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Chlorine in PDB 6fz3: Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound

Enzymatic activity of 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;

Protein crystallography data

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound, PDB code: 6fz3 was solved by F.C.Kersten, R.Brenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.87 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.278, 58.000, 153.309, 90.00, 92.18, 90.00
R / Rfree (%) 19.9 / 23.5

Other elements in 6fz3:

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

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound (pdb code 6fz3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound, PDB code: 6fz3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6fz3

Go back to Chlorine Binding Sites List in 6fz3
Chlorine binding site 1 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1000

b:52.7
occ:1.00
 CL A:EBK1000 0.0 52.7 1.0
C14 A:EBK1000 1.8 40.0 1.0
OH A:TYR420 2.7 19.9 1.0
C20 A:EBK1000 2.7 44.3 1.0
O1 A:EBK1000 2.8 48.4 1.0
C5 A:EBK1000 2.9 39.3 1.0
S A:EBK1000 3.2 49.1 1.0
CZ A:TYR420 3.6 19.3 1.0
CE2 A:TYR420 3.7 18.8 1.0
CE1 A:PHE190 3.8 32.4 1.0
CZ A:PHE190 3.8 31.8 1.0
C19 A:EBK1000 3.9 45.1 1.0
ND2 A:ASN451 4.1 23.3 1.0
C15 A:EBK1000 4.1 43.6 1.0
N3 A:EBK1000 4.1 45.7 1.0
C17 A:EBK1000 4.1 37.3 1.0
C12 A:EBK1000 4.2 42.3 1.0
C13 A:EBK1000 4.3 43.5 1.0
CE1 A:TYR296 4.5 37.2 1.0
O A:EBK1000 4.5 55.8 1.0
N1 A:EBK1000 4.6 40.3 1.0
CD1 A:TYR296 4.6 36.2 1.0
N5 A:EBK1000 4.6 42.5 1.0
C A:EBK1000 4.7 44.0 1.0
C6 A:EBK1000 4.7 37.8 1.0
CG A:ASN451 4.7 22.3 1.0
O A:HOH1128 4.7 24.2 1.0
CZ A:TYR296 4.8 37.8 1.0
CE1 A:TYR420 4.9 18.6 1.0
C1 A:EBK1000 4.9 41.0 1.0

Chlorine binding site 2 out of 4 in 6fz3

Go back to Chlorine Binding Sites List in 6fz3
Chlorine binding site 2 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl1000

b:39.0
occ:1.00
 CL1 A:EBK1000 0.0 39.0 1.0
C15 A:EBK1000 1.7 43.6 1.0
C6 A:EBK1000 2.7 37.8 1.0
C20 A:EBK1000 2.8 44.3 1.0
O A:EBK1000 3.0 55.8 1.0
S A:EBK1000 3.2 49.1 1.0
N3 A:EBK1000 3.4 45.7 1.0
N A:GLY472 3.6 38.2 1.0
CA A:GLY472 3.8 40.4 1.0
C1 A:EBK1000 3.9 41.0 1.0
C14 A:EBK1000 4.0 40.0 1.0
C17 A:EBK1000 4.1 37.3 1.0
O A:HOH1182 4.2 25.6 1.0
C19 A:EBK1000 4.4 45.1 1.0
C5 A:EBK1000 4.5 39.3 1.0
CB A:ASP471 4.5 46.7 1.0
C13 A:EBK1000 4.6 43.5 1.0
C A:ASP471 4.6 41.8 1.0
O1 A:EBK1000 4.6 48.4 1.0
N A:ASP471 4.7 39.0 1.0
CA A:ASP471 4.8 42.8 1.0

Chlorine binding site 3 out of 4 in 6fz3

Go back to Chlorine Binding Sites List in 6fz3
Chlorine binding site 3 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1000

b:42.2
occ:1.00
 CL B:EBK1000 0.0 42.2 1.0
C14 B:EBK1000 1.8 40.5 1.0
OH B:TYR420 2.7 30.4 1.0
C20 B:EBK1000 2.7 43.4 1.0
C5 B:EBK1000 2.8 41.8 1.0
O1 B:EBK1000 3.0 41.4 1.0
S B:EBK1000 3.4 42.5 1.0
CZ B:TYR420 3.5 27.9 1.0
CE2 B:TYR420 3.5 27.3 1.0
CE1 B:PHE190 3.9 33.8 1.0
ND2 B:ASN451 4.0 31.9 1.0
CZ B:PHE190 4.0 35.1 1.0
C19 B:EBK1000 4.0 38.4 1.0
C17 B:EBK1000 4.0 42.8 1.0
C15 B:EBK1000 4.1 46.2 1.0
C12 B:EBK1000 4.2 39.0 1.0
N3 B:EBK1000 4.2 41.6 1.0
CE1 B:TYR296 4.3 43.6 1.0
C13 B:EBK1000 4.4 35.5 1.0
CD1 B:TYR296 4.5 43.5 1.0
CG B:ASN451 4.6 31.5 1.0
C6 B:EBK1000 4.6 43.4 1.0
C B:EBK1000 4.6 40.7 1.0
O B:EBK1000 4.6 45.4 1.0
O B:HOH1111 4.6 21.1 1.0
N1 B:EBK1000 4.6 35.8 1.0
CZ B:TYR296 4.6 44.0 1.0
N5 B:EBK1000 4.7 34.8 1.0
CE1 B:TYR420 4.8 27.2 1.0
CD2 B:TYR420 4.9 26.1 1.0
CG B:TYR296 4.9 43.3 1.0
CE1 B:HIS298 5.0 52.6 1.0

Chlorine binding site 4 out of 4 in 6fz3

Go back to Chlorine Binding Sites List in 6fz3
Chlorine binding site 4 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1000

b:48.4
occ:1.00
 CL1 B:EBK1000 0.0 48.4 1.0
C15 B:EBK1000 1.7 46.2 1.0
C6 B:EBK1000 2.6 43.4 1.0
C20 B:EBK1000 2.8 43.4 1.0
O B:EBK1000 3.0 45.4 1.0
S B:EBK1000 3.2 42.5 1.0
N3 B:EBK1000 3.3 41.6 1.0
C1 B:EBK1000 3.7 35.5 1.0
N B:GLY472 3.8 53.0 1.0
CA B:GLY472 3.9 50.9 1.0
C14 B:EBK1000 4.0 40.5 1.0
C17 B:EBK1000 4.1 42.8 1.0
C19 B:EBK1000 4.2 38.4 1.0
C13 B:EBK1000 4.3 35.5 1.0
C5 B:EBK1000 4.5 41.8 1.0
O1 B:EBK1000 4.7 41.4 1.0
C B:ASP471 4.9 54.0 1.0
CB B:ASP471 5.0 58.9 1.0

Reference:

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
Page generated: Sat Jul 27 23:36:27 2024

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