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Zinc in PDB 6n3g: Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol

Enzymatic activity of Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol

All present enzymatic activity of Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol, PDB code: 6n3g was solved by E.Perry, N.Spellmon, J.Brunzelle, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.92 / 2.43
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 151.840, 151.840, 53.740, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.2

Other elements in 6n3g:

The structure of Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol (pdb code 6n3g). 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 Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol, PDB code: 6n3g:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6n3g

Go back to Zinc Binding Sites List in 6n3g
Zinc binding site 1 out of 3 in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol


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 Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:52.9
occ:1.00
SG A:CYS78 2.3 47.6 1.0
SG A:CYS74 2.3 44.7 1.0
SG A:CYS55 2.4 41.4 1.0
SG A:CYS52 2.6 45.5 1.0
CB A:CYS52 3.4 42.0 1.0
CB A:CYS55 3.5 35.8 1.0
CB A:CYS78 3.5 48.1 1.0
CB A:CYS74 3.6 45.6 1.0
N A:CYS55 3.8 31.5 1.0
N A:CYS74 4.0 36.7 1.0
CA A:CYS55 4.2 30.6 1.0
CA A:CYS74 4.5 42.4 1.0
CB A:TYR54 4.7 35.5 1.0
CB A:THR57 4.8 38.1 1.0
ND2 A:ASN75 4.9 61.5 1.0
C A:TYR54 4.9 34.6 1.0
CA A:CYS78 4.9 49.1 1.0
CA A:CYS52 4.9 40.8 1.0

Zinc binding site 2 out of 3 in 6n3g

Go back to Zinc Binding Sites List in 6n3g
Zinc binding site 2 out of 3 in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol


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 Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:36.4
occ:1.00
NE2 A:HIS86 2.2 34.7 1.0
SG A:CYS90 2.2 37.2 1.0
SG A:CYS68 2.4 29.8 1.0
SG A:CYS65 2.4 50.1 1.0
CE1 A:HIS86 3.1 32.5 1.0
CB A:CYS65 3.2 45.7 1.0
CD2 A:HIS86 3.2 35.2 1.0
CB A:CYS68 3.4 30.4 1.0
CB A:CYS90 3.6 38.8 1.0
N A:CYS68 3.6 33.3 1.0
CA A:CYS68 4.1 32.2 1.0
CA A:CYS90 4.1 36.7 1.0
ND1 A:HIS86 4.2 30.2 1.0
CG A:HIS86 4.3 32.1 1.0
CB A:ARG67 4.4 51.2 1.0
CA A:CYS65 4.6 43.6 1.0
C A:ARG67 4.6 50.5 1.0
CB A:ALA71 4.6 50.5 1.0
N A:LYS69 4.8 41.1 1.0
CA A:ARG67 4.8 51.3 1.0
N A:ARG67 4.8 52.1 1.0
C A:CYS65 4.9 47.5 1.0
C A:CYS68 4.9 32.6 1.0
O A:CYS65 5.0 48.6 1.0

Zinc binding site 3 out of 3 in 6n3g

Go back to Zinc Binding Sites List in 6n3g
Zinc binding site 3 out of 3 in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol


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 Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn512

b:35.7
occ:1.00
SG A:CYS262 2.3 23.8 1.0
SG A:CYS264 2.4 33.1 1.0
SG A:CYS267 2.4 28.8 1.0
SG A:CYS209 2.4 37.4 1.0
CB A:CYS209 3.1 31.1 1.0
CB A:CYS267 3.1 26.1 1.0
CB A:CYS262 3.2 24.0 1.0
CB A:CYS264 3.8 32.0 1.0
N A:CYS209 3.8 28.4 1.0
N A:CYS267 3.9 36.7 1.0
N A:CYS264 4.1 33.0 1.0
CA A:CYS267 4.1 27.2 1.0
CA A:CYS209 4.1 27.7 1.0
NE2 A:HIS207 4.3 23.9 1.0
CA A:CYS262 4.5 23.7 1.0
CA A:CYS264 4.5 30.2 1.0
C A:CYS262 4.5 29.2 1.0
N A:GLU263 4.5 33.1 1.0
NE A:ARG250 4.6 19.5 1.0
NH2 A:ARG250 4.7 24.8 1.0
O A:CYS264 4.8 29.3 1.0
CD2 A:HIS207 4.8 21.9 1.0
C A:CYS264 4.9 30.6 1.0
C A:SER208 4.9 26.8 1.0
O A:CYS262 4.9 29.6 1.0
C A:GLU266 5.0 31.6 1.0

Reference:

E.Perry, Z.Yang. Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with Polyethylene Glycol To Be Published.
Page generated: Wed Dec 16 12:21:00 2020

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