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Chlorine in PDB 4c2z: 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: 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

Other elements in 4c2z:

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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound, PDB code: 4c2z:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 4c2z

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Chlorine binding site 1 out of 12 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:Cl1498

b:54.0
occ:1.00
 CLF A:6461498 0.0 54.0 1.0
CAW A:6461498 1.8 47.6 1.0
OAE A:6461498 2.7 50.1 1.0
CAJ A:6461498 2.7 44.6 1.0
CBC A:6461498 2.7 46.1 1.0
O A:ASP471 2.7 47.4 1.0
SBF A:6461498 3.2 49.5 1.0
NAT A:6461498 3.5 36.8 1.0
C A:ASP471 3.9 48.4 1.0
CAX A:6461498 4.0 43.1 1.0
CAZ A:6461498 4.0 41.7 1.0
CAB A:6461498 4.1 29.2 1.0
CAK A:6461498 4.5 41.7 1.0
CBB A:6461498 4.5 32.7 1.0
CAV A:6461498 4.6 30.9 1.0
OAD A:6461498 4.6 44.4 1.0
CA A:GLY472 4.6 50.2 1.0
N A:ASP471 4.7 40.4 1.0
O A:HOH2268 4.8 33.5 1.0
CD2 A:TYR296 4.8 29.2 1.0
N A:GLY472 4.8 52.3 1.0
CA A:ASP471 4.8 49.8 1.0
CB A:ASP471 4.9 55.7 1.0
O A:GLY472 4.9 50.0 1.0

Chlorine binding site 2 out of 12 in 4c2z

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Chlorine binding site 2 out of 12 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:Cl1498

b:40.0
occ:1.00
 CLG A:6461498 0.0 40.0 1.0
CAX A:6461498 1.8 43.1 1.0
CBC A:6461498 2.7 46.1 1.0
CAK A:6461498 2.7 41.7 1.0
OAD A:6461498 2.8 44.4 1.0
OH A:TYR420 2.9 24.5 1.0
SBF A:6461498 3.1 49.5 1.0
CE2 A:TYR420 3.6 20.4 1.0
CZ A:TYR420 3.7 21.6 1.0
CE1 A:PHE190 3.7 24.5 1.0
CBB A:6461498 3.7 32.7 1.0
CZ A:PHE190 3.8 26.1 1.0
CAW A:6461498 3.9 47.6 1.0
NAT A:6461498 4.0 36.8 1.0
CAU A:6461498 4.0 36.7 1.0
CAZ A:6461498 4.0 41.7 1.0
CAV A:6461498 4.1 30.9 1.0
ND2 A:ASN451 4.3 30.2 1.0
OAE A:6461498 4.4 50.1 1.0
CE1 A:TYR296 4.4 37.2 1.0
NAR A:6461498 4.4 33.7 1.0
CAJ A:6461498 4.5 44.6 1.0
CAA A:6461498 4.5 37.3 1.0
NBE A:6461498 4.5 30.8 1.0
CZ A:TYR296 4.6 37.4 1.0
CD1 A:TYR296 4.6 33.3 1.0
CAB A:6461498 4.7 29.2 1.0
CG A:ASN451 4.9 25.0 1.0
CE2 A:TYR296 4.9 36.7 1.0
CD2 A:TYR420 4.9 17.1 1.0
CG A:TYR296 5.0 30.3 1.0
OH A:TYR296 5.0 43.4 1.0
CE1 A:TYR420 5.0 18.1 1.0

Chlorine binding site 3 out of 12 in 4c2z

Go back to Chlorine Binding Sites List in 4c2z
Chlorine binding site 3 out of 12 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
A:Cl1503

b:31.3
occ:1.00
 OG A:SER300 2.7 25.2 0.5
OG A:SER312 3.1 40.9 1.0
OG A:SER300 3.4 20.9 0.5
CB A:SER300 3.6 24.1 0.5
CB A:SER300 3.6 25.9 0.5
CB A:PRO303 3.6 32.0 1.0
CA A:PRO303 3.7 30.2 1.0
CB A:SER312 3.9 38.9 1.0
CE2 A:TYR327 4.0 30.2 1.0
O A:PRO303 4.1 33.8 1.0
CB A:LEU306 4.4 25.2 1.0
CD1 A:LEU306 4.4 25.6 1.0
C A:PRO303 4.4 33.4 1.0
CD2 A:TYR327 4.4 30.8 1.0
CD1 A:ILE307 4.5 38.6 1.0
CG2 A:THR323 4.5 47.7 1.0
CG1 A:ILE307 4.5 36.1 1.0
CG A:PRO303 4.7 30.9 1.0
CZ A:TYR327 4.7 35.8 1.0
OH A:TYR327 4.9 35.7 1.0
N A:PRO303 4.9 29.4 1.0
CG A:LEU306 5.0 25.4 1.0
CA A:SER300 5.0 24.0 0.5

