Chlorine in PDB 8fbq: Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B

The structure of Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B, PDB code: 8fbq was solved by M.K.Fenwick, B.L.Staker, S.W.Lovell, I.Q.Phan, J.Early, P.J.Myler, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.97 / 1.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.93, 91.93, 101.286, 90, 90, 90
R / Rfree (%)	13.6 / 16.5

The binding sites of Chlorine atom in the Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B (pdb code 8fbq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B, PDB code: 8fbq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl512 b:13.9 occ:1.00 H A:GLY199 2.3 13.5 1.0 H222 A:XOQ502 2.8 21.7 1.0 H2 A:MYA501 2.9 11.5 1.0 H271 A:XOQ502 2.9 15.3 1.0 O A:HOH992 3.0 31.8 1.0 O A:HOH732 3.1 14.6 1.0 N A:GLY199 3.1 11.3 1.0 HB1 A:ALA198 3.2 13.3 1.0 H A:VAL200 3.2 13.2 1.0 HA A:ALA198 3.4 10.4 1.0 HG22 A:VAL200 3.5 15.1 1.0 HG13 A:VAL200 3.6 24.3 1.0 HA3 A:GLY199 3.7 12.8 1.0 C2 A:MYA501 3.8 9.6 1.0 HG22 A:VAL96 3.8 15.8 1.0 CA A:GLY199 3.9 10.7 1.0 HN6B A:MYA501 3.9 17.2 1.0 C22 A:XOQ502 3.9 18.1 1.0 S1 A:MYA501 3.9 10.8 1.0 N A:VAL200 3.9 11.0 1.0 H3A A:MYA501 3.9 11.0 1.0 CA A:ALA198 4.0 8.7 1.0 CB A:ALA198 4.0 11.1 1.0 HN6A A:MYA501 4.0 17.2 1.0 HG11 A:VAL96 4.0 15.0 1.0 C27 A:XOQ502 4.0 12.8 1.0 C A:ALA198 4.0 10.1 1.0 HG21 A:VAL96 4.1 15.8 1.0 H221 A:XOQ502 4.2 21.7 1.0 O5 A:MYA501 4.2 10.7 1.0 HG13 A:VAL96 4.3 15.0 1.0 HB2 A:ALA198 4.3 13.3 1.0 N6A A:MYA501 4.4 14.3 1.0 C A:GLY199 4.4 10.7 1.0 CG2 A:VAL200 4.4 12.6 1.0 CG2 A:VAL96 4.4 13.2 1.0 H231 A:XOQ502 4.4 28.1 1.0 C3 A:MYA501 4.4 9.2 1.0 CG1 A:VAL200 4.5 20.2 1.0 H281 A:XOQ502 4.5 15.6 1.0 CG1 A:VAL96 4.6 12.5 1.0 H2A A:MYA501 4.6 11.5 1.0 C23 A:XOQ502 4.7 23.4 1.0 HG21 A:VAL200 4.7 15.1 1.0 HB3 A:ALA198 4.7 13.3 1.0 HG11 A:VAL200 4.7 24.3 1.0 HA2 A:GLY199 4.8 12.8 1.0 C28 A:XOQ502 4.8 13.0 1.0 H232 A:XOQ502 4.8 28.1 1.0 N21 A:XOQ502 4.8 19.6 1.0 CB A:VAL200 4.8 15.6 1.0 C20 A:XOQ502 4.9 11.6 1.0 O A:HOH1016 4.9 44.0 1.0 O A:HOH889 5.0 18.3 1.0 CA A:VAL200 5.0 12.2 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl513 b:24.7 occ:1.00 H A:SER236 2.3 15.0 0.5 H A:SER236 2.3 15.0 0.5 HG A:SER236 2.4 20.1 0.5 O A:HOH819 2.8 20.8 1.0 HB A:THR234 3.0 16.5 1.0 HB3 A:MET235 3.0 16.2 1.0 HB2 A:SER236 3.0 17.2 0.5 OG A:SER236 3.0 16.7 0.5 HB2 A:SER236 3.1 17.4 0.5 N A:SER236 3.1 12.5 0.5 N A:SER236 3.1 12.5 0.5 HB3 A:SER236 3.3 17.2 0.5 H A:MET235 3.3 15.2 1.0 CB A:SER236 3.5 14.5 0.5 CB A:SER236 3.5 14.4 0.5 N A:MET235 3.7 12.7 1.0 CB A:MET235 3.9 13.5 1.0 CB A:THR234 3.9 13.8 1.0 CA A:SER236 3.9 13.1 0.5 CA A:SER236 3.9 13.1 0.5 C A:MET235 4.1 11.9 1.0 CA A:MET235 4.1 12.2 1.0 OG1 A:THR234 4.2 13.4 1.0 HG1 A:THR234 4.2 16.0 1.0 HB2 A:MET235 4.4 16.2 1.0 HA A:SER236 4.4 15.7 0.5 HB3 A:SER236 4.4 17.4 0.5 HA A:SER236 4.4 15.7 0.5 C A:THR234 4.4 12.6 1.0 CA A:THR234 4.7 13.3 1.0 O4 A:SO4505 4.7 10.9 1.0 O A:HOH796 4.7 41.0 1.0 H A:ARG237 4.7 14.6 1.0 HG21 A:THR234 4.7 17.4 1.0 HA A:THR234 4.7 15.9 1.0 OG A:SER236 4.8 17.4 0.5 HG3 A:MET235 4.8 21.3 1.0 CG2 A:THR234 4.8 14.5 1.0 CG A:MET235 4.8 17.8 1.0 HG2 A:MET235 4.9 21.3 1.0 HG22 A:THR234 5.0 17.