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Zinc in PDB 5v37: Crystal Structure of SMYD3 with Sam and EPZ028862

Enzymatic activity of Crystal Structure of SMYD3 with Sam and EPZ028862

All present enzymatic activity of Crystal Structure of SMYD3 with Sam and EPZ028862:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of SMYD3 with Sam and EPZ028862, PDB code: 5v37 was solved by P.A.Boriack-Sjodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.26 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.818, 65.868, 107.015, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SMYD3 with Sam and EPZ028862 (pdb code 5v37). 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 SMYD3 with Sam and EPZ028862, PDB code: 5v37:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5v37

Go back to Zinc Binding Sites List in 5v37
Zinc binding site 1 out of 4 in the Crystal Structure of SMYD3 with Sam and EPZ028862


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 SMYD3 with Sam and EPZ028862 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:13.7
occ:1.00
 SG A:CYS75 2.3 15.3 1.0
SG A:CYS52 2.3 13.5 1.0
SG A:CYS49 2.3 11.0 1.0
SG A:CYS71 2.3 13.7 1.0
O A:HOH658 3.0 33.3 1.0
CB A:CYS75 3.2 13.1 1.0
CB A:CYS49 3.2 14.0 1.0
CB A:CYS52 3.3 11.9 1.0
CB A:CYS71 3.4 16.3 1.0
N A:CYS52 3.7 10.8 1.0
O A:HOH1095 3.9 20.9 1.0
N A:CYS71 3.9 14.4 1.0
CA A:CYS52 4.1 10.8 1.0
CA A:CYS71 4.2 13.7 1.0
OG A:SER72 4.5 15.4 1.0
CB A:ARG51 4.5 14.4 0.5
CB A:ARG51 4.6 12.5 0.5
CA A:CYS75 4.6 11.4 1.0
CA A:CYS49 4.7 13.0 1.0
N A:SER72 4.8 17.1 1.0
C A:ARG51 4.8 12.1 0.5
O A:HOH1083 4.8 38.0 1.0
O A:HOH993 4.9 29.1 1.0
C A:ARG51 4.9 11.8 0.5
C A:CYS71 4.9 15.8 1.0
C A:CYS52 5.0 10.4 1.0
CG A:ARG51 5.0 16.5 0.5

Zinc binding site 2 out of 4 in 5v37

Go back to Zinc Binding Sites List in 5v37
Zinc binding site 2 out of 4 in the Crystal Structure of SMYD3 with Sam and EPZ028862


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 SMYD3 with Sam and EPZ028862 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:13.0
occ:1.00
 SG A:CYS261 2.3 12.2 1.0
SG A:CYS266 2.3 11.7 1.0
SG A:CYS208 2.3 11.4 1.0
SG A:CYS263 2.3 14.2 1.0
CB A:CYS261 3.3 10.2 1.0
CB A:CYS208 3.4 10.0 1.0
CB A:CYS263 3.4 13.1 1.0
CB A:CYS266 3.4 11.6 1.0
N A:CYS266 4.1 9.1 1.0
N A:CYS263 4.1 14.8 1.0
CA A:CYS263 4.2 13.3 1.0
N A:CYS208 4.2 8.2 1.0
CA A:CYS266 4.3 9.6 1.0
CA A:CYS208 4.4 10.1 1.0
CA A:CYS261 4.6 11.1 1.0
NE2 A:HIS206 4.6 8.3 1.0
NH2 A:ARG249 4.6 10.8 1.0
O A:CYS263 4.6 12.9 1.0
NE A:ARG249 4.6 9.7 1.0
C A:CYS261 4.7 12.1 1.0
C A:CYS263 4.7 12.4 1.0
O A:CYS261 4.8 12.2 1.0
CD2 A:HIS206 4.9 8.9 1.0

Zinc binding site 3 out of 4 in 5v37

Go back to Zinc Binding Sites List in 5v37
Zinc binding site 3 out of 4 in the Crystal Structure of SMYD3 with Sam and EPZ028862


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 SMYD3 with Sam and EPZ028862 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:15.0
occ:0.50
 ZN A:ZN503 0.0 15.0 0.5
ZN A:ZN503 0.8 9.6 0.5
NE2 A:HIS83 1.9 12.5 1.0
SG A:CYS87 2.3 9.0 0.5
SG A:CYS65 2.3 17.1 0.5
SG A:CYS87 2.3 19.6 0.5
SG A:CYS62 2.3 19.3 0.5
SG A:CYS62 2.3 8.8 0.5
CD2 A:HIS83 2.8 12.3 1.0
CE1 A:HIS83 2.9 12.7 1.0
CB A:CYS87 3.0 9.7 0.5
CB A:CYS65 3.1 25.6 0.5
SG A:CYS65 3.1 8.3 0.5
CB A:CYS87 3.3 21.6 0.5
CB A:CYS62 3.4 11.5 0.5
CB A:CYS62 3.4 21.7 0.5
N A:CYS65 3.7 35.9 0.5
CA A:CYS87 3.8 9.7 0.5
CA A:CYS87 3.9 21.8 0.5
CG A:HIS83 3.9 12.8 1.0
ND1 A:HIS83 4.0 12.5 1.0
CA A:CYS65 4.0 31.7 0.5
CB A:CYS65 4.0 7.3 0.5
N A:CYS65 4.2 7.3 0.5
CZ3 A:TRP80 4.3 19.9 1.0
CB A:GLN64 4.3 12.6 0.5
C A:GLN64 4.4 41.4 0.5
O A:HOH973 4.5 18.6 1.0
N A:ARG66 4.6 32.8 0.5
OE1 A:GLN64 4.7 14.9 0.5
CB A:ALA68 4.7 11.4 0.5
CA A:CYS65 4.7 7.7 0.5
C A:CYS87 4.7 10.1 0.5
C A:CYS65 4.8 32.6 0.5
CB A:GLN64 4.8 39.3 0.5
CA A:CYS62 4.8 20.3 0.5
CB A:ALA68 4.8 16.4 0.5
CA A:CYS62 4.8 12.0 0.5
C A:CYS87 4.8 22.9 0.5
N A:CYS87 4.9 9.9 0.5
O A:HIS83 4.9 14.4 1.0
N A:CYS87 4.9 20.6 0.5
CA A:GLN64 4.9 39.8 0.5
O A:GLN64 5.0 41.0 0.5
O A:CYS87 5.0 10.3 0.5
O A:CYS87 5.0 22.4 0.5

