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Magnesium in PDB 5hi7: Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound

Enzymatic activity of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound

All present enzymatic activity of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound:
2.1.1.43;

Protein crystallography data

The structure of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound, PDB code: 5hi7 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) 44.71 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.470, 66.401, 104.851, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.6

Other elements in 5hi7:

The structure of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound (pdb code 5hi7). 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 An Aza-Sah Compound, PDB code: 5hi7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5hi7

Go back to Magnesium Binding Sites List in 5hi7
Magnesium binding site 1 out of 2 in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound


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 An Aza-Sah Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:55.6
occ:1.00
O A:HOH604 2.2 34.4 1.0
O A:HOH612 2.2 39.0 1.0
O A:HOH626 2.2 43.2 1.0
O A:HOH695 2.2 44.0 1.0
OE2 A:GLU130 3.8 31.1 1.0
HD21 A:ASN134 3.8 37.8 1.0
HE2 A:LYS135 4.0 29.0 0.5
OE1 A:GLU130 4.0 32.0 1.0
HE3 A:LYS135 4.0 32.4 0.6
O A:HOH719 4.0 41.3 1.0
CD A:GLU130 4.2 30.5 1.0
OD1 A:ASN134 4.2 31.2 1.0
HZ2 A:LYS135 4.3 31.3 0.6
HA A:ASN132 4.4 29.2 1.0
ND2 A:ASN134 4.5 31.5 1.0
O A:HOH685 4.5 0.7 1.0
OD1 A:ASN132 4.6 27.0 1.0
HD2 A:LYS135 4.6 30.6 0.6
CE A:LYS135 4.7 27.0 0.6
CG A:ASN134 4.8 30.4 1.0
NZ A:LYS135 4.8 26.1 0.6
HZ1 A:LYS135 4.9 31.3 0.6
CE A:LYS135 4.9 24.2 0.5
HG3 A:LYS135 4.9 28.4 0.5
HZ3 A:LYS135 5.0 29.0 0.5
HG3 A:LYS135 5.0 28.4 0.6

Magnesium binding site 2 out of 2 in 5hi7

Go back to Magnesium Binding Sites List in 5hi7
Magnesium binding site 2 out of 2 in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound


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 An Aza-Sah Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:45.9
occ:1.00
O A:HOH605 2.2 31.9 1.0
O A:HOH713 2.2 28.7 1.0
O A:HOH621 2.2 25.9 1.0
O A:HOH606 2.2 45.8 1.0
OD1 A:ASP332 2.8 31.6 1.0
OE1 A:GLN372 2.8 29.2 1.0
OD2 A:ASP332 3.2 30.7 1.0
O A:HOH669 3.3 30.8 1.0
CG A:ASP332 3.3 30.5 1.0
HZ2 A:LYS375 3.5 44.5 1.0
HG2 A:MET190 3.6 69.1 1.0
CD A:GLN372 3.6 27.4 1.0
HE22 A:GLN372 3.7 33.0 1.0
HH A:TYR358 3.7 28.4 1.0
OD2 A:ASP336 3.8 30.9 1.0
NE2 A:GLN372 4.0 27.5 1.0
O A:ALA188 4.0 43.8 1.0
HD2 A:LYS375 4.0 38.1 1.0
OD1 A:ASP336 4.2 31.4 1.0
OH A:TYR358 4.3 23.6 1.0
HG3 A:MET190 4.3 69.1 1.0
HB2 A:GLN372 4.3 28.8 1.0
HA A:GLU189 4.3 56.2 1.0
NZ A:LYS375 4.3 37.1 1.0
HA A:GLN372 4.4 27.1 1.0
CG A:MET190 4.4 57.6 1.0
CG A:ASP336 4.4 30.5 1.0
HZ3 A:LYS375 4.5 44.5 1.0
HE21 A:GLN372 4.8 33.0 1.0
HB2 A:MET190 4.8 66.5 1.0
HE2 A:TYR358 4.8 25.7 1.0
CB A:ASP332 4.8 28.8 1.0
H12 A:DMS506 4.8 55.8 1.0
CG A:GLN372 4.8 25.8 1.0
CD A:LYS375 4.8 31.8 1.0
HZ1 A:LYS375 4.9 44.5 1.0
CB A:GLN372 4.9 24.0 1.0
HD3 A:LYS375 4.9 38.1 1.0
HG12 A:VAL371 4.9 27.6 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 20:27:00 2020

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