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Zinc in PDB 4o6f: Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2

Enzymatic activity of Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2

All present enzymatic activity of Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2:
2.1.1.43;

Protein crystallography data

The structure of Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2, PDB code: 4o6f was solved by Y.Jiang, L.Trescott, J.Holcomb, J.Brunzelle, N.Sirinupong, X.Shi, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.90 / 2.82
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 151.810, 151.810, 52.873, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.5

Other elements in 4o6f:

The structure of Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2 (pdb code 4o6f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2, PDB code: 4o6f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4o6f

Go back to Zinc Binding Sites List in 4o6f
Zinc binding site 1 out of 3 in the Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:28.6
occ:1.00
 SG A:CYS78 2.3 47.5 1.0
SG A:CYS55 2.3 31.3 1.0
SG A:CYS74 2.4 35.3 1.0
SG A:CYS52 2.6 32.4 1.0
CB A:CYS74 3.1 37.5 1.0
CB A:CYS52 3.3 28.4 1.0
CB A:CYS55 3.5 33.4 1.0
CB A:CYS78 3.6 38.1 1.0
N A:CYS55 4.0 27.9 1.0
N A:CYS74 4.1 36.6 1.0
CA A:CYS74 4.2 35.3 1.0
CA A:CYS55 4.3 26.4 1.0
OG1 A:THR57 4.5 39.8 1.0
CB A:TYR54 4.7 24.9 1.0
CB A:THR57 4.8 33.7 1.0
CA A:CYS52 4.8 25.7 1.0
C A:CYS55 4.9 26.9 1.0
CA A:CYS78 5.0 35.9 1.0

Zinc binding site 2 out of 3 in 4o6f

Go back to Zinc Binding Sites List in 4o6f
Zinc binding site 2 out of 3 in the Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:24.3
occ:1.00
 NE2 A:HIS86 2.0 24.1 1.0
SG A:CYS68 2.2 31.0 1.0
SG A:CYS90 2.4 25.3 1.0
SG A:CYS65 2.5 30.7 1.0
CE1 A:HIS86 3.0 19.5 1.0
CD2 A:HIS86 3.0 27.1 1.0
CB A:CYS68 3.2 30.7 1.0
CB A:CYS90 3.3 35.2 1.0
CB A:CYS65 3.4 25.6 1.0
N A:CYS68 3.5 32.7 1.0
CA A:CYS90 3.9 33.5 1.0
CA A:CYS68 4.0 39.5 1.0
ND1 A:HIS86 4.1 21.6 1.0
CG A:HIS86 4.1 24.7 1.0
CB A:ARG67 4.4 33.9 1.0
O A:HOH621 4.5 25.2 1.0
C A:ARG67 4.6 32.7 1.0
C A:CYS90 4.7 29.3 1.0
CB A:ALA71 4.8 30.6 1.0
CA A:CYS65 4.8 26.5 1.0
CA A:ARG67 4.8 23.3 1.0
N A:LYS69 4.8 32.3 1.0
N A:ARG67 4.8 31.2 1.0
C A:CYS68 4.9 34.2 1.0
O A:CYS90 4.9 28.3 1.0
N A:CYS90 4.9 22.1 1.0
CZ3 A:TRP83 4.9 24.9 1.0

Zinc binding site 3 out of 3 in 4o6f

Go back to Zinc Binding Sites List in 4o6f
Zinc binding site 3 out of 3 in the Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of Estrogen Receptor Alpha Methylation Mediated By Histone Methyltransferase SMYD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:17.5
occ:1.00
 SG A:CYS262 2.3 12.0 1.0
SG A:CYS267 2.3 16.0 1.0
SG A:CYS264 2.4 21.1 1.0
SG A:CYS209 2.4 14.4 1.0
CB A:CYS262 3.0 18.9 1.0
CB A:CYS209 3.2 22.0 1.0
CB A:CYS267 3.4 19.6 1.0
CB A:CYS264 3.5 18.5 1.0
N A:CYS209 3.6 21.0 1.0
N A:CYS264 3.9 24.5 1.0
CA A:CYS209 4.0 19.3 1.0
N A:CYS267 4.1 21.8 1.0
CA A:CYS264 4.2 15.6 1.0
CA A:CYS262 4.2 17.0 1.0
C A:CYS262 4.3 22.9 1.0
CA A:CYS267 4.3 18.8 1.0
NH2 A:ARG250 4.4 13.4 1.0
NE2 A:HIS207 4.5 17.6 1.0
O A:CYS262 4.5 21.8 1.0
N A:GLU263 4.6 29.9 1.0
C A:SER208 4.6 16.5 1.0
NE A:ARG250 4.8 12.2 1.0
C A:CYS264 4.8 19.6 1.0
CD2 A:HIS207 4.8 17.2 1.0
O A:CYS264 4.8 26.8 1.0
CA A:SER208 4.9 22.5 1.0

Reference:

Y.Jiang, L.Trescott, J.Holcomb, X.Zhang, J.Brunzelle, N.Sirinupong, X.Shi, Z.Yang. Structural Insights Into Estrogen Receptor Alpha Methylation By Histone Methyltransferase SMYD2, A Cellular Event Implicated in Estrogen Signaling Regulation. J.Mol.Biol. V. 426 3413 2014.
ISSN: ISSN 0022-2836
PubMed: 24594358
DOI: 10.1016/J.JMB.2014.02.019
Page generated: Wed Dec 16 05:38:15 2020

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