Atomistry » Magnesium » PDB 5hif-5hr6 » 5hq8
Atomistry »
  Magnesium »
    PDB 5hif-5hr6 »
      5hq8 »

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: Sun Sep 29 16:05:51 2024

Last articles

Cl in 2PFH
Cl in 2PD4
Cl in 2PFG
Cl in 2PF8
Cl in 2PEV
Cl in 2PDQ
Cl in 2PDU
Cl in 2PDP
Cl in 2PDN
Cl in 2PDJ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy