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Chlorine in PDB 6fz5: 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: 6fz5 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) 76.94 / 1.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.390, 58.160, 154.001, 90.00, 92.36, 90.00
R / Rfree (%) 18.9 / 22.3

Other elements in 6fz5:

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 6fz5). 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: 6fz5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6fz5

Go back to Chlorine Binding Sites List in 6fz5
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:93.2
occ:1.00
 CL1 A:BXN1000 0.0 93.2 1.0
C15 A:BXN1000 1.8 80.1 1.0
C17 A:BXN1000 2.8 76.1 1.0
C14 A:BXN1000 2.8 77.5 1.0
O12 A:BXN1000 3.1 83.8 1.0
S11 A:BXN1000 3.3 79.7 1.0
O A:HOH1238 3.4 43.6 1.0
N09 A:BXN1000 3.5 73.2 1.0
C10 A:BXN1000 3.5 71.1 1.0
N A:GLY472 3.9 46.6 1.0
C07 A:BXN1000 4.0 64.0 1.0
CA A:GLY472 4.1 49.2 1.0
C18 A:BXN1000 4.1 71.9 1.0
C32 A:BXN1000 4.1 74.4 1.0
O A:HOH1252 4.2 49.6 1.0
C08 A:BXN1000 4.5 67.4 1.0
C31 A:BXN1000 4.6 71.0 1.0
C06 A:BXN1000 4.8 63.7 1.0
C A:ASP471 4.8 48.5 1.0
CB A:ASP471 4.8 48.8 1.0
N A:ASP471 4.9 45.2 1.0
O13 A:BXN1000 4.9 73.0 1.0

Chlorine binding site 2 out of 4 in 6fz5

Go back to Chlorine Binding Sites List in 6fz5
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:79.9
occ:1.00
 CL2 A:BXN1000 0.0 79.9 1.0
C32 A:BXN1000 1.8 74.4 1.0
O13 A:BXN1000 2.6 73.0 1.0
C31 A:BXN1000 2.7 71.0 1.0
C14 A:BXN1000 2.8 77.5 1.0
OH A:TYR420 2.9 32.8 1.0
S11 A:BXN1000 3.3 79.7 1.0
CE2 A:TYR420 3.6 28.5 1.0
CZ A:TYR420 3.7 29.8 1.0
CZ A:PHE190 4.0 45.0 1.0
CE1 A:PHE190 4.0 43.7 1.0
C18 A:BXN1000 4.1 71.9 1.0
C15 A:BXN1000 4.1 80.1 1.0
C08 A:BXN1000 4.2 67.4 1.0
N09 A:BXN1000 4.3 73.2 1.0
ND2 A:ASN451 4.4 31.9 1.0
C06 A:BXN1000 4.4 63.7 1.0
CE1 A:TYR296 4.4 45.0 1.0
CD1 A:TYR296 4.5 43.1 1.0
O12 A:BXN1000 4.6 83.8 1.0
CZ A:TYR296 4.6 45.7 1.0
C17 A:BXN1000 4.6 76.1 1.0
C02 A:BXN1000 4.7 64.6 1.0
C07 A:BXN1000 4.7 64.0 1.0
CG A:TYR296 4.8 39.2 1.0
N04 A:BXN1000 4.8 59.8 1.0
CE2 A:TYR296 4.9 44.1 1.0
CG A:ASN451 4.9 30.3 1.0
CE1 A:HIS298 4.9 36.2 1.0
CD2 A:TYR296 4.9 43.2 1.0
CD2 A:TYR420 4.9 26.7 1.0

Chlorine binding site 3 out of 4 in 6fz5

Go back to Chlorine Binding Sites List in 6fz5
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:76.0
occ:1.00
 CL1 B:BXN1000 0.0 76.0 1.0
C15 B:BXN1000 1.8 62.4 1.0
C17 B:BXN1000 2.7 59.6 1.0
C14 B:BXN1000 2.8 59.5 1.0
O12 B:BXN1000 3.0 61.5 1.0
S11 B:BXN1000 3.3 63.5 1.0
N09 B:BXN1000 3.6 57.4 1.0
C10 B:BXN1000 3.6 58.2 1.0
N B:GLY472 3.7 44.3 1.0
CA B:GLY472 3.8 43.9 1.0
C18 B:BXN1000 4.1 54.9 1.0
C32 B:BXN1000 4.1 58.5 1.0
C07 B:BXN1000 4.1 46.2 1.0
C31 B:BXN1000 4.6 56.8 1.0
C08 B:BXN1000 4.6 50.6 1.0
C B:ASP471 4.7 46.4 1.0
C06 B:BXN1000 4.8 47.0 1.0
N B:ASP471 4.9 44.9 1.0
O13 B:BXN1000 4.9 60.2 1.0
CB B:ASP471 4.9 50.3 1.0

Chlorine binding site 4 out of 4 in 6fz5

Go back to Chlorine Binding Sites List in 6fz5
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:62.5
occ:1.00
 CL2 B:BXN1000 0.0 62.5 1.0
C32 B:BXN1000 1.8 58.5 1.0
O13 B:BXN1000 2.7 60.2 1.0
C14 B:BXN1000 2.7 59.5 1.0
C31 B:BXN1000 2.8 56.8 1.0
OH B:TYR420 2.9 33.6 1.0
S11 B:BXN1000 3.2 63.5 1.0
CZ B:TYR420 3.8 31.4 1.0
CZ B:PHE190 3.8 35.6 1.0
CE2 B:TYR420 3.8 30.8 1.0
CE1 B:PHE190 3.8 35.5 1.0
C08 B:BXN1000 4.0 50.6 1.0
C15 B:BXN1000 4.0 62.4 1.0
C18 B:BXN1000 4.1 54.9 1.0
C06 B:BXN1000 4.2 47.0 1.0
N09 B:BXN1000 4.2 57.4 1.0
CE1 B:TYR296 4.4 37.7 1.0
C02 B:BXN1000 4.4 49.7 1.0
CZ B:TYR296 4.5 38.7 1.0
N04 B:BXN1000 4.5 45.5 1.0
C17 B:BXN1000 4.6 59.6 1.0
CD1 B:TYR296 4.6 37.8 1.0
ND2 B:ASN451 4.6 33.6 1.0
C07 B:BXN1000 4.6 46.2 1.0
O12 B:BXN1000 4.6 61.5 1.0
N03 B:BXN1000 4.7 46.1 1.0
CE2 B:TYR296 4.8 37.7 1.0
CG B:TYR296 4.9 38.2 1.0
OH B:TYR296 4.9 39.6 1.0
CD2 B:TYR296 5.0 39.7 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 23:36:40 2024

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