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl514 b:42.8 occ:1.00 H A:LYS283 2.4 18.5 0.2 H A:LYS283 2.4 18.4 0.4 H A:LYS283 2.4 18.4 0.4 HE1 A:HIS265 2.8 22.5 0.5 HZ2 A:LYS283 2.9 30.9 0.4 HG3 A:LYS283 3.0 23.6 0.4 HB A:THR282 3.1 23.0 1.0 N A:LYS283 3.2 15.4 0.2 N A:LYS283 3.2 15.4 0.4 N A:LYS283 3.2 15.4 0.4 HA A:THR282 3.2 16.1 1.0 HZ3 A:LYS283 3.3 30.9 0.4 HB2 A:LYS283 3.3 22.1 0.4 HB3 A:LYS283 3.4 22.1 0.2 HB2 A:LYS283 3.5 22.0 0.4 NZ A:LYS283 3.5 25.7 0.4 HB2 A:LYS283 3.6 22.1 0.2 CE1 A:HIS265 3.6 18.7 0.5 O A:HOH938 3.7 44.3 1.0 HB3 A:LYS283 3.7 22.1 0.4 CG A:LYS283 3.8 19.7 0.4 CB A:THR282 3.8 19.2 1.0 CA A:THR282 3.8 13.4 1.0 CB A:LYS283 3.8 18.4 0.2 CB A:LYS283 3.9 18.4 0.4 HE1 A:HIS265 3.9 23.4 0.5 CB A:LYS283 4.0 18.3 0.4 HD2 A:LYS283 4.0 24.1 0.4 OE1 A:GLU284 4.0 13.7 0.5 HG22 A:THR282 4.0 26.0 1.0 C A:THR282 4.0 14.2 1.0 HE2 A:HIS265 4.1 20.5 0.5 HZ1 A:LYS283 4.1 30.9 0.4 CA A:LYS283 4.2 13.1 0.2 CA A:LYS283 4.2 13.1 0.4 CE1 A:HIS265 4.2 19.5 0.5 CA A:LYS283 4.2 13.0 0.4 NE2 A:HIS265 4.3 17.1 0.5 CD A:LYS283 4.3 20.0 0.4 CG2 A:THR282 4.4 21.6 1.0 NE2 A:HIS265 4.4 18.2 0.5 ND1 A:HIS265 4.4 17.1 0.5 HE2 A:HIS265 4.5 21.8 0.5 CE A:LYS283 4.5 31.8 0.4 H A:GLU284 4.6 15.8 0.2 HG2 A:LYS283 4.6 23.6 0.4 H A:GLU284 4.6 15.8 0.4 HA A:LYS283 4.7 15.7 0.4 HA A:LYS283 4.7 15.8 0.2 HA A:LYS283 4.7 15.7 0.4 HG21 A:THR282 4.8 26.0 1.0 O A:HOH1017 4.8 32.8 1.0 HB3 A:LYS283 4.9 22.0 0.4 HE2 A:LYS283 4.9 21.1 0.2 OG1 A:THR282 5.0 16.5 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Plasmodium Vivax Glycylpeptide N- Tetradecanoyltransferase (N-Myristoyltransferase, Nmt) Bound to Myristoyl-Coa and Inhibitor 12B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl515 b:32.2 occ:1.00 HH22 A:ARG84 2.2 20.6 1.0 O A:HOH962 2.6 40.4 1.0 O A:HOH790 2.8 28.7 1.0 NH2 A:ARG84 3.0 17.2 1.0 HG3 A:GLU81 3.0 51.4 1.0 HG2 A:GLU81 3.2 51.4 1.0 HH12 A:ARG84 3.3 20.0 1.0 HH21 A:ARG84 3.4 20.6 1.0 CG A:GLU81 3.5 42.8 1.0 OE2 A:GLU81 3.6 68.7 1.0 CZ A:ARG84 3.9 17.2 1.0 NH1 A:ARG84 3.9 16.7 1.0 CD A:GLU81 4.1 72.1 1.0 O A:LYS79 4.5 20.6 1.0 O A:HOH830 4.5 37.4 1.0 HH11 A:ARG84 4.7 20.0 1.0 HA A:GLU81 4.7 23.6 1.0 CB A:GLU81 4.9 37.1 1.0 H A:GLU81 4.9 21.9 1.0

D.Rodriguez-Hernandez, K.Vijayan, R.Zigweid, M.K.Fenwick, B.Sankaran, W.Roobsoong, J.Sattabongkot, E.K.K.Glennon, P.J.Myler, P.Sunnerhagen, B.L.Staker, A.Kaushansky, M.Grotli. Identification of Potent and Selective N-Myristoyltransferase Inhibitors of Plasmodium Vivax Liver Stage Hypnozoites and Schizonts. Nat Commun V. 14 5408 2023.
ISSN: ESSN 2041-1723
PubMed: 37669940
DOI: 10.1038/S41467-023-41119-7