Magnesium in PDB 6f56: Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa

All present enzymatic activity of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa:
2.3.1.97;

The structure of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa, PDB code: 6f56 was solved by R.Brenk, J.Kehrein, C.Kersten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.50 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.190, 159.130, 174.990, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.9

The binding sites of Magnesium atom in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa (pdb code 6f56). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa, PDB code: 6f56:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:42.7 occ:1.00 O A:LEU254 2.6 32.0 1.0 N A:LYS257 2.8 36.6 1.0 O4A A:MYA501 3.0 32.0 1.0 O2A A:MYA501 3.1 30.8 1.0 N A:VAL259 3.2 31.0 1.0 N A:ARG258 3.4 38.6 1.0 N A:SER256 3.4 37.2 1.0 CA A:LYS257 3.4 33.5 1.0 C A:LYS257 3.4 37.0 1.0 CB A:VAL259 3.5 30.3 1.0 CG2 A:VAL259 3.6 34.8 1.0 CB A:LYS257 3.6 36.2 1.0 C A:ARG255 3.6 38.6 1.0 C A:LEU254 3.7 31.4 1.0 CA A:ARG255 3.9 31.8 1.0 C A:SER256 3.9 37.3 1.0 CA A:VAL259 3.9 31.2 1.0 P1A A:MYA501 4.0 33.4 1.0 CG1 A:VAL250 4.0 34.6 1.0 CA A:SER256 4.1 32.8 1.0 O1A A:MYA501 4.1 36.2 1.0 O A:LYS257 4.2 34.3 1.0 C A:ARG258 4.2 35.5 1.0 N A:ARG255 4.3 33.1 1.0 CA A:ARG258 4.3 35.4 1.0 O A:ARG255 4.3 39.5 1.0 P2A A:MYA501 4.3 36.1 1.0 CG A:LYS257 4.4 37.7 1.0 N A:ALA260 4.5 28.1 1.0 O3A A:MYA501 4.6 32.2 1.0 C A:VAL259 4.7 30.8 1.0 O6A A:MYA501 4.8 37.6 1.0 CG1 A:VAL259 4.8 27.1 1.0 CB A:VAL250 4.9 32.7 1.0 CA A:LEU254 4.9 30.5 1.0 CG2 A:VAL250 5.0 28.8 1.0 CB A:LEU254 5.0 30.1 1.0 O A:SER256 5.0 35.6 1.0

Magnesium binding site 2 out of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.8 occ:1.00 O2A B:MYA501 2.7 28.5 1.0 N B:VAL259 2.8 27.9 1.0 N B:LYS257 2.9 42.0 1.0 O B:LEU254 2.9 33.5 1.0 O4A B:MYA501 3.0 35.2 1.0 N B:ARG258 3.0 32.9 1.0 C B:LYS257 3.3 40.6 1.0 CB B:VAL259 3.3 28.8 1.0 CA B:LYS257 3.4 36.8 1.0 CG2 B:VAL259 3.5 32.4 1.0 N B:SER256 3.6 38.6 1.0 CA B:VAL259 3.6 31.9 1.0 P1A B:MYA501 3.7 29.2 1.0 C B:ARG258 3.7 31.8 1.0 CB B:LYS257 3.8 36.1 1.0 CA B:ARG258 3.8 35.5 1.0 C B:ARG255 3.9 38.5 1.0 O1A B:MYA501 3.9 33.4 1.0 C B:SER256 4.0 41.5 1.0 C B:LEU254 4.1 34.7 1.0 O B:LYS257 4.1 40.9 1.0 CA B:ARG255 4.1 33.3 1.0 N B:ALA260 4.2 22.3 1.0 CG1 B:VAL250 4.2 25.5 1.0 CA B:SER256 4.2 35.4 1.0 P2A B:MYA501 4.2 32.9 1.0 O3A B:MYA501 4.4 27.4 1.0 C B:VAL259 4.4 30.9 1.0 CG B:LYS257 4.5 38.8 1.0 O B:ARG255 4.6 38.9 1.0 N B:ARG255 4.6 32.6 1.0 CG1 B:VAL259 4.7 27.0 1.0 O6A B:MYA501 4.7 32.8 1.0 O B:ARG258 4.9 34.5 1.0 CG2 B:VAL250 4.9 24.6 1.0 CB B:VAL250 5.0 25.9 1.0