Chlorine binding site 4 out of 12 in 4c2z

Go back to Chlorine Binding Sites List in 4c2z
Chlorine binding site 4 out of 12 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
A:Cl1504

b:21.2
occ:1.00
 NH2 A:ARG258 2.9 38.1 1.0
NE A:ARG258 3.2 46.0 1.0
CZ A:ARG258 3.4 47.5 1.0
OE1 A:GLN118 3.7 38.2 1.0
CB A:PHE119 3.9 21.4 1.0
CG A:GLN118 3.9 31.8 1.0
CG A:PRO261 4.0 17.1 1.0
CA A:PHE119 4.2 21.8 1.0
N A:PHE119 4.2 24.6 1.0
CD A:GLN118 4.3 34.7 1.0
CB A:PRO261 4.3 16.1 1.0
CD A:ARG258 4.4 33.2 1.0
C A:GLN118 4.4 25.5 1.0
O A:GLN118 4.6 28.3 1.0
CB A:ARG258 4.6 27.6 1.0
CB A:GLN118 4.6 27.9 1.0
CG A:ARG258 4.6 31.7 1.0
NH1 A:ARG258 4.7 45.0 1.0
CG A:PHE119 4.8 21.6 1.0
CD1 A:PHE119 4.8 20.8 1.0

Chlorine binding site 5 out of 12 in 4c2z

Go back to Chlorine Binding Sites List in 4c2z
Chlorine binding site 5 out of 12 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 5 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1505

b:40.0
occ:1.00
 N A:SER485 3.5 27.6 1.0
N A:VAL132 3.6 49.5 1.0
OG A:SER485 3.7 30.1 1.0
CA A:PRO484 3.8 28.1 1.0
O A:VAL132 4.1 49.2 1.0
C A:PRO484 4.1 28.4 1.0
CB A:VAL132 4.3 45.5 1.0
CB A:SER485 4.3 28.7 1.0
CA A:VAL131 4.3 52.5 1.0
CG1 A:VAL131 4.4 50.8 1.0
CA A:VAL132 4.4 49.7 1.0
CB A:PRO484 4.4 28.0 1.0
CE A:LYS289 4.4 38.4 1.0
C A:VAL131 4.5 51.1 1.0
CA A:SER485 4.5 27.5 1.0
CG2 A:VAL131 4.6 51.6 1.0
CB A:VAL131 4.7 53.2 1.0
CG2 A:VAL132 4.7 39.3 1.0
C A:VAL132 4.7 54.1 1.0
NZ A:LYS289 4.7 41.9 1.0
O A:CYS483 4.8 32.7 1.0
O A:GLU130 5.0 63.3 1.0

Chlorine binding site 6 out of 12 in 4c2z

Go back to Chlorine Binding Sites List in 4c2z
Chlorine binding site 6 out of 12 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 6 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1498

b:0.5
occ:1.00
 CLF B:6461498 0.0 0.5 1.0
CAW B:6461498 1.8 0.2 1.0
CAJ B:6461498 2.7 99.2 1.0
OAE B:6461498 2.7 97.5 1.0
CBC B:6461498 2.8 95.9 1.0
O B:ASP471 2.9 39.6 1.0
SBF B:6461498 3.2 0.2 1.0
OD1 B:ASP184 3.3 75.8 1.0
OD2 B:ASP184 3.8 92.1 1.0
CG B:ASP184 4.0 84.1 1.0
NAT B:6461498 4.0 79.2 1.0
C B:ASP471 4.1 37.1 1.0
CAZ B:6461498 4.1 92.5 1.0
CAX B:6461498 4.1 89.3 1.0
CAB B:6461498 4.2 62.8 1.0
OAD B:6461498 4.6 0.1 1.0
CAK B:6461498 4.6 88.8 1.0
CA B:GLY472 4.7 37.9 1.0
CBB B:6461498 4.8 70.3 1.0
N B:GLY472 4.8 35.4 1.0
CAV B:6461498 4.8 65.7 1.0
C B:GLY472 4.9 39.1 1.0
CD2 B:TYR296 4.9 30.9 1.0

Chlorine binding site 7 out of 12 in 4c2z

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Chlorine binding site 7 out of 12 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 7 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1498

