.9 11.7 1.0
C A:TYR54 5.0 11.1 1.0
C A:TYR73 5.0 10.5 1.0

Zinc binding site 4 out of 4 in 4wuy

Go back to Zinc Binding Sites List in 4wuy
Zinc binding site 4 out of 4 in the Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Protein Lysine Methyltransferase SMYD2 in Complex with Lly-507, A Cell-Active, Potent and Selective Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:45.8
occ:0.50
 SG A:CYS210 2.1 20.4 0.5
CB A:CYS210 3.2 16.3 0.5
CB A:CYS210 3.3 20.7 0.5
OE2 A:GLU266 3.5 59.0 1.0
SG A:CYS210 3.6 40.6 0.5
O A:HOH836 4.1 25.1 1.0
O A:HOH1026 4.2 56.5 1.0
CD A:GLU266 4.4 42.1 1.0
CA A:CYS210 4.4 11.5 0.5
CA A:CYS210 4.4 12.9 0.5
CG A:GLU266 4.5 30.2 1.0

Reference:

H.Nguyen, A.Allali-Hassani, S.Antonysamy, S.Chang, L.H.Chen, C.Curtis, S.Emtage, L.Fan, T.Gheyi, F.Li, S.Liu, J.R.Martin, D.Mendel, J.B.Olsen, L.Pelletier, T.Shatseva, S.Wu, F.F.Zhang, C.H.Arrowsmith, P.J.Brown, R.M.Campbell, B.A.Garcia, D.Barsyte-Lovejoy, M.Mader, M.Vedadi. Lly-507, A Cell-Active, Potent and Selective Inhibitor of Protein Lysine Methyltransferase SMYD2 J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.626861
Page generated: Sun Oct 27 10:06:44 2024

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