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Zinc 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:

Chlorine (Cl) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid, PDB code: 5fic:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5fic

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Zinc binding site 1 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn701

b:37.8
occ:1.00
 OD1 A:ASP204 2.0 23.2 1.0
NE2 A:HIS206 2.0 57.8 1.0
NE2 A:HIS457 2.0 27.7 1.0
OD1 A:ASP276 2.3 30.9 1.0
O2 A:PO4709 2.3 51.8 1.0
CG A:ASP204 2.5 42.4 1.0
HB3 A:ASP204 2.7 37.0 1.0
CE1 A:HIS206 3.0 40.8 1.0
CE1 A:HIS457 3.0 32.9 1.0
CD2 A:HIS457 3.0 40.1 1.0
CD2 A:HIS206 3.0 34.9 1.0
CB A:ASP204 3.1 30.9 1.0
HE1 A:HIS206 3.2 48.9 1.0
OD2 A:ASP204 3.2 46.3 1.0
HD2 A:HIS457 3.2 48.1 1.0
HE1 A:HIS457 3.2 39.5 1.0
HB3 A:ASP276 3.2 54.5 1.0
HD2 A:HIS206 3.2 41.9 1.0
CG A:ASP276 3.3 33.4 1.0
HA A:ASP204 3.5 34.8 1.0
ZN A:ZN702 3.5 45.1 1.0
HA A:HIS455 3.5 41.9 1.0
CB A:ASP276 3.7 45.4 1.0
P A:PO4709 3.7 60.2 1.0
HE1 A:HIS423 3.8 40.7 1.0
HB2 A:ASP276 3.9 54.5 1.0
CA A:ASP204 3.9 29.0 1.0
HB2 A:ASP204 3.9 37.0 1.0
O A:HIS455 4.1 44.0 1.0
ND1 A:HIS206 4.1 29.8 1.0
O4 A:PO4709 4.1 59.8 1.0
ND1 A:HIS457 4.1 25.7 1.0
CG A:HIS206 4.2 31.1 1.0
CG A:HIS457 4.2 30.2 1.0
HE1 A:HIS280 4.2 42.5 1.0
O3 A:PO4709 4.3 46.4 1.0
HD1 A:HIS317 4.4 80.8 1.0
CA A:HIS455 4.4 34.9 1.0
OD2 A:ASP276 4.4 36.2 1.0
HE2 A:HIS280 4.4 60.6 1.0
CE1 A:HIS423 4.5 33.9 1.0
NE2 A:HIS423 4.5 35.2 1.0
C A:HIS455 4.6 36.5 1.0
ND1 A:HIS455 4.6 65.6 1.0
H A:HIS455 4.7 53.2 1.0
O1 A:PO4709 4.7 54.5 1.0
HG21 A:THR484 4.7 37.5 1.0
HB3 A:SER482 4.8 40.0 1.0
C A:ASP204 4.8 29.3 1.0
CE1 A:HIS280 4.8 35.4 1.0
HD1 A:HIS206 4.9 35.8 1.0
HD1 A:HIS457 4.9 30.9 1.0
N A:ASP204 4.9 42.9 1.0
NE2 A:HIS280 4.9 50.5 1.0
H A:ASP204 5.0 51.4 1.0
ND1 A:HIS317 5.0 67.3 1.0

Zinc binding site 2 out of 8 in 5fic

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Zinc binding site 2 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn702

