Magnesium in PDB 4c2z: Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound

All present enzymatic activity of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound:
2.3.1.97;

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound, PDB code: 4c2z was solved by E.Thinon, R.A.Serwa, J.A.Brannigan, U.Brassat, M.H.Wright, W.P.Heal, A.J.Wilkinson, D.J.Mann, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.56 / 2.08
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.630, 179.120, 58.590, 90.00, 90.00, 90.00
R / Rfree (%)	16.939 / 23.814

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Magnesium atom in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound (pdb code 4c2z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound, PDB code: 4c2z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1499 b:28.2 occ:1.00 O4A A:MYA1497 2.6 22.3 1.0 O2A A:MYA1497 2.8 24.1 1.0 N A:LYS257 2.8 25.5 1.0 O A:LEU254 2.9 25.1 1.0 N A:VAL259 3.1 21.6 1.0 N A:SER256 3.2 22.5 1.0 N A:ARG258 3.5 26.4 1.0 CB A:VAL259 3.5 18.6 1.0 C A:LYS257 3.5 23.4 1.0 CA A:LYS257 3.5 25.1 1.0 O1A A:MYA1497 3.6 23.4 1.0 P1A A:MYA1497 3.6 23.4 1.0 C A:ARG255 3.6 24.4 1.0 CA A:ARG255 3.8 21.6 1.0 C A:SER256 3.8 25.2 1.0 CG2 A:VAL259 3.8 19.0 1.0 CB A:LYS257 3.8 26.0 1.0 CA A:VAL259 3.9 17.6 1.0 P2A A:MYA1497 3.9 20.4 1.0 C A:LEU254 3.9 25.1 1.0 CA A:SER256 3.9 23.7 1.0 C A:ARG258 4.1 24.2 1.0 O3A A:MYA1497 4.2 22.2 1.0 CA A:ARG258 4.2 26.1 1.0 O A:LYS257 4.2 22.8 1.0 CG1 A:VAL250 4.2 13.7 1.0 N A:ARG255 4.2 22.9 1.0 N A:ALA260 4.3 16.7 1.0 O A:ARG255 4.3 22.5 1.0 O6A A:MYA1497 4.5 21.1 1.0 C A:VAL259 4.6 18.1 1.0 CG A:LYS257 4.6 31.6 1.0 CG1 A:VAL259 4.7 19.0 1.0 CD2 A:LEU254 4.8 23.4 0.5 CG2 A:VAL250 4.9 13.3 1.0 O A:SER256 4.9 27.1 1.0 CB A:VAL250 4.9 13.9 1.0

Magnesium binding site 2 out of 2 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1499 b:27.7 occ:1.00 N B:LYS257 2.8 30.1 1.0 O2A B:MYA1497 2.8 22.6 1.0 O B:LEU254 2.8 24.6 1.0 N B:VAL259 3.0 19.8 1.0 O4A B:MYA1497 3.0 22.5 1.0 N B:ARG258 3.3 31.5 1.0 N B:SER256 3.3 24.6 1.0 C B:LYS257 3.4 27.2 1.0 CA B:LYS257 3.4 27.4 1.0 CB B:VAL259 3.5 18.4 1.0 CG2 B:VAL259 3.7 18.9 1.0 P1A B:MYA1497 3.7 20.3 1.0 C B:ARG255 3.7 25.1 1.0 CA B:VAL259 3.8 18.6 1.0 CB B:LYS257 3.8 29.7 1.0 C B:SER256 3.8 28.0 1.0 O1A B:MYA1497 3.8 22.5 1.0 C B:LEU254 3.9 25.6 1.0 CA B:ARG255 3.9 26.0 1.0 C B:ARG258 4.0 24.6 1.0 CA B:SER256 4.0 26.4 1.0 CG1 B:VAL250 4.0 18.1 1.0 CA B:ARG258 4.1 27.4 1.0 O B:LYS257 4.1 25.7 1.0 P2A B:MYA1497 4.2 23.2 1.0 N B:ALA260 4.3 17.5 1.0 O3A B:MYA1497 4.4 22.3 1.0 N B:ARG255 4.4 26.4 1.0 O B:ARG255 4.5 22.4 1.0 C B:VAL259 4.6 19.4 1.0 CG B:LYS257 4.7 35.2 1.0 O6A B:MYA1497 4.7 22.5 1.0 CG2 B:VAL250 4.9 17.4 1.0 CB B:VAL250 4.9 17.8 1.0 CG B:LEU254 4.9 28.7 1.0 CG1 B:VAL259 4.9 18.8 1.0 O B:SER256 4.9 27.0 1.0

E.Thinon, R.A.Serwa, M.Broncel, J.A.Brannigan, U.Brassat, M.H.Wright, W.P.Heal, A.J.Wilkinson, D.J.Mann, E.W.Tate. Chemical Proteomics Defines the Mammalian N- Myristoylated Proteome in Live Cells Global Profiling of Co- and Post-Translationally N-Myristoylated Proteomes in Human Cells. Nat.Commun. V. 5 4919 2014.
ISSN: ISSN 2041-1723
PubMed: 25255805
DOI: 10.1038/NCOMMS5919