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Zinc in PDB 3ru0: Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound

Enzymatic activity of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound

All present enzymatic activity of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound:
2.1.1.43;

Protein crystallography data

The structure of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound, PDB code: 3ru0 was solved by K.W.Foreman, M.Brown, F.Park, S.Emtage, J.Harriss, C.Das, L.Zhu, A.Crew, L.Arnold, S.Shaaban, P.Tucker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.83 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.175, 118.073, 82.901, 90.00, 91.58, 90.00
R / Rfree (%) 20 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound (pdb code 3ru0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound, PDB code: 3ru0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3ru0

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Zinc binding site 1 out of 6 in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn438

b:24.3
occ:0.80
 SG A:CYS263 2.3 22.6 1.0
SG A:CYS266 2.3 18.8 1.0
SG A:CYS261 2.4 20.8 1.0
SG A:CYS208 2.4 18.6 1.0
CB A:CYS266 3.3 17.3 1.0
CB A:CYS208 3.3 17.0 1.0
CB A:CYS263 3.3 17.0 1.0
CB A:CYS261 3.4 15.3 1.0
N A:CYS266 4.0 17.1 1.0
N A:CYS263 4.1 23.9 1.0
N A:CYS208 4.2 17.0 1.0
CA A:CYS266 4.2 17.3 1.0
CA A:CYS263 4.2 19.4 1.0
CA A:CYS208 4.4 18.2 1.0
CE1 A:HIS206 4.4 11.2 1.0
NE A:ARG249 4.5 15.8 1.0
CA A:CYS261 4.6 20.9 1.0
C A:CYS261 4.6 20.6 1.0
NH2 A:ARG249 4.6 15.5 1.0
O A:CYS261 4.7 20.7 1.0
O A:CYS263 4.7 15.5 1.0
C A:CYS263 4.8 16.5 1.0
CD1 A:LEU253 4.9 16.1 1.0
N A:ASP262 5.0 22.9 1.0
ND1 A:HIS206 5.0 20.0 1.0

Zinc binding site 2 out of 6 in 3ru0

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Zinc binding site 2 out of 6 in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn439

b:31.4
occ:0.80
 NE2 A:HIS83 2.1 21.8 1.0
SG A:CYS65 2.3 27.5 1.0
SG A:CYS62 2.4 28.6 1.0
SG A:CYS87 2.4 25.6 1.0
CE1 A:HIS83 3.1 25.9 1.0
CD2 A:HIS83 3.1 25.5 1.0
CB A:CYS65 3.3 30.1 1.0
CB A:CYS62 3.3 30.9 1.0
CB A:CYS87 3.4 20.2 1.0
N A:CYS65 3.5 31.9 1.0
CA A:CYS87 3.8 21.6 1.0
CA A:CYS65 4.0 29.2 1.0
ND1 A:HIS83 4.2 20.8 1.0
CG A:HIS83 4.2 21.2 1.0
CB A:GLN64 4.4 28.0 1.0
C A:GLN64 4.4 30.8 1.0
O A:HOH686 4.5 29.2 1.0
CB A:ALA68 4.6 27.2 1.0
O A:CYS87 4.6 27.0 1.0
C A:CYS87 4.6 23.3 1.0
CA A:CYS62 4.7 30.1 1.0
CA A:GLN64 4.8 29.2 1.0
N A:GLN64 4.8 29.8 1.0
C A:CYS65 4.9 31.6 1.0
C A:CYS62 4.9 28.9 1.0
N A:ARG66 4.9 28.6 1.0
N A:CYS87 5.0 23.2 1.0
O A:CYS62 5.0 27.3 1.0

Zinc binding site 3 out of 6 in 3ru0

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Zinc binding site 3 out of 6 in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn440

b:31.4
occ:0.80
 SG A:CYS75 2.2 28.0 1.0
SG A:CYS52 2.3 26.5 1.0
SG A:CYS49 2.4 23.7 1.0
SG A:CYS71 2.4 30.9 1.0
CB A:CYS49 3.1 22.7 1.0
CB A:CYS75 3.2 31.2 1.0
CB A:CYS52 3.3 22.4 1.0
CB A:CYS71 3.6 30.5 1.0
N A:CYS52 3.7 22.5 1.0
N A:CYS71 4.0 31.8 1.0
CA A:CYS52 4.1 24.1 1.0
CA A:CYS71 4.4 32.5 1.0
OG A:SER72 4.5 32.8 1.0
CA A:CYS49 4.6 21.1 1.0
CB A:ARG51 4.6 19.1 1.0
CA A:CYS75 4.6 30.3 1.0
N A:SER72 4.8 35.2 1.0
C A:ARG51 4.8 21.3 1.0
C A:CYS52 4.9 22.2 1.0
C A:CYS71 5.0 33.5 1.0

