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Magnesium 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:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Co-Crystal Structure of Human SMYD3 with A MEKK2 Peptide at 2.13A, PDB code: 5hq8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5hq8

Go back to Magnesium Binding Sites List in 5hq8
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg504

b:42.7
occ:1.00
O A:HOH924 2.2 30.4 1.0
O A:HOH873 2.2 48.1 1.0
O A:PHE169 2.4 26.0 1.0
O A:PRO167 2.4 26.6 1.0
O A:HOH934 3.1 49.1 1.0
C A:PHE169 3.5 23.5 1.0
C A:PRO167 3.5 26.8 1.0
N A:PHE169 4.1 19.7 1.0
CA A:ASP170 4.2 22.3 1.0
N A:ASP170 4.2 20.0 1.0
C A:ALA168 4.2 24.4 1.0
CA A:PRO167 4.3 24.5 1.0
O A:HOH680 4.3 23.6 1.0
CB A:ASP170 4.3 23.6 1.0
N A:ALA168 4.5 23.1 1.0
CA A:PHE169 4.5 19.7 1.0
CA A:ALA168 4.6 24.6 1.0
O A:ALA168 4.6 23.7 1.0
O A:PRO166 4.6 19.8 1.0
OD1 A:ASP170 4.6 34.7 1.0
O A:HOH885 4.7 30.6 1.0

Magnesium binding site 2 out of 2 in 5hq8

Go back to Magnesium Binding Sites List in 5hq8
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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
B:Mg504

b:40.8
occ:1.00
O B:HOH766 2.1 47.9 1.0
O B:HOH852 2.2 36.5 1.0
O B:HOH848 2.2 44.5 1.0
O B:HOH853 2.3 31.2 1.0
O B:PRO167 2.4 24.4 1.0
O B:PHE169 2.5 25.2 1.0
C B:PHE169 3.5 22.7 1.0
C B:PRO167 3.5 21.5 1.0
N B:ASP170 4.2 18.0 1.0
N B:PHE169 4.2 19.2 1.0
CA B:ASP170 4.2 19.4 1.0
C B:ALA168 4.2 22.9 1.0
CA B:PRO167 4.3 20.5 1.0
O B:HOH697 4.4 26.3 1.0
CB B:ASP170 4.4 24.0 1.0
N B:ALA168 4.5 21.5 1.0
CA B:PHE169 4.5 21.7 1.0
O B:ALA168 4.5 23.9 1.0
CA B:ALA168 4.6 21.1 1.0
OD1 B:ASP170 4.6 33.8 1.0
O B:PRO166 4.6 19.4 1.0
O B:HOH756 4.6 26.4 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: Mon Dec 14 20:28:32 2020

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