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Sodium in PDB 4w9n: Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan

Enzymatic activity of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan

All present enzymatic activity of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan:
2.3.1.39;

Protein crystallography data

The structure of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan, PDB code: 4w9n was solved by K.H.Sippel, N.K.Vyas, B.Sankaran, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.43 / 1.84
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 68.564, 75.834, 83.264, 65.38, 88.87, 65.08
R / Rfree (%) 20.6 / 23.3

Other elements in 4w9n:

The structure of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan (pdb code 4w9n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan, PDB code: 4w9n:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4w9n

Go back to Sodium Binding Sites List in 4w9n
Sodium binding site 1 out of 4 in the Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1904

b:27.8
occ:1.00
 H B:PHE1772 2.4 59.2 1.0
HD2 B:PHE1772 2.6 70.0 1.0
HD2 B:PHE1573 3.1 68.1 1.0
HB2 B:PHE1772 3.1 68.1 1.0
HA B:ARG1574 3.1 29.9 1.0
HG3 B:MET1577 3.1 52.0 1.0
HA B:LYS1771 3.2 39.8 1.0
N B:PHE1772 3.2 49.4 1.0
O B:HOH2084 3.3 36.9 1.0
HB2 B:ARG1574 3.4 29.9 1.0
CD2 B:PHE1772 3.5 58.3 1.0
HD3 B:LYS1771 3.6 48.3 1.0
CA B:ARG1574 3.8 24.9 1.0
CB B:PHE1772 3.8 56.7 1.0
HB3 B:PHE1573 3.9 39.1 1.0
N B:ARG1574 3.9 27.5 1.0
CD2 B:PHE1573 3.9 56.8 1.0
CA B:LYS1771 4.0 33.1 1.0
CB B:ARG1574 4.0 24.9 1.0
H B:ARG1574 4.0 33.0 1.0
CG B:MET1577 4.0 43.3 1.0
C B:LYS1771 4.1 46.5 1.0
CA B:PHE1772 4.1 52.9 1.0
CG B:PHE1772 4.1 55.2 1.0
HB3 B:LYS1771 4.2 45.4 1.0
CD B:LYS1771 4.2 40.2 1.0
HG2 B:MET1577 4.2 52.0 1.0
HG3 B:ARG1574 4.3 39.6 1.0
HE B:ARG1574 4.3 29.7 1.0
H B:ASP1773 4.3 74.5 1.0
HE2 B:MET1577 4.4 67.5 1.0
C B:PHE1573 4.4 31.5 1.0
HD22 B:LEU1583 4.5 38.3 1.0
CE2 B:PHE1772 4.5 51.3 1.0
HE2 B:PHE1772 4.5 61.5 1.0
HE2 B:PHE1573 4.5 73.9 1.0
CB B:LYS1771 4.5 37.9 1.0
HB2 B:MET1577 4.5 43.2 1.0
HB3 B:PHE1772 4.6 68.1 1.0
CB B:PHE1573 4.7 32.6 1.0
CE2 B:PHE1573 4.7 61.5 1.0
O B:PHE1573 4.7 38.0 1.0
CG B:ARG1574 4.7 33.0 1.0
CG B:PHE1573 4.8 43.2 1.0
HB3 B:ARG1574 4.8 29.9 1.0
O B:GLY1770 4.8 25.0 1.0
HA B:PHE1772 4.9 63.5 1.0
CB B:MET1577 4.9 36.0 1.0
N B:ASP1773 4.9 62.1 1.0
HD2 B:LYS1771 4.9 48.3 1.0
OD1 B:ASP1773 5.0 77.4 1.0
C B:PHE1772 5.0 57.1 1.0

Sodium binding site 2 out of 4 in 4w9n

Go back to Sodium Binding Sites List in 4w9n
Sodium binding site 2 out of 4 in the Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1902

