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Zinc in PDB 5v3h: Crystal Structure of SMYD2 with Sam and EPZ033294

Enzymatic activity of Crystal Structure of SMYD2 with Sam and EPZ033294

All present enzymatic activity of Crystal Structure of SMYD2 with Sam and EPZ033294:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of SMYD2 with Sam and EPZ033294, PDB code: 5v3h 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) 50.00 / 2.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.560, 54.775, 79.702, 90.00, 114.22, 90.00
R / Rfree (%) 21.8 / 27

Other elements in 5v3h:

The structure of Crystal Structure of SMYD2 with Sam and EPZ033294 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SMYD2 with Sam and EPZ033294 (pdb code 5v3h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of SMYD2 with Sam and EPZ033294, PDB code: 5v3h:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5v3h

Go back to Zinc Binding Sites List in 5v3h
Zinc binding site 1 out of 3 in the Crystal Structure of SMYD2 with Sam and EPZ033294


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 SMYD2 with Sam and EPZ033294 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:24.7
occ:1.00
SG A:CYS262 2.3 40.0 1.0
SG A:CYS267 2.3 43.0 1.0
SG A:CYS209 2.3 35.8 1.0
SG A:CYS264 2.4 40.1 1.0
CB A:CYS209 3.2 33.6 1.0
CB A:CYS267 3.3 45.5 1.0
CB A:CYS262 3.4 42.0 1.0
CB A:CYS264 3.5 41.9 1.0
N A:CYS209 3.7 31.4 1.0
CA A:CYS209 4.1 31.1 1.0
N A:CYS264 4.1 46.0 1.0
N A:CYS267 4.1 42.4 1.0
CA A:CYS264 4.3 44.8 1.0
CA A:CYS267 4.3 44.9 1.0
C A:CYS262 4.5 47.4 1.0
CA A:CYS262 4.6 44.9 1.0
O A:CYS262 4.6 49.0 1.0
NE2 A:HIS207 4.7 29.2 1.0
NH2 A:ARG250 4.7 38.3 1.0
C A:CYS264 4.8 45.8 1.0
C A:SER208 4.8 30.0 1.0
N A:GLU263 4.9 48.2 1.0
NE A:ARG250 4.9 35.9 1.0
O A:CYS264 5.0 47.6 1.0

Zinc binding site 2 out of 3 in 5v3h

Go back to Zinc Binding Sites List in 5v3h
Zinc binding site 2 out of 3 in the Crystal Structure of SMYD2 with Sam and EPZ033294


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 SMYD2 with Sam and EPZ033294 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:29.1
occ:1.00
SG A:CYS74 2.3 49.3 1.0
SG A:CYS52 2.3 43.2 1.0
SG A:CYS78 2.4 48.7 1.0
SG A:CYS55 2.4 42.2 1.0
CB A:CYS52 3.3 42.9 1.0
CB A:CYS74 3.4 52.3 1.0
CB A:CYS78 3.4 48.9 1.0
CB A:CYS55 3.4 39.2 1.0
N A:CYS74 3.9 49.3 1.0
N A:CYS55 4.0 35.1 1.0
CA A:CYS74 4.2 52.4 1.0
CA A:CYS55 4.3 35.6 1.0
CA A:CYS52 4.8 41.2 1.0
CA A:CYS78 4.8 48.8 1.0
CB A:TYR54 4.9 35.4 1.0
CB A:THR57 4.9 40.7 1.0
C A:CYS55 4.9 34.1 1.0

Zinc binding site 3 out of 3 in 5v3h

Go back to Zinc Binding Sites List in 5v3h
Zinc binding site 3 out of 3 in the Crystal Structure of SMYD2 with Sam and EPZ033294


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 SMYD2 with Sam and EPZ033294 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:34.2
occ:1.00
NE2 A:HIS86 2.2 54.6 1.0
SG A:CYS68 2.3 57.8 1.0
SG A:CYS65 2.4 62.0 1.0
SG A:CYS90 2.4 58.1 1.0
CE1 A:HIS86 3.1 51.8 1.0
CD2 A:HIS86 3.2 52.3 1.0
CB A:CYS90 3.4 54.1 1.0
CB A:CYS65 3.4 60.5 1.0
CB A:CYS68 3.4 61.8 1.0
N A:CYS68 4.0 66.0 1.0
CA A:CYS90 4.0 52.3 1.0
ND1 A:HIS86 4.3 48.1 1.0
CA A:CYS68 4.3 65.0 1.0
CG A:HIS86 4.3 47.9 1.0
CB A:ALA71 4.8 45.1 1.0
CA A:CYS65 4.8 62.3 1.0
CB A:ARG67 4.8 68.4 1.0
C A:CYS90 4.9 54.9 1.0

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: Wed Dec 16 11:07:34 2020

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