Zinc binding site 4 out of 6 in 3ru0

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Zinc binding site 4 out of 6 in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn438

b:26.5
occ:0.80
 SG B:CYS71 2.3 22.9 1.0
SG B:CYS52 2.3 20.6 1.0
SG B:CYS49 2.4 19.6 1.0
SG B:CYS75 2.4 22.9 1.0
CB B:CYS49 3.1 19.9 1.0
CB B:CYS75 3.3 20.2 1.0
CB B:CYS52 3.3 22.2 1.0
CB B:CYS71 3.5 22.8 1.0
N B:CYS52 3.7 19.4 1.0
N B:CYS71 4.0 20.1 1.0
O B:HOH614 4.1 28.4 1.0
CA B:CYS52 4.1 20.4 1.0
CA B:CYS71 4.4 19.1 1.0
CB B:ARG51 4.5 18.0 1.0
OG B:SER72 4.5 20.3 1.0
CA B:CYS49 4.6 19.1 1.0
CA B:CYS75 4.7 21.0 1.0
C B:ARG51 4.8 19.1 1.0
C B:CYS52 4.9 20.3 1.0
CG B:ARG51 5.0 24.8 1.0
N B:ARG51 5.0 18.1 1.0
CA B:ARG51 5.0 19.4 1.0

Zinc binding site 5 out of 6 in 3ru0

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Zinc binding site 5 out of 6 in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn439

b:23.9
occ:0.80
 NE2 B:HIS83 2.1 14.9 1.0
SG B:CYS65 2.2 21.1 1.0
SG B:CYS62 2.3 20.5 1.0
SG B:CYS87 2.4 19.3 1.0
CE1 B:HIS83 2.9 14.1 1.0
CD2 B:HIS83 3.1 22.4 1.0
CB B:CYS62 3.2 17.7 1.0
CB B:CYS65 3.2 18.4 1.0
CB B:CYS87 3.3 16.8 1.0
N B:CYS65 3.5 23.4 1.0
CA B:CYS87 3.8 17.6 1.0
CA B:CYS65 4.0 18.7 1.0
ND1 B:HIS83 4.1 13.5 1.0
CG B:HIS83 4.2 15.9 1.0
CB B:GLN64 4.4 24.4 1.0
C B:GLN64 4.5 22.7 1.0
CA B:CYS62 4.6 18.3 1.0
C B:CYS87 4.6 16.6 1.0
O B:CYS87 4.7 18.8 1.0
O B:HOH566 4.7 31.3 1.0
CB B:ALA68 4.7 13.9 1.0
CA B:GLN64 4.8 24.5 1.0
N B:GLN64 4.9 23.5 1.0
C B:CYS62 4.9 18.2 1.0
N B:CYS87 4.9 17.4 1.0
N B:ARG66 4.9 20.8 1.0
C B:CYS65 4.9 20.0 1.0
O B:CYS62 5.0 15.5 1.0

Zinc binding site 6 out of 6 in 3ru0

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Zinc binding site 6 out of 6 in the Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cocrystal Structure of Human SMYD3 with Inhibitor Sinefungin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn440

b:35.4
occ:0.80
 SG B:CYS263 2.3 30.9 1.0
SG B:CYS266 2.3 29.4 1.0
SG B:CYS261 2.4 31.3 1.0
SG B:CYS208 2.4 24.0 1.0
CB B:CYS208 3.3 28.3 1.0
CB B:CYS261 3.4 24.2 1.0
CB B:CYS266 3.4 31.2 1.0
CB B:CYS263 3.5 31.9 1.0
N B:CYS208 3.9 24.5 1.0
N B:CYS266 3.9 29.2 1.0
N B:CYS263 4.0 33.4 1.0
CA B:CYS263 4.2 32.4 1.0
CA B:CYS208 4.2 24.5 1.0
CA B:CYS266 4.2 30.4 1.0
CE1 B:HIS206 4.4 18.8 1.0
NH2 B:ARG249 4.5 26.6 1.0
O B:CYS263 4.6 28.8 1.0
C B:CYS261 4.6 34.7 1.0
CA B:CYS261 4.6 31.9 1.0
C B:CYS263 4.6 30.0 1.0
NE B:ARG249 4.7 27.7 1.0
O B:CYS261 4.7 32.5 1.0
CB B:ARG265 4.9 27.6 1.0
C B:ARG265 5.0 27.5 1.0
C B:SER207 5.0 23.4 1.0

Reference:

K.W.Foreman, M.Brown, F.Park, S.Emtage, J.Harriss, C.Das, L.Zhu, A.Crew, L.Arnold, S.Shaaban, P.Tucker. Structural and Functional Profiling of the Human Histone Methyltransferase SMYD3. Plos One V. 6 22290 2011.
ISSN: ESSN 1932-6203
PubMed: 21779408
DOI: 10.1371/JOURNAL.PONE.0022290
Page generated: Wed Aug 20 13:40:36 2025

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