Magnesium binding site 3 out of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:50.3 occ:1.00 N C:LYS257 2.7 41.7 1.0 O C:LEU254 2.8 40.6 1.0 O4A C:MYA501 2.8 41.3 1.0 O2A C:MYA501 2.9 45.7 1.0 N C:ARG258 2.9 43.4 1.0 N C:VAL259 3.0 41.5 1.0 C C:LYS257 3.2 44.4 1.0 N C:SER256 3.3 44.5 1.0 CA C:LYS257 3.3 45.5 1.0 C C:ARG255 3.6 46.5 1.0 CB C:VAL259 3.7 40.7 1.0 C C:SER256 3.7 46.3 1.0 CB C:LYS257 3.8 41.7 1.0 P1A C:MYA501 3.8 42.6 1.0 O1A C:MYA501 3.8 47.1 1.0 CA C:ARG258 3.8 43.4 1.0 CG2 C:VAL259 3.9 40.9 1.0 CA C:VAL259 3.9 38.1 1.0 CA C:ARG255 3.9 41.8 1.0 C C:LEU254 3.9 35.2 1.0 CA C:SER256 3.9 48.3 1.0 C C:ARG258 3.9 42.6 1.0 O C:LYS257 4.1 44.7 1.0 P2A C:MYA501 4.1 43.1 1.0 O C:ARG255 4.2 47.7 1.0 N C:ALA260 4.3 40.1 1.0 CG1 C:VAL250 4.3 33.3 1.0 O3A C:MYA501 4.4 31.0 1.0 N C:ARG255 4.4 38.6 1.0 CG C:LYS257 4.6 42.0 1.0 C C:VAL259 4.7 40.9 1.0 O6A C:MYA501 4.8 42.5 1.0 O C:SER256 4.8 48.7 1.0

Magnesium binding site 4 out of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:47.7 occ:1.00 O D:LEU254 2.4 43.3 1.0 N D:LYS257 2.9 43.1 1.0 CG2 D:VAL259 3.1 42.2 1.0 N D:VAL259 3.1 34.8 1.0 O2A D:MYA501 3.2 43.6 1.0 CB D:VAL259 3.2 41.2 1.0 O4A D:MYA501 3.3 39.5 1.0 C D:LYS257 3.3 42.9 1.0 CA D:LYS257 3.4 43.5 1.0 N D:ARG258 3.4 42.8 1.0 CB D:LYS257 3.6 40.1 1.0 C D:LEU254 3.6 39.5 1.0 N D:SER256 3.6 47.4 1.0 CA D:VAL259 3.8 38.5 1.0 C D:ARG255 3.8 45.4 1.0 O D:LYS257 3.8 46.3 1.0 CA D:ARG255 3.9 41.3 1.0 C D:SER256 4.1 45.8 1.0 C D:ARG258 4.1 39.1 1.0 P1A D:MYA501 4.2 39.9 1.0 CG1 D:VAL250 4.2 37.2 1.0 O1A D:MYA501 4.2 40.0 1.0 N D:ARG255 4.2 42.0 1.0 CA D:ARG258 4.3 40.8 1.0 CA D:SER256 4.4 45.4 1.0 O D:ARG255 4.4 39.1 1.0 N D:ALA260 4.5 33.2 1.0 P2A D:MYA501 4.5 41.8 1.0 CG1 D:VAL259 4.6 38.3 1.0 C D:VAL259 4.7 33.2 1.0 CB D:LEU254 4.8 40.1 1.0 CA D:LEU254 4.8 41.9 1.0 O3A D:MYA501 4.8 32.8 1.0 CE D:LYS257 4.9 42.8 0.0 CG D:LYS257 5.0 44.6 1.0 O6A D:MYA501 5.0 39.0 1.0

C.Kersten, E.Fleischer, J.Kehrein, C.Borek, E.Jaenicke, C.Sotriffer, R.Brenk. How to Design Selective Ligands For Highly Conserved Binding Sites: A Case Study Usingn-Myristoyltransferases As A Model System. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31423787
DOI: 10.1021/ACS.JMEDCHEM.9B00586