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Zinc in PDB 3oxf: Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)

Enzymatic activity of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)

All present enzymatic activity of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I):
2.1.1.43;

Protein crystallography data

The structure of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I), PDB code: 3oxf was solved by S.Xu, J.Wu, B.Sun, 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 / 2.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.991, 117.990, 82.808, 90.00, 91.78, 90.00
R / Rfree (%) 21.1 / 26.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I) (pdb code 3oxf). 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 SMYD3 in Complex with Adohcy (Form I), PDB code: 3oxf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3oxf

Go back to Zinc Binding Sites List in 3oxf
Zinc binding site 1 out of 6 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)


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 SMYD3 in Complex with Adohcy (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn438

b:47.4
occ:1.00
 SG A:CYS71 2.2 45.8 1.0
SG A:CYS52 2.2 45.4 1.0
SG A:CYS75 2.3 49.4 1.0
SG A:CYS49 2.3 38.8 1.0
CB A:CYS49 3.1 41.4 1.0
CB A:CYS75 3.2 49.8 1.0
CB A:CYS71 3.3 46.2 1.0
CB A:CYS52 3.3 45.7 1.0
N A:CYS52 3.8 45.5 1.0
N A:CYS71 3.9 45.7 1.0
CA A:CYS52 4.1 45.9 1.0
CA A:CYS71 4.2 46.2 1.0
CA A:CYS49 4.6 41.7 1.0
CA A:CYS75 4.7 49.7 1.0
CB A:ARG51 4.8 44.7 1.0
N A:SER72 4.8 47.2 1.0
C A:CYS52 4.9 46.4 1.0
C A:ARG51 4.9 45.0 1.0
OG A:SER72 4.9 47.7 1.0
C A:CYS71 4.9 46.7 1.0
N A:ARG51 5.0 44.1 1.0
N A:LEU53 5.0 46.9 1.0

Zinc binding site 2 out of 6 in 3oxf

Go back to Zinc Binding Sites List in 3oxf
Zinc binding site 2 out of 6 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)


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 SMYD3 in Complex with Adohcy (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn439

b:44.6
occ:1.00
 NE2 A:HIS83 2.1 43.7 1.0
SG A:CYS87 2.2 45.7 1.0
SG A:CYS62 2.2 51.2 1.0
SG A:CYS65 2.3 48.1 1.0
CE1 A:HIS83 3.0 43.5 1.0
CB A:CYS62 3.0 53.1 1.0
CD2 A:HIS83 3.1 44.1 1.0
CB A:CYS65 3.4 48.9 1.0
CB A:CYS87 3.6 46.7 1.0
N A:CYS65 3.7 49.6 1.0
CA A:CYS65 4.1 48.9 1.0
ND1 A:HIS83 4.1 43.8 1.0
CG A:HIS83 4.2 44.9 1.0
CA A:CYS87 4.3 46.8 1.0
CB A:GLN64 4.4 51.1 1.0
CA A:CYS62 4.4 53.2 1.0
CB A:ALA68 4.5 44.5 1.0
C A:GLN64 4.6 50.2 1.0
CG A:GLN64 4.6 52.8 1.0
N A:GLN64 4.7 51.0 1.0
N A:ARG66 4.7 48.2 1.0
C A:CYS62 4.8 52.9 1.0
CA A:GLN64 4.8 50.8 1.0
C A:CYS65 4.8 48.6 1.0
O A:CYS87 4.9 47.0 1.0

Zinc binding site 3 out of 6 in 3oxf

Go back to Zinc Binding Sites List in 3oxf
Zinc binding site 3 out of 6 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)


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 SMYD3 in Complex with Adohcy (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn440

b:32.1
occ:1.00
 SG A:CYS261 2.2 32.8 1.0
SG A:CYS266 2.2 27.4 1.0
SG A:CYS208 2.2 29.7 1.0
SG A:CYS263 2.2 30.4 1.0
CB A:CYS208 3.1 28.6 1.0
CB A:CYS266 3.3 29.0 1.0
CB A:CYS263 3.5 31.2 1.0
CB A:CYS261 3.5 33.2 1.0
N A:CYS208 4.0 28.1 1.0
N A:CYS266 4.1 29.2 1.0
CA A:CYS208 4.2 28.7 1.0
CA A:CYS266 4.2 29.2 1.0
N A:CYS263 4.3 32.3 1.0
NE2 A:HIS206 4.3 24.7 1.0
CA A:CYS263 4.4 31.4 1.0
NE A:ARG249 4.4 32.5 1.0
CA A:CYS261 4.7 33.4 1.0
C A:CYS261 4.8 33.5 1.0
NH2 A:ARG249 4.8 31.8 1.0
C A:CYS263 4.9 31.2 1.0
CD2 A:HIS206 4.9 24.3 1.0
O A:CYS263 4.9 30.9 1.0
C A:SER207 5.0 27.6 1.0

Zinc binding site 4 out of 6 in 3oxf

Go back to Zinc Binding Sites List in 3oxf
Zinc binding site 4 out of 6 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)