Zinc binding site 4 out of 4 in 5v37

Go back to Zinc Binding Sites List in 5v37
Zinc binding site 4 out of 4 in the Crystal Structure of SMYD3 with Sam and EPZ028862


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 SMYD3 with Sam and EPZ028862 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:9.6
occ:0.50
 ZN A:ZN503 0.0 9.6 0.5
ZN A:ZN503 0.8 15.0 0.5
SG A:CYS65 1.5 17.1 0.5
NE2 A:HIS83 2.3 12.5 1.0
SG A:CYS87 2.3 9.0 0.5
SG A:CYS62 2.3 8.8 0.5
SG A:CYS65 2.3 8.3 0.5
CB A:CYS65 2.5 25.6 0.5
SG A:CYS62 2.5 19.3 0.5
SG A:CYS87 2.7 19.6 0.5
CE1 A:HIS83 3.1 12.7 1.0
CB A:CYS62 3.2 11.5 0.5
CB A:CYS65 3.2 7.3 0.5
CB A:CYS87 3.3 9.7 0.5
CB A:CYS62 3.3 21.7 0.5
N A:CYS65 3.3 35.9 0.5
CD2 A:HIS83 3.4 12.3 1.0
CA A:CYS65 3.4 31.7 0.5
N A:CYS65 3.5 7.3 0.5
CB A:CYS87 3.7 21.6 0.5
CA A:CYS87 3.9 9.7 0.5
N A:ARG66 3.9 32.8 0.5
CA A:CYS65 4.0 7.7 0.5
CA A:CYS87 4.0 21.8 0.5
C A:CYS65 4.1 32.6 0.5
C A:GLN64 4.2 41.4 0.5
CB A:GLN64 4.2 12.6 0.5
ND1 A:HIS83 4.3 12.5 1.0
CB A:ALA68 4.4 11.4 0.5
CG A:HIS83 4.5 12.8 1.0
C A:CYS87 4.6 10.1 0.5
O A:CYS87 4.6 10.3 0.5
C A:GLN64 4.6 8.5 0.5
CA A:CYS62 4.6 12.0 0.5
O A:CYS62 4.6 22.5 0.5
CB A:ALA68 4.6 16.4 0.5
CA A:CYS62 4.6 20.3 0.5
N A:VAL67 4.7 28.1 0.5
N A:ALA68 4.7 12.0 0.5
C A:CYS62 4.7 21.2 0.5
N A:ARG66 4.8 7.5 0.5
CA A:GLN64 4.8 10.9 0.5
O A:GLN64 4.8 41.0 0.5
O A:CYS87 4.8 22.4 0.5
C A:CYS65 4.9 7.4 0.5
C A:CYS87 4.9 22.9 0.5
C A:CYS62 4.9 11.5 0.5
N A:GLN64 4.9 37.6 0.5
N A:GLN64 4.9 11.4 0.5
CA A:GLN64 4.9 39.8 0.5
O A:CYS62 5.0 11.2 0.5
OE1 A:GLN64 5.0 14.9 0.5

Reference:

M.J.Thomenius, J.Totman, D.Harvey, L.H.Mitchell, T.V.Riera, K.Cosmopoulos, A.R.Grassian, C.Klaus, M.Foley, E.A.Admirand, H.Jahic, C.Majer, T.Wigle, S.L.Jacques, J.Gureasko, D.Brach, T.Lingaraj, K.West, S.Smith, N.Rioux, N.J.Waters, C.Tang, A.Raimondi, M.Munchhof, J.E.Mills, S.Ribich, M.Porter Scott, K.W.Kuntz, W.P.Janzen, M.Moyer, J.J.Smith, R.Chesworth, R.A.Copeland, P.A.Boriack-Sjodin. Small Molecule Inhibitors and Crispr/CAS9 Mutagenesis Demonstrate That SMYD2 and SMYD3 Activity Are Dispensable For Autonomous Cancer Cell Proliferation. Plos One V. 13 97372 2018.
ISSN: ESSN 1932-6203
PubMed: 29856759
DOI: 10.1371/JOURNAL.PONE.0197372
Page generated: Mon Oct 28 12:35:18 2024

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