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Zinc in PDB 5hq8: Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A

Enzymatic activity of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A

All present enzymatic activity of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A:
2.1.1.43;

Protein crystallography data

The structure of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A, PDB code: 5hq8 was solved by P.A.Elkins, W.G.Bonnette, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.43 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.109, 118.155, 84.782, 90.00, 90.61, 90.00
R / Rfree (%) 17.4 / 20.1

Other elements in 5hq8:

The structure of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A (pdb code 5hq8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A, PDB code: 5hq8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5hq8

Go back to Zinc Binding Sites List in 5hq8
Zinc binding site 1 out of 6 in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:16.2
occ:1.00
 SG A:CYS263 2.3 16.3 1.0
SG A:CYS266 2.3 15.1 1.0
SG A:CYS261 2.3 16.4 1.0
SG A:CYS208 2.4 13.7 1.0
CB A:CYS208 3.3 16.2 1.0
CB A:CYS266 3.4 13.8 1.0
CB A:CYS261 3.4 16.3 1.0
CB A:CYS263 3.5 15.2 1.0
N A:CYS266 4.0 13.6 1.0
N A:CYS208 4.1 14.4 1.0
N A:CYS263 4.2 15.1 1.0
CA A:CYS266 4.3 13.0 1.0
NE2 A:HIS206 4.3 12.8 1.0
CA A:CYS263 4.3 13.4 1.0
CA A:CYS208 4.4 13.4 1.0
NE A:ARG249 4.5 13.0 1.0
NH2 A:ARG249 4.6 14.0 1.0
CA A:CYS261 4.6 15.2 1.0
C A:CYS261 4.6 17.8 1.0
O A:CYS261 4.8 19.3 1.0
C A:CYS263 4.8 15.2 1.0
CD1 A:LEU253 4.8 12.8 1.0
CD2 A:HIS206 4.9 11.9 1.0
O A:CYS263 4.9 14.8 1.0

Zinc binding site 2 out of 6 in 5hq8

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Zinc binding site 2 out of 6 in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:22.2
occ:1.00
 NE2 A:HIS83 2.1 22.1 1.0
SG A:CYS65 2.3 24.6 1.0
SG A:CYS62 2.3 25.4 1.0
SG A:CYS87 2.4 25.1 1.0
CE1 A:HIS83 3.0 21.2 1.0
CD2 A:HIS83 3.1 27.0 1.0
CB A:CYS62 3.2 25.1 1.0
CB A:CYS65 3.3 26.6 1.0
CB A:CYS87 3.3 23.4 1.0
N A:CYS65 3.4 29.1 1.0
CA A:CYS87 3.9 24.4 1.0
CA A:CYS65 4.0 29.0 1.0
ND1 A:HIS83 4.1 20.4 1.0
CG A:HIS83 4.2 20.8 1.0
CB A:GLN64 4.3 31.4 1.0
C A:GLN64 4.4 28.0 1.0
CA A:CYS62 4.7 27.4 1.0
CA A:GLN64 4.7 28.6 1.0
C A:CYS87 4.7 26.4 1.0
O A:CYS87 4.7 26.3 1.0
O A:HOH908 4.7 27.9 1.0
N A:GLN64 4.8 28.7 1.0
CB A:ALA68 4.8 23.9 1.0
C A:CYS65 4.9 31.8 1.0
C A:CYS62 5.0 28.3 1.0
N A:ARG66 5.0 32.6 1.0

Zinc binding site 3 out of 6 in 5hq8

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Zinc binding site 3 out of 6 in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:26.5
occ:1.00
 SG A:CYS75 2.1 29.0 1.0
SG A:CYS52 2.3 25.3 1.0
SG A:CYS71 2.3 28.1 1.0
SG A:CYS49 2.4 23.7 1.0
CB A:CYS49 3.1 27.4 1.0
CB A:CYS75 3.2 26.9 1.0
CB A:CYS52 3.3 23.3 1.0
CB A:CYS71 3.4 28.8 1.0
N A:CYS52 3.8 20.8 1.0
N A:CYS71 4.0 27.4 1.0
CA A:CYS52 4.2 22.0 1.0
CA A:CYS71 4.3 31.2 1.0
OG A:SER72 4.4 28.8 1.0
CB A:ARG51 4.6 25.8 0.6
CA A:CYS49 4.6 25.4 1.0
CA A:CYS75 4.6 26.3 1.0
CB A:ARG51 4.7 26.0 0.4
N A:SER72 4.9 32.2 1.0
C A:ARG51 4.9 24.2 1.0
C A:CYS71 4.9 33.7 1.0
C A:CYS52 5.0 23.3 1.0

