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Chlorine in PDB 5fic: Open Form of Murine Acid Sphingomyelinase in Presence of Lipid

Enzymatic activity of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid

All present enzymatic activity of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid:
3.1.4.12;

Protein crystallography data

The structure of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid, PDB code: 5fic was solved by A.Gorelik, K.Illes, L.X.Heinz, G.Superti-Furga, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.32 / 2.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 101.750, 101.750, 401.830, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.6

Other elements in 5fic:

The structure of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid (pdb code 5fic). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid, PDB code: 5fic:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5fic

Go back to Chlorine Binding Sites List in 5fic
Chlorine binding site 1 out of 5 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl712

b:58.1
occ:1.00
 HH22 B:ARG253 2.1 43.1 1.0
HE A:ARG472 2.3 39.8 1.0
HD3 A:ARG472 2.7 36.7 1.0
NH2 B:ARG253 2.9 35.9 1.0
NE A:ARG472 2.9 33.1 1.0
HH12 B:ARG253 2.9 35.0 1.0
H B:GLU213 3.0 59.7 1.0
CD A:ARG472 3.2 30.6 1.0
HH21 B:ARG253 3.4 43.1 1.0
HA B:LEU212 3.4 39.3 1.0
NH1 B:ARG253 3.5 29.1 1.0
HD12 B:LEU212 3.5 38.0 1.0
CZ B:ARG253 3.6 41.2 1.0
HB2 B:GLU213 3.7 49.9 1.0
N B:GLU213 3.8 49.7 1.0
HB2 A:ARG472 3.8 31.7 1.0
HD2 A:ARG472 3.8 36.7 1.0
HH21 A:ARG472 3.9 51.6 1.0
CZ A:ARG472 3.9 43.4 1.0
HD2 B:TYR211 4.0 53.0 1.0
HB3 B:GLU213 4.0 49.9 1.0
O B:TYR211 4.1 42.4 1.0
NH2 A:ARG472 4.2 43.0 1.0
CB B:GLU213 4.3 41.6 1.0
CA B:LEU212 4.3 32.8 1.0
HB3 A:ARG472 4.3 31.7 1.0
HH11 B:ARG253 4.3 35.0 1.0
CB A:ARG472 4.3 26.4 1.0
CG A:ARG472 4.4 31.9 1.0
CD1 B:LEU212 4.5 31.7 1.0
C B:LEU212 4.5 38.0 1.0
CA B:GLU213 4.7 47.8 1.0
HE2 B:TYR211 4.7 45.2 1.0
HE1 B:PHE241 4.8 54.7 1.0
HD13 B:LEU212 4.8 38.0 1.0
HG2 A:PRO184 4.8 39.8 1.0
CD2 B:TYR211 4.8 44.1 1.0
C B:TYR211 4.8 47.0 1.0
NE B:ARG253 4.9 43.9 1.0
HD11 B:LEU212 4.9 38.0 1.0
HG3 A:ARG472 4.9 38.2 1.0
HB3 B:PRO251 4.9 39.8 1.0
NH1 A:ARG472 4.9 47.6 1.0
N B:LEU212 5.0 39.3 1.0

Chlorine binding site 2 out of 5 in 5fic

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Chlorine binding site 2 out of 5 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl713

