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Zinc in PDB 3rib: Human Lysine Methyltransferase SMYD2 in Complex with Adohcy

Enzymatic activity of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy

All present enzymatic activity of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy:
2.1.1.43;

Protein crystallography data

The structure of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy, PDB code: 3rib was solved by S.Xu, T.Zhang, C.Zhong, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 194.560, 57.185, 96.607, 90.00, 103.95, 90.00
R / Rfree (%) 24.6 / 30

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy (pdb code 3rib). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy, PDB code: 3rib:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3rib

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Zinc binding site 1 out of 6 in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn442

b:47.2
occ:1.00
 SG A:CYS78 2.2 28.1 1.0
SG A:CYS55 2.3 30.4 1.0
SG A:CYS52 2.4 29.7 1.0
SG A:CYS74 2.6 27.9 1.0
CB A:CYS74 3.2 28.3 1.0
CB A:CYS52 3.2 29.6 1.0
CB A:CYS78 3.3 27.6 1.0
CB A:CYS55 3.5 30.5 1.0
N A:CYS74 3.8 28.5 1.0
N A:CYS55 3.8 30.3 1.0
CA A:CYS74 4.1 28.5 1.0
CA A:CYS55 4.2 30.5 1.0
CB A:TYR54 4.6 29.6 1.0
CA A:CYS78 4.7 27.6 1.0
CA A:CYS52 4.7 29.7 1.0
CD2 A:TYR54 4.7 28.5 1.0
OG1 A:THR57 4.8 33.4 1.0
C A:TYR54 4.9 30.0 1.0
C A:CYS55 4.9 30.8 1.0
C A:TYR73 4.9 28.6 1.0

Zinc binding site 2 out of 6 in 3rib

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Zinc binding site 2 out of 6 in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn443

b:39.0
occ:1.00
 SG A:CYS90 2.3 26.0 1.0
SG A:CYS65 2.5 40.2 1.0
SG A:CYS68 2.5 35.1 1.0
NE2 A:HIS86 2.5 17.8 1.0
CB A:CYS65 2.7 39.3 1.0
CB A:CYS90 3.2 25.5 1.0
CB A:CYS68 3.2 35.3 1.0
CD2 A:HIS86 3.3 18.4 1.0
CE1 A:HIS86 3.5 18.0 1.0
N A:CYS68 3.6 36.4 1.0
CA A:CYS90 3.8 26.5 1.0
CA A:CYS68 4.0 35.6 1.0
CA A:CYS65 4.2 39.5 1.0
CG A:HIS86 4.5 19.4 1.0
ND1 A:HIS86 4.6 18.6 1.0
N A:LYS69 4.7 34.9 1.0
CB A:ARG67 4.7 37.7 1.0
C A:ARG67 4.7 37.1 1.0
C A:CYS90 4.7 26.8 1.0
N A:ARG67 4.8 38.2 1.0
CZ3 A:TRP83 4.8 21.0 1.0
C A:CYS68 4.8 35.3 1.0
C A:CYS65 4.9 39.3 1.0
O A:CYS90 4.9 27.1 1.0
CB A:ALA71 4.9 30.9 1.0
CA A:ARG67 4.9 37.6 1.0
N A:CYS90 5.0 26.0 1.0

Zinc binding site 3 out of 6 in 3rib

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Zinc binding site 3 out of 6 in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn444

b:40.7
occ:1.00
 SG A:CYS264 2.4 33.8 1.0
SG A:CYS262 2.4 30.0 1.0
SG A:CYS209 2.4 21.9 1.0
SG A:CYS267 2.4 34.9 1.0
CB A:CYS209 3.1 21.5 1.0
CB A:CYS262 3.3 30.3 1.0
N A:CYS209 3.5 21.8 1.0
CB A:CYS267 3.6 35.5 1.0
CB A:CYS264 3.9 33.4 1.0
CA A:CYS209 3.9 21.9 1.0
N A:CYS264 4.1 33.0 1.0
N A:CYS267 4.2 35.5 1.0
NE2 A:HIS207 4.4 19.7 1.0
C A:CYS262 4.4 30.9 1.0
CA A:CYS262 4.5 30.4 1.0
CA A:CYS267 4.5 35.6 1.0
CA A:CYS264 4.5 33.5 1.0
C A:SER208 4.6 21.6 1.0
NH2 A:ARG250 4.6 25.1 1.0
O A:CYS262 4.6 31.1 1.0
CD2 A:HIS207 4.6 20.3 1.0
N A:GLU263 4.7 31.6 1.0
CB A:GLU266 4.8 35.3 1.0
CA A:SER208 4.9 21.6 1.0
O A:CYS264 4.9 33.7 1.0
C A:CYS209 4.9 22.0 1.0
C A:CYS264 4.9 33.8 1.0