Zinc binding site 4 out of 6 in 5hq8

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Zinc binding site 4 out of 6 in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:27.6
occ:1.00
 SG B:CYS261 2.3 26.8 1.0
SG B:CYS266 2.3 28.5 1.0
SG B:CYS208 2.4 21.9 1.0
SG B:CYS263 2.4 28.4 1.0
CB B:CYS261 3.1 21.9 1.0
CB B:CYS208 3.3 21.0 1.0
CB B:CYS263 3.5 25.7 1.0
CB B:CYS266 3.5 29.0 1.0
N B:CYS208 3.9 23.0 1.0
N B:CYS266 4.0 24.4 1.0
N B:CYS263 4.1 29.5 1.0
CA B:CYS208 4.2 22.6 1.0
CA B:CYS263 4.3 26.9 1.0
NE2 B:HIS206 4.3 18.9 1.0
CA B:CYS266 4.4 27.8 1.0
CA B:CYS261 4.4 27.9 1.0
C B:CYS261 4.5 32.4 1.0
O B:CYS263 4.6 29.8 1.0
O B:CYS261 4.6 31.1 1.0
C B:CYS263 4.7 28.1 1.0
NH2 B:ARG249 4.7 23.8 1.0
NE B:ARG249 4.7 24.8 1.0
CD2 B:HIS206 4.8 21.7 1.0
C B:SER207 5.0 22.7 1.0
CB B:ARG265 5.0 24.0 1.0

Zinc binding site 5 out of 6 in 5hq8

Go back to Zinc Binding Sites List in 5hq8
Zinc binding site 5 out of 6 in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:16.1
occ:1.00
 NE2 B:HIS83 2.1 13.6 1.0
SG B:CYS65 2.3 15.0 1.0
SG B:CYS87 2.3 16.8 1.0
SG B:CYS62 2.3 16.6 1.0
CD2 B:HIS83 3.0 13.7 1.0
CE1 B:HIS83 3.1 16.1 1.0
CB B:CYS62 3.2 15.9 1.0
CB B:CYS65 3.3 12.9 1.0
CB B:CYS87 3.3 17.3 1.0
N B:CYS65 3.5 16.1 1.0
CA B:CYS87 3.9 15.1 1.0
CA B:CYS65 4.0 14.5 1.0
ND1 B:HIS83 4.2 12.7 1.0
CG B:HIS83 4.2 12.8 1.0
CB B:GLN64 4.5 18.4 1.0
O B:HOH794 4.5 26.1 1.0
CA B:CYS62 4.6 15.8 1.0
C B:GLN64 4.6 20.7 1.0
C B:CYS87 4.6 16.7 1.0
O B:CYS87 4.6 15.8 1.0
CZ3 B:TRP80 4.9 32.3 1.0
N B:GLN64 4.9 17.7 1.0
CB B:ALA68 4.9 13.9 1.0
CA B:GLN64 4.9 17.6 1.0
C B:CYS65 4.9 17.2 1.0
N B:ARG66 4.9 15.2 1.0
C B:CYS62 4.9 16.3 1.0

Zinc binding site 6 out of 6 in 5hq8

Go back to Zinc Binding Sites List in 5hq8
Zinc binding site 6 out of 6 in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:18.6
occ:1.00
 SG B:CYS75 2.3 22.6 1.0
SG B:CYS52 2.3 18.6 1.0
SG B:CYS49 2.4 14.5 1.0
SG B:CYS71 2.4 19.5 1.0
CB B:CYS49 3.2 16.9 1.0
CB B:CYS75 3.2 16.8 1.0
CB B:CYS52 3.3 17.6 1.0
CB B:CYS71 3.5 14.8 1.0
N B:CYS52 3.7 15.9 1.0
N B:CYS71 4.0 14.4 1.0
CA B:CYS52 4.1 19.8 1.0
CA B:CYS71 4.3 15.8 1.0
CB B:ARG51 4.5 16.5 0.6
OG B:SER72 4.5 19.2 1.0
CA B:CYS75 4.7 15.7 1.0
CB B:ARG51 4.7 17.1 0.5
CA B:CYS49 4.7 17.2 1.0
C B:ARG51 4.8 16.9 1.0
C B:CYS52 5.0 21.2 1.0
N B:SER72 5.0 17.3 1.0
O B:HOH885 5.0 43.0 1.0

Reference:

G.S.Van Aller, A.P.Graves, P.A.Elkins, W.G.Bonnette, P.J.Mcdevitt, F.Zappacosta, R.S.Annan, T.W.Dean, D.S.Su, C.L.Carpenter, H.P.Mohammad, R.G.Kruger. Structure-Based Design of A Novel SMYD3 Inhibitor That Bridges the Sam-and MEKK2-Binding Pockets. Structure V. 24 774 2016.
ISSN: ISSN 0969-2126
PubMed: 27066749
DOI: 10.1016/J.STR.2016.03.010
Page generated: Sun Oct 27 17:37:52 2024

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