b:55.3
occ:1.00
 H A:GLU213 2.0 48.5 1.0
HH22 A:ARG253 2.1 85.3 1.0
HH21 A:ARG253 2.5 85.3 1.0
HA A:LEU212 2.6 49.1 1.0
NH2 A:ARG253 2.6 71.1 1.0
HD12 A:LEU212 2.7 60.5 1.0
N A:GLU213 2.9 40.4 1.0
HB2 A:GLU213 3.3 52.1 1.0
CA A:LEU212 3.4 40.9 1.0
HB3 A:GLU213 3.4 52.1 1.0
C A:LEU212 3.6 38.8 1.0
CD1 A:LEU212 3.7 50.4 1.0
CB A:GLU213 3.7 43.4 1.0
HD2 A:TYR211 3.8 65.2 1.0
CA A:GLU213 3.9 40.1 1.0
HD13 A:LEU212 3.9 60.5 1.0
CZ A:ARG253 3.9 70.0 1.0
O A:TYR211 4.0 43.9 1.0
HD11 A:LEU212 4.2 60.5 1.0
N A:LEU212 4.3 47.8 1.0
HH12 A:ARG253 4.3 70.6 1.0
HE2 A:TYR211 4.4 46.9 1.0
HA A:GLU213 4.4 48.2 1.0
CB A:LEU212 4.5 62.7 1.0
C A:TYR211 4.5 55.9 1.0
CG A:LEU212 4.5 54.8 1.0
NH1 A:ARG253 4.6 58.8 1.0
CD2 A:TYR211 4.6 54.4 1.0
HG A:LEU212 4.6 65.8 1.0
HB2 A:LEU212 4.7 75.2 1.0
O A:LEU212 4.8 35.7 1.0
HE A:ARG253 4.8 86.4 1.0
CE2 A:TYR211 4.9 39.1 1.0
H A:LEU212 4.9 57.4 1.0
NE A:ARG253 4.9 72.0 1.0
C A:GLU213 4.9 49.8 1.0
O A:GLU213 5.0 65.2 1.0

Chlorine binding site 3 out of 5 in 5fic

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Chlorine binding site 3 out of 5 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl708

b:50.2
occ:1.00
 HB2 B:ALA293 2.7 86.0 1.0
HH11 B:ARG292 2.7 74.3 1.0
HH12 B:ARG292 2.7 74.3 1.0
O B:ASP289 2.9 70.5 1.0
NH1 B:ARG292 3.0 62.0 1.0
H B:ALA293 3.2 55.2 1.0
HB3 B:ARG292 3.4 76.6 1.0
CB B:ALA293 3.6 71.6 1.0
HZ3 B:TRP207 3.6 63.0 1.0
N B:ALA293 3.7 46.0 1.0
HB3 B:HIS209 3.8 76.9 1.0
C B:ASP289 3.9 70.4 1.0
ND1 B:HIS209 3.9 45.3 1.0
CZ3 B:TRP207 3.9 52.5 1.0
HB3 B:ALA293 3.9 86.0 1.0
HB3 B:ASP289 4.0 83.5 1.0
CA B:ALA293 4.1 53.6 1.0
HA B:ALA293 4.1 64.3 1.0
HA B:ASP289 4.1 90.7 1.0
CZ B:ARG292 4.1 61.0 1.0
HD2 B:ARG292 4.2 85.0 1.0
HE3 B:TRP207 4.2 55.0 1.0
CE3 B:TRP207 4.3 45.8 1.0
HB1 B:ALA293 4.3 86.0 1.0
CB B:ARG292 4.3 63.8 1.0
CG B:HIS209 4.4 60.1 1.0
CA B:ASP289 4.5 75.6 1.0
HA B:GLN290 4.5 85.2 1.0
CB B:HIS209 4.5 64.0 1.0
CE1 B:HIS209 4.6 57.2 1.0
CH2 B:TRP207 4.6 49.1 1.0
C B:ARG292 4.6 60.6 1.0
HB2 B:ARG292 4.7 76.6 1.0
HH2 B:TRP207 4.7 58.9 1.0
HE1 B:HIS209 4.7 68.7 1.0
CB B:ASP289 4.7 69.6 1.0
HH22 B:ARG292 4.7 71.7 1.0
H B:HIS209 4.8 54.9 1.0
H B:ARG292 4.9 62.4 1.0
CD B:ARG292 4.9 70.8 1.0
NH2 B:ARG292 4.9 59.7 1.0
NE B:ARG292 4.9 63.0 1.0
N B:GLN290 4.9 65.4 1.0
CA B:ARG292 4.9 64.2 1.0