b:41.5
occ:1.00
 HG22 C:VAL1699 2.3 49.2 1.0
OD1 C:ASN1722 2.4 54.8 1.0
HB3 C:PHE1720 2.5 43.4 1.0
H C:ASN1722 2.7 38.2 1.0
H C:VAL1699 3.0 31.2 1.0
HA C:THR1698 3.1 28.2 1.0
CG2 C:VAL1699 3.3 41.0 1.0
HD1 C:PHE1720 3.3 36.5 1.0
H C:ALA1721 3.4 37.5 1.0
CB C:PHE1720 3.4 36.1 1.0
HA C:PHE1720 3.4 39.0 1.0
OG C:SER1723 3.5 75.4 1.0
N C:ASN1722 3.5 31.9 1.0
HG23 C:VAL1699 3.6 49.2 1.0
CG C:ASN1722 3.6 39.5 1.0
N C:VAL1699 3.6 26.0 1.0
HG21 C:VAL1699 3.6 49.2 1.0
O C:THR1697 3.6 22.9 1.0
N C:ALA1721 3.7 31.3 1.0
CA C:PHE1720 3.7 32.5 1.0
C C:PHE1720 3.7 32.4 1.0
H C:SER1723 3.8 57.8 1.0
N C:SER1723 3.9 48.1 1.0
HG C:SER1723 3.9 90.5 1.0
HG13 C:VAL1699 4.0 50.0 1.0
C C:ASN1722 4.0 41.9 1.0
HB2 C:PHE1720 4.0 43.4 1.0
CA C:THR1698 4.0 23.5 1.0
CD1 C:PHE1720 4.1 30.4 1.0
CA C:ASN1722 4.2 44.1 1.0
HD3 C:ARG1705 4.2 69.1 1.0
CG C:PHE1720 4.2 37.0 1.0
HG23 C:THR1697 4.2 28.6 1.0
C C:THR1698 4.2 25.8 1.0
CB C:VAL1699 4.3 44.8 1.0
O C:PHE1720 4.3 28.3 1.0
HA C:SER1723 4.4 70.5 1.0
CB C:ASN1722 4.4 41.4 1.0
CB C:SER1723 4.5 46.2 1.0
CA C:VAL1699 4.5 38.6 1.0
C C:THR1697 4.5 21.1 1.0
CA C:SER1723 4.5 58.8 1.0
HD21 C:ASN1722 4.5 47.1 1.0
C C:ALA1721 4.5 31.1 1.0
ND2 C:ASN1722 4.5 39.3 1.0
CG1 C:VAL1699 4.6 41.6 1.0
O C:ASN1722 4.6 61.1 1.0
HB2 C:ARG1705 4.6 43.2 1.0
HB2 C:SER1723 4.6 55.5 1.0
CA C:ALA1721 4.7 29.4 1.0
O C:VAL1699 4.7 47.5 1.0
HG3 C:ARG1705 4.7 45.8 1.0
N C:THR1698 4.7 21.0 1.0
CD C:ARG1705 4.7 57.6 1.0
HG11 C:VAL1699 4.8 50.0 1.0
HG22 C:THR1698 4.8 27.4 1.0
HB3 C:ASN1722 4.8 49.6 1.0
HB C:THR1698 5.0 31.1 1.0

Sodium binding site 3 out of 4 in 4w9n

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Sodium binding site 3 out of 4 in the Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1902

b:28.7
occ:1.00
 H D:GLN1714 2.5 44.9 1.0
HE21 D:GLN1714 2.6 70.3 1.0
HD2 D:PRO1713 2.7 51.0 1.0
HG3 D:GLN1714 2.7 64.2 1.0
HA D:PHE1712 2.8 39.8 1.0
HB2 D:GLN1714 2.9 59.5 1.0
HD13 D:LEU1689 3.3 41.8 1.0
HD1 D:PHE1712 3.3 36.2 1.0
NE2 D:GLN1714 3.4 58.6 1.0
N D:GLN1714 3.4 37.4 1.0
HB3 D:PHE1712 3.4 39.9 1.0
CG D:GLN1714 3.4 53.5 1.0
CD D:PRO1713 3.5 42.5 1.0
CA D:PHE1712 3.5 33.2 1.0
N D:PRO1713 3.5 37.5 1.0
CB D:GLN1714 3.5 49.5 1.0
C D:PHE1712 3.6 45.3 1.0
CD D:GLN1714 3.8 56.8 1.0
CB D:PHE1712 3.9 33.3 1.0
HD3 D:PRO1713 4.0 51.0 1.0
HE22 D:GLN1714 4.0 70.3 1.0
CD1 D:LEU1689 4.1 34.8 1.0
CA D:GLN1714 4.1 37.9 1.0
CD1 D:PHE1712 4.1 30.1 1.0
HD12 D:LEU1689 4.1 41.8 1.0
HG2 D:GLN1714 4.3 64.2 1.0
C D:PRO1713 4.4 34.7 1.0
HD11 D:LEU1689 4.4 41.8 1.0
HB3 D:GLN1714 4.4 59.5 1.0
HB2 D:PRO1713 4.4 51.1 1.0
O D:PHE1712 4.4 33.1 1.0
CA D:PRO1713 4.4 38.3 1.0
CG D:PHE1712 4.5 28.1 1.0
H D:LEU1715 4.5 38.1 1.0
O D:ARG1711 4.6 32.6 1.0
CG D:PRO1713 4.6 59.0 1.0
HA D:GLN1714 4.7 45.5 1.0
CB D:PRO1713 4.7 42.6 1.0
HG2 D:PRO1713 4.7 70.7 1.0
HB2 D:PHE1712 4.8 39.9 1.0
N D:PHE1712 4.8 33.5 1.0
HB3 D:LEU1689 5.0 36.6 1.0