b:68.0
occ:1.00
 CLG B:6461498 0.0 68.0 1.0
CAX B:6461498 1.8 89.3 1.0
OAD B:6461498 2.6 0.1 1.0
CBC B:6461498 2.8 95.9 1.0
CAK B:6461498 2.8 88.8 1.0
OH B:TYR420 2.9 28.4 1.0
SBF B:6461498 3.1 0.2 1.0
CE2 B:TYR420 3.4 24.1 1.0
CZ B:TYR420 3.6 23.8 1.0
CBB B:6461498 3.7 70.3 1.0
CZ B:PHE190 3.7 35.0 1.0
NAT B:6461498 3.7 79.2 1.0
CE1 B:PHE190 3.8 37.1 1.0
CAW B:6461498 4.1 0.2 1.0
CAZ B:6461498 4.1 92.5 1.0
CAV B:6461498 4.1 65.7 1.0
CE2 B:TYR296 4.2 37.3 1.0
CAU B:6461498 4.2 71.1 1.0
CZ B:TYR296 4.2 39.9 1.0
CD2 B:TYR296 4.4 30.9 1.0
OAE B:6461498 4.4 97.5 1.0
CE1 B:TYR296 4.5 39.0 1.0
CAJ B:6461498 4.6 99.2 1.0
ND2 B:ASN451 4.6 20.0 1.0
CG B:TYR296 4.6 32.1 1.0
CD2 B:TYR420 4.6 21.2 1.0
OH B:TYR296 4.7 42.0 1.0
CD1 B:TYR296 4.7 36.5 1.0
CAA B:6461498 4.7 71.5 1.0
CAB B:6461498 4.7 62.8 1.0
NAR B:6461498 4.7 67.3 1.0
NBE B:6461498 4.8 64.7 1.0
CE1 B:TYR420 4.9 21.4 1.0

Chlorine binding site 8 out of 12 in 4c2z

Go back to Chlorine Binding Sites List in 4c2z
Chlorine binding site 8 out of 12 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 8 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1503

b:25.8
occ:1.00
 OG B:SER312 3.0 38.6 0.5
OG B:SER300 3.0 31.8 1.0
OG B:SER312 3.5 31.6 0.5
CB B:PRO303 3.6 31.0 1.0
CB B:SER312 3.6 34.5 0.5
CB B:SER300 3.6 26.5 1.0
CB B:SER312 3.6 37.3 0.5
CA B:PRO303 3.7 28.4 1.0
CE2 B:TYR327 4.1 25.7 1.0
O B:PRO303 4.2 34.1 1.0
CD1 B:LEU306 4.3 32.1 1.0
CB B:LEU306 4.3 34.1 1.0
CG2 B:THR323 4.3 33.4 1.0
CG1 B:ILE307 4.3 31.7 1.0
CD1 B:ILE307 4.4 32.9 1.0
CD2 B:TYR327 4.4 25.4 1.0
C B:PRO303 4.5 32.5 1.0
CG B:PRO303 4.6 28.7 1.0
CG B:LEU306 4.8 33.5 1.0
N B:PRO303 4.9 27.3 1.0
CZ B:TYR327 5.0 27.6 1.0

Chlorine binding site 9 out of 12 in 4c2z

Go back to Chlorine Binding Sites List in 4c2z
Chlorine binding site 9 out of 12 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 9 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1504

b:22.4
occ:1.00
 NH2 B:ARG258 3.2 36.2 1.0
NE B:ARG258 3.4 44.4 1.0
OE1 B:GLN118 3.5 34.3 1.0
CZ B:ARG258 3.6 43.9 1.0
CG B:GLN118 3.9 28.7 1.0
CG B:PRO261 3.9 17.3 1.0
CB B:PHE119 4.0 16.9 1.0
CD B:GLN118 4.1 30.3 1.0
CB B:PRO261 4.2 15.8 1.0
CA B:PHE119 4.3 17.5 1.0
N B:PHE119 4.3 19.1 1.0
C B:GLN118 4.5 23.4 1.0
CD B:ARG258 4.5 35.4 1.0
CB B:GLN118 4.6 25.5 1.0
O B:GLN118 4.7 25.4 1.0
CB B:ARG258 4.8 31.0 1.0
CD1 B:PHE119 4.8 17.6 1.0
NH1 B:ARG258 4.9 44.5 1.0
CG B:ARG258 4.9 34.0 1.0
CG B:PHE119 4.9 16.6 1.0
NH1 B:ARG265 4.9 20.7 1.0

Chlorine binding site 10 out of 12 in 4c2z

Go back to Chlorine Binding Sites List in 4c2z
Chlorine binding site 10 out of 12 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 10 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1505

b:24.3
occ:1.00
 NZ B:LYS289 3.1 27.9 1.0
N B:SER485 3.4 18.1 1.0
N B:VAL132 3.5 43.7 1.0
OG B:SER485 3.6 25.1 1.0
CA B:PRO484 3.8 18.2 1.0
O B:VAL132 3.9 39.9 1.0
C B:PRO484 4.1 18.5 1.0
CB B:SER485 4.2 22.8 1.0
CB B:VAL132 4.3 33.9 1.0
CB B:PRO484 4.3 16.4 1.0
CA B:VAL132 4.3 34.1 1.0
CA B:VAL131 4.4 53.0 1.0
CA B:SER485 4.4 21.5 1.0
C B:VAL131 4.5 45.0 1.0
O B:GLU130 4.5 58.9 1.0
CE B:LYS289 4.6 31.9 1.0
C B:VAL132 4.6 38.4 1.0
CG2 B:VAL132 4.6 28.2 1.0
CG1 B:VAL131 4.9 52.7 1.0
O B:CYS483 4.9 20.8 1.0

Reference:

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
Page generated: Sun Jul 21 10:46:15 2024

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