Zinc binding site 4 out of 6 in 3rib

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Zinc binding site 4 out of 6 in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn442

b:48.1
occ:1.00
 SG B:CYS55 2.2 33.1 1.0
SG B:CYS52 2.3 32.7 1.0
SG B:CYS74 2.4 31.7 1.0
SG B:CYS78 2.4 27.8 1.0
CB B:CYS52 3.1 33.1 1.0
CB B:CYS74 3.5 31.4 1.0
CB B:CYS78 3.5 27.8 1.0
CB B:CYS55 3.6 33.0 1.0
N B:CYS55 3.8 32.5 1.0
N B:CYS74 3.9 31.3 1.0
CA B:CYS55 4.2 33.0 1.0
CA B:CYS74 4.3 31.4 1.0
CA B:CYS52 4.6 33.1 1.0
CB B:TYR54 4.6 31.6 1.0
OG1 B:THR57 4.7 36.0 1.0
C B:TYR54 4.8 32.0 1.0
CD2 B:TYR54 4.9 30.2 1.0
N B:TYR54 4.9 31.9 1.0
CA B:CYS78 4.9 27.7 1.0
C B:CYS55 4.9 33.3 1.0
CB B:THR57 5.0 35.8 1.0
CA B:TYR54 5.0 31.8 1.0
N B:PHE56 5.0 33.8 1.0
C B:TYR73 5.0 31.4 1.0

Zinc binding site 5 out of 6 in 3rib

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Zinc binding site 5 out of 6 in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn443

b:51.1
occ:1.00
 SG B:CYS68 2.1 34.0 1.0
NE2 B:HIS86 2.2 24.3 1.0
SG B:CYS65 2.3 38.1 1.0
SG B:CYS90 2.3 27.3 1.0
CE1 B:HIS86 3.0 24.1 1.0
CB B:CYS68 3.0 34.9 1.0
CB B:CYS65 3.2 38.2 1.0
CD2 B:HIS86 3.3 23.9 1.0
CB B:CYS90 3.4 27.6 1.0
N B:CYS68 3.6 35.5 1.0
CA B:CYS68 3.9 35.0 1.0
CA B:CYS90 4.0 27.6 1.0
ND1 B:HIS86 4.2 23.9 1.0
CG B:HIS86 4.3 23.7 1.0
CA B:CYS65 4.6 38.2 1.0
C B:CYS68 4.7 34.9 1.0
N B:LYS69 4.7 34.7 1.0
C B:ARG67 4.7 35.9 1.0
CB B:ALA71 4.7 32.2 1.0
C B:CYS90 4.8 27.9 1.0
C B:CYS65 4.9 37.9 1.0
N B:ARG67 5.0 36.5 1.0
CB B:ARG67 5.0 36.4 1.0

Zinc binding site 6 out of 6 in 3rib

Go back to Zinc Binding Sites List in 3rib
Zinc binding site 6 out of 6 in the Human Lysine Methyltransferase SMYD2 in Complex with Adohcy


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Lysine Methyltransferase SMYD2 in Complex with Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn444

b:69.4
occ:1.00
 SG B:CYS267 2.3 61.6 1.0
SG B:CYS262 2.5 57.4 1.0
SG B:CYS209 2.5 45.5 1.0
SG B:CYS264 2.9 59.6 1.0
CB B:CYS209 3.1 45.3 1.0
CB B:CYS262 3.3 57.7 1.0
N B:CYS209 3.4 45.3 1.0
CB B:CYS267 3.4 61.4 1.0
CA B:CYS209 3.9 45.3 1.0
CB B:CYS264 4.0 59.6 1.0
NE2 B:HIS207 4.3 45.6 1.0
NH1 B:ARG250 4.4 52.0 1.0
N B:CYS267 4.4 61.2 1.0
C B:SER208 4.4 45.4 1.0
CA B:CYS267 4.5 61.4 1.0
N B:CYS264 4.5 59.4 1.0
O B:CYS262 4.5 58.3 1.0
CD2 B:HIS207 4.5 45.2 1.0
CA B:CYS262 4.6 57.8 1.0
C B:CYS262 4.6 58.2 1.0
CA B:SER208 4.7 45.3 1.0
CA B:CYS264 4.8 59.6 1.0
ND2 B:ASN251 5.0 52.4 1.0

Reference:

S.Xu, C.Zhong, T.Zhang, J.Ding. Structure of Human Lysine Methyltransferase SMYD2 Reveals Insights Into the Substrate Divergence in Smyd Proteins J Mol Cell Biol V. 3 293 2011.
ISSN: ISSN 1674-2788
PubMed: 21724641
DOI: 10.1093/JMCB/MJR015
Page generated: Wed Dec 16 04:47:29 2020

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