b:45.1
occ:1.00
 NE2 A:HIS423 2.0 35.2 1.0
ND1 A:HIS455 2.1 65.6 1.0
OD1 A:ASN316 2.1 55.8 1.0
OD1 A:ASP276 2.1 30.9 1.0
O2 A:PO4709 2.7 51.8 1.0
CG A:ASP276 2.8 33.4 1.0
HD21 A:ASN316 2.9 63.2 1.0
CE1 A:HIS455 2.9 67.6 1.0
HA A:HIS455 2.9 41.9 1.0
CE1 A:HIS423 3.0 33.9 1.0
CD2 A:HIS423 3.0 40.3 1.0
HE1 A:HIS455 3.0 81.1 1.0
CG A:ASN316 3.0 44.0 1.0
OD2 A:ASP276 3.1 36.2 1.0
CG A:HIS455 3.2 53.5 1.0
HD2 A:HIS423 3.2 48.4 1.0
HE1 A:HIS423 3.2 40.7 1.0
ND2 A:ASN316 3.3 52.7 1.0
HB2 A:HIS455 3.5 52.1 1.0
ZN A:ZN701 3.5 37.8 1.0
OD1 A:ASP204 3.6 23.2 1.0
P A:PO4709 3.6 60.2 1.0
HD1 A:HIS317 3.6 80.8 1.0
O1 A:PO4709 3.6 54.5 1.0
CB A:HIS455 3.6 43.4 1.0
CA A:HIS455 3.7 34.9 1.0
H A:ASN316 3.7 43.8 1.0
O3 A:PO4709 4.0 46.4 1.0
HB2 A:ASP276 4.0 54.5 1.0
CB A:ASP276 4.0 45.4 1.0
NE2 A:HIS455 4.1 51.0 1.0
ND1 A:HIS423 4.1 30.6 1.0
CG A:HIS423 4.1 32.8 1.0
HD22 A:ASN316 4.1 63.2 1.0
CD2 A:HIS455 4.2 51.4 1.0
O A:HIS455 4.3 44.0 1.0
HB3 A:ASP276 4.4 54.5 1.0
ND1 A:HIS317 4.4 67.3 1.0
CB A:ASN316 4.4 42.0 1.0
C A:HIS455 4.5 36.5 1.0
HE1 A:HIS206 4.5 48.9 1.0
CG A:ASP204 4.5 42.4 1.0
H A:HIS317 4.6 73.2 1.0
N A:ASN316 4.6 36.5 1.0
HB3 A:HIS455 4.6 52.1 1.0
HB3 A:ASN316 4.6 50.4 1.0
N A:HIS455 4.7 44.3 1.0
H A:HIS455 4.7 53.2 1.0
OD2 A:ASP204 4.8 46.3 1.0
HG12 A:ILE424 4.8 54.7 1.0
HE2 A:HIS455 4.8 61.1 1.0
HE1 A:HIS317 4.8 71.3 1.0
HD1 A:HIS423 4.9 36.8 1.0
NE2 A:HIS206 4.9 57.8 1.0
O4 A:PO4709 4.9 59.8 1.0

Zinc binding site 3 out of 8 in 5fic

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Zinc binding site 3 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn701

b:56.7
occ:1.00
 OD1 B:ASP204 2.0 39.7 1.0
NE2 B:HIS457 2.0 47.9 1.0
NE2 B:HIS206 2.0 49.3 1.0
OD1 B:ASP276 2.3 71.0 1.0
O1 B:PO4706 2.5 59.3 1.0
CE1 B:HIS206 2.7 58.7 1.0
HE1 B:HIS206 2.8 70.4 1.0
CE1 B:HIS457 2.8 58.4 1.0
HE1 B:HIS457 2.8 70.0 1.0
CG B:ASP204 3.0 40.2 1.0
HD2 B:HIS317 3.1 69.8 1.0
ZN B:ZN702 3.2 42.6 1.0
CD2 B:HIS457 3.2 47.1 1.0
CD2 B:HIS206 3.2 58.1 1.0
HB3 B:ASP204 3.3 51.0 1.0
CG B:ASP276 3.3 69.9 1.0
HB3 B:ASP276 3.4 74.7 1.0
HE1 B:HIS423 3.4 53.7 1.0
HD2 B:HIS457 3.5 56.5 1.0
O4 B:PO4706 3.5 47.0 1.0
HE2 B:HIS280 3.6 64.0 1.0
HD2 B:HIS206 3.6 69.7 1.0
P B:PO4706 3.6 87.8 1.0
CB B:ASP204 3.7 42.5 1.0
HE1 B:HIS280 3.7 60.4 1.0
CB B:ASP276 3.8 62.3 1.0
HA B:HIS455 3.9 49.0 1.0
ND1 B:HIS206 3.9 60.2 1.0
OD2 B:ASP204 4.0 46.8 1.0
CD2 B:HIS317 4.0 58.2 1.0
ND1 B:HIS457 4.0 55.6 1.0
HA B:ASP204 4.0 74.1 1.0
HB2 B:ASP276 4.1 74.7 1.0
NE2 B:HIS280 4.1 53.3 1.0
CE1 B:HIS423 4.2 44.8 1.0
CG B:HIS206 4.2 52.4 1.0
CG B:HIS457 4.2 45.7 1.0
CE1 B:HIS280 4.2 50.3 1.0
OD2 B:ASP276 4.4 57.8 1.0
O B:HIS455 4.4 42.3 1.0
O3 B:PO4706 4.4 74.0 1.0
CA B:ASP204 4.5 61.7 1.0
HB2 B:ASP204 4.5 51.0 1.0
NE2 B:HIS317 4.6 59.4 1.0
NE2 B:HIS423 4.6 40.7 1.0
HD1 B:HIS206 4.7 72.3 1.0
O2 B:PO4706 4.7 51.0 1.0
HD21 B:ASN316 4.7 58.0 1.0
HD1 B:HIS457 4.7 66.7 1.0
CA B:HIS455 4.8 40.8 1.0
ND1 B:HIS455 4.8 51.6 1.0
HG21 B:THR484 4.8 53.3 1.0
OD1 B:ASN316 5.0 46.4 1.0
C B:HIS455 5.0 48.0 1.0