Chlorine binding site 4 out of 5 in 5fic

Go back to Chlorine Binding Sites List in 5fic
Chlorine binding site 4 out of 5 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl707

b:44.4
occ:1.00
 HH21 C:ARG253 2.4 83.4 1.0
HA C:LEU212 2.7 46.8 1.0
HD2 C:TYR211 2.9 52.6 1.0
H C:GLU213 2.9 42.5 1.0
NH2 C:ARG253 3.0 69.5 1.0
HH22 C:ARG253 3.2 83.4 1.0
O C:TYR211 3.2 28.9 1.0
HD12 C:LEU212 3.4 50.1 1.0
CA C:LEU212 3.6 39.0 1.0
N C:GLU213 3.6 35.4 1.0
CD2 C:TYR211 3.7 43.9 1.0
C C:TYR211 3.8 33.8 1.0
N C:LEU212 4.0 38.3 1.0
HE2 C:TYR211 4.0 73.1 1.0
C C:LEU212 4.1 36.2 1.0
HE C:ARG253 4.1 90.3 1.0
CZ C:ARG253 4.2 62.5 1.0
HB2 C:GLU213 4.2 65.2 1.0
HB3 C:PRO251 4.3 53.0 1.0
CD1 C:LEU212 4.3 41.8 1.0
CE2 C:TYR211 4.3 60.9 1.0
HB3 C:TYR211 4.4 52.5 1.0
HD13 C:LEU212 4.5 50.1 1.0
NE C:ARG253 4.6 75.3 1.0
HB3 C:GLU213 4.6 65.2 1.0
H C:LEU212 4.7 45.9 1.0
CB C:LEU212 4.7 48.2 1.0
CB C:GLU213 4.7 54.3 1.0
CA C:GLU213 4.8 41.9 1.0
CG C:TYR211 4.8 50.8 1.0
HB2 C:LEU212 4.8 57.9 1.0
HD11 C:LEU212 4.9 50.1 1.0
HB2 C:PRO251 4.9 53.0 1.0
CB C:TYR211 4.9 43.7 1.0

Chlorine binding site 5 out of 5 in 5fic

Go back to Chlorine Binding Sites List in 5fic
Chlorine binding site 5 out of 5 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl710

b:26.6
occ:1.00
 HH22 D:ARG253 1.9 60.5 1.0
H D:GLU213 2.3 55.7 1.0
NH2 D:ARG253 2.8 50.5 1.0
HD12 D:LEU212 2.9 38.2 1.0
HA D:LEU212 3.0 36.3 1.0
N D:GLU213 3.1 46.4 1.0
HB2 D:GLU213 3.1 42.4 1.0
HH21 D:ARG253 3.2 60.5 1.0
HB3 D:GLU213 3.3 42.4 1.0
HH12 D:ARG253 3.3 39.0 1.0
CB D:GLU213 3.6 35.3 1.0
CZ D:ARG253 3.8 37.6 1.0
CA D:LEU212 3.9 30.2 1.0
NH1 D:ARG253 3.9 32.5 1.0
CD1 D:LEU212 3.9 31.8 1.0
CA D:GLU213 3.9 34.8 1.0
C D:LEU212 4.0 31.4 1.0
HD2 D:TYR211 4.0 56.7 1.0
HD13 D:LEU212 4.2 38.2 1.0
HD11 D:LEU212 4.3 38.2 1.0
O D:TYR211 4.3 35.0 1.0
HE2 D:TYR211 4.4 57.4 1.0
HD1 D:PHE241 4.4 44.8 1.0
HE1 D:PHE241 4.5 52.0 1.0
HA D:GLU213 4.5 41.8 1.0
OE2 D:GLU213 4.6 73.3 1.0
HH11 D:ARG253 4.7 39.0 1.0
N D:LEU212 4.7 27.1 1.0
HG D:LEU212 4.8 45.1 1.0
CD2 D:TYR211 4.8 47.3 1.0
CG D:LEU212 4.8 37.6 1.0
CB D:LEU212 4.9 45.8 1.0
C D:TYR211 4.9 26.1 1.0
CD1 D:PHE241 4.9 37.3 1.0
CE1 D:PHE241 4.9 43.3 1.0
HA D:PHE241 5.0 62.5 1.0
CG D:GLU213 5.0 55.1 1.0
CE2 D:TYR211 5.0 47.9 1.0

Reference:

A.Gorelik, K.Illes, L.X.Heinz, G.Superti-Furga, B.Nagar. Crystal Structure of Mammalian Acid Sphingomyelinase. Nat Commun V. 7 12196 2016.
ISSN: ESSN 2041-1723
PubMed: 27435900
DOI: 10.1038/NCOMMS12196
Page generated: Fri Jul 26 07:54:40 2024

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