Sodium binding site 4 out of 4 in 4w9n

Go back to Sodium Binding Sites List in 4w9n
Sodium binding site 4 out of 4 in the Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Enoyl-Acyl Carrier Protein-Reductase Domain From Human Fatty Acid Synthase Complexed with Triclosan within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1903

b:40.3
occ:1.00
 O D:HOH2050 2.7 36.9 1.0
O B:HOH2041 2.7 31.6 1.0
O D:HOH2016 2.9 25.5 1.0
CD2 D:TRP1811 3.0 29.2 1.0
CE2 D:TRP1811 3.0 23.8 1.0
HA B:GLU1809 3.1 43.0 1.0
CE3 D:TRP1811 3.2 29.1 1.0
CZ2 D:TRP1811 3.2 28.6 1.0
HB3 B:ALA1812 3.3 24.0 1.0
CZ3 D:TRP1811 3.4 26.8 1.0
CH2 D:TRP1811 3.4 32.1 1.0
NE1 D:TRP1811 3.6 25.3 1.0
CG D:TRP1811 3.7 23.6 1.0
HG3 B:GLU1809 3.7 41.2 1.0
HE3 D:TRP1811 3.7 35.0 1.0
HZ2 D:TRP1811 3.7 34.3 1.0
HG3 D:ARG1808 3.8 42.5 1.0
HA D:ASP1631 3.9 30.6 1.0
HZ3 D:TRP1811 4.0 32.1 1.0
HB1 B:ALA1812 4.0 24.0 1.0
CB B:ALA1812 4.0 20.0 1.0
CD1 D:TRP1811 4.0 25.8 1.0
HH2 D:TRP1811 4.0 38.5 1.0
HB2 B:ALA1812 4.0 24.0 1.0
CA B:GLU1809 4.1 35.8 1.0
HE1 D:TRP1811 4.1 30.3 1.0
O D:ASP1631 4.2 24.8 1.0
HB3 D:TRP1811 4.3 34.0 1.0
HG2 B:ARG1808 4.3 42.5 1.0
HB2 B:GLU1809 4.5 37.8 1.0
CG B:GLU1809 4.5 34.3 1.0
CB D:TRP1811 4.6 28.3 1.0
CB B:GLU1809 4.6 31.5 1.0
O B:GLU1809 4.6 35.6 1.0
HD1 D:TRP1811 4.7 31.0 1.0
O D:HOH2008 4.7 30.7 1.0
O B:ARG1808 4.8 33.8 1.0
CG D:ARG1808 4.8 35.4 1.0
CA D:ASP1631 4.8 25.5 1.0
N B:GLU1809 4.8 31.0 1.0
C D:ASP1631 4.9 25.1 1.0
C B:GLU1809 4.9 24.1 1.0
HD2 D:ARG1808 4.9 51.7 1.0
O D:HOH2048 4.9 33.2 1.0
HB2 D:TRP1811 4.9 34.0 1.0
HG2 B:GLU1809 4.9 41.2 1.0
HA D:ARG1808 5.0 36.6 1.0

Reference:

K.H.Sippel, N.K.Vyas, W.Zhang, B.Sankaran, F.A.Quiocho. Crystal Structure of the Human Fatty Acid Synthase Enoyl-Acyl Carrier Protein-Reductase Domain Complexed with Triclosan Reveals Allosteric Protein-Protein Interface Inhibition. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25301948
DOI: 10.1074/JBC.M114.608547
Page generated: Mon Oct 7 18:50:06 2024

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