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 SMYD3 in Complex with Adohcy (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn438

b:35.2
occ:1.00
 SG B:CYS75 2.2 39.4 1.0
SG B:CYS71 2.3 33.6 1.0
SG B:CYS52 2.4 35.1 1.0
SG B:CYS49 2.4 31.8 1.0
CB B:CYS75 3.1 39.5 1.0
CB B:CYS49 3.2 33.3 1.0
CB B:CYS52 3.2 34.7 1.0
CB B:CYS71 3.5 34.1 1.0
N B:CYS52 3.7 34.7 1.0
CA B:CYS52 4.0 34.8 1.0
N B:CYS71 4.1 33.7 1.0
CA B:CYS71 4.3 34.2 1.0
OG B:SER72 4.5 36.8 1.0
CA B:CYS75 4.6 39.5 1.0
CA B:CYS49 4.7 33.4 1.0
CB B:ARG51 4.7 34.7 1.0
N B:SER72 4.8 35.5 1.0
C B:CYS52 4.8 35.0 1.0
C B:ARG51 4.8 34.5 1.0
C B:CYS71 4.9 34.9 1.0
N B:LEU53 4.9 34.9 1.0

Zinc binding site 5 out of 6 in 3oxf

Go back to Zinc Binding Sites List in 3oxf
Zinc binding site 5 out of 6 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)


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 SMYD3 in Complex with Adohcy (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn439

b:32.1
occ:1.00
 NE2 B:HIS83 2.1 35.3 1.0
SG B:CYS62 2.2 36.4 1.0
SG B:CYS87 2.2 35.9 1.0
SG B:CYS65 2.3 38.4 1.0
CE1 B:HIS83 2.9 34.9 1.0
CB B:CYS62 3.2 37.3 1.0
CD2 B:HIS83 3.2 36.0 1.0
CB B:CYS65 3.2 37.1 1.0
CB B:CYS87 3.4 36.2 1.0
N B:CYS65 3.5 37.6 1.0
CA B:CYS87 3.9 36.3 1.0
CA B:CYS65 4.0 37.3 1.0
ND1 B:HIS83 4.1 35.6 1.0
CG B:HIS83 4.3 36.8 1.0
CB B:GLN64 4.3 38.6 1.0
C B:GLN64 4.5 38.0 1.0
CA B:CYS62 4.6 37.4 1.0
C B:CYS87 4.7 36.4 1.0
CA B:GLN64 4.7 38.3 1.0
O B:CYS87 4.8 36.5 1.0
CB B:ALA68 4.8 33.4 1.0
N B:GLN64 4.8 38.3 1.0
N B:ARG66 4.9 37.0 1.0
O B:CYS62 4.9 37.6 1.0
C B:CYS65 4.9 37.0 1.0
C B:CYS62 4.9 37.7 1.0
N B:CYS87 4.9 36.3 1.0

Zinc binding site 6 out of 6 in 3oxf

Go back to Zinc Binding Sites List in 3oxf
Zinc binding site 6 out of 6 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form I)


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 SMYD3 in Complex with Adohcy (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn440

b:45.0
occ:1.00
 SG B:CYS266 2.2 47.9 1.0
SG B:CYS261 2.3 48.2 1.0
SG B:CYS263 2.4 49.3 1.0
SG B:CYS208 2.5 37.6 1.0
CB B:CYS266 3.2 49.0 1.0
CB B:CYS261 3.3 49.5 1.0
CB B:CYS208 3.4 38.3 1.0
CB B:CYS263 3.7 50.0 1.0
N B:CYS266 3.8 49.2 1.0
N B:CYS208 4.0 38.5 1.0
N B:CYS263 4.1 50.3 1.0
CA B:CYS266 4.1 49.0 1.0
CA B:CYS263 4.3 50.1 1.0
CA B:CYS208 4.3 38.5 1.0
NE B:ARG249 4.4 41.0 1.0
NH2 B:ARG249 4.5 40.0 1.0
O B:CYS263 4.6 50.1 1.0
NE2 B:HIS206 4.6 35.6 1.0
CA B:CYS261 4.6 49.7 1.0
C B:CYS263 4.7 50.2 1.0
C B:CYS261 4.8 50.1 1.0
CB B:ARG265 4.9 49.6 1.0
C B:ARG265 4.9 49.5 1.0
N B:ASP262 4.9 50.4 1.0
CZ B:ARG249 5.0 40.2 1.0

Reference:

S.Xu, J.Wu, B.Sun, C.Zhong, J.Ding. Structural and Biochemical Studies of Human Lysine Methyltransferase SMYD3 Reveal the Important Functional Roles of Its Post-Set and Tpr Domains and the Regulation of Its Activity By Dna Binding. Nucleic Acids Res. V. 39 4438 2011.
ISSN: ISSN 0305-1048
PubMed: 21266482
DOI: 10.1093/NAR/GKR019
Page generated: Sat Oct 26 11:10:42 2024

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