Zinc binding site 4 out of 8 in 5fic

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Zinc binding site 4 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn702

b:42.6
occ:1.00
 OD1 B:ASN316 2.1 46.4 1.0
NE2 B:HIS423 2.1 40.7 1.0
ND1 B:HIS455 2.1 51.6 1.0
OD1 B:ASP276 2.1 71.0 1.0
O4 B:PO4706 2.2 47.0 1.0
HE1 B:HIS423 2.5 53.7 1.0
HD21 B:ASN316 2.6 58.0 1.0
CE1 B:HIS423 2.6 44.8 1.0
CE1 B:HIS455 2.8 62.9 1.0
HE1 B:HIS455 2.8 75.5 1.0
CG B:ASN316 2.9 46.4 1.0
HA B:HIS455 3.0 49.0 1.0
ND2 B:ASN316 3.0 48.3 1.0
CG B:ASP276 3.1 69.9 1.0
ZN B:ZN701 3.2 56.7 1.0
HD2 B:HIS317 3.3 69.8 1.0
CG B:HIS455 3.3 37.2 1.0
CD2 B:HIS423 3.3 48.0 1.0
P B:PO4706 3.3 87.8 1.0
OD2 B:ASP276 3.6 57.8 1.0
OD1 B:ASP204 3.6 39.7 1.0
O1 B:PO4706 3.6 59.3 1.0
HD2 B:HIS423 3.8 57.6 1.0
CA B:HIS455 3.8 40.8 1.0
O3 B:PO4706 3.8 74.0 1.0
HB2 B:HIS455 3.8 50.0 1.0
CD2 B:HIS317 3.8 58.2 1.0
H B:ASN316 3.9 63.8 1.0
CB B:HIS455 3.9 41.7 1.0
HD22 B:ASN316 3.9 58.0 1.0
ND1 B:HIS423 3.9 45.5 1.0
NE2 B:HIS455 4.1 43.4 1.0
O B:HIS455 4.1 42.3 1.0
CG B:HIS423 4.2 50.4 1.0
HB2 B:ASP276 4.3 74.7 1.0
CB B:ASP276 4.3 62.3 1.0
H B:HIS317 4.3 78.6 1.0
NE2 B:HIS317 4.3 59.4 1.0
CD2 B:HIS455 4.3 42.8 1.0
CB B:ASN316 4.3 45.7 1.0
HE1 B:HIS206 4.3 70.4 1.0
C B:HIS455 4.5 48.0 1.0
NE2 B:HIS457 4.5 47.9 1.0
HB3 B:ASN316 4.6 54.8 1.0
HD1 B:HIS423 4.6 54.5 1.0
HB3 B:ASP276 4.6 74.7 1.0
O2 B:PO4706 4.6 51.0 1.0
HG12 B:ILE424 4.7 70.9 1.0
N B:ASN316 4.7 53.2 1.0
CG B:ASP204 4.7 40.2 1.0
HE2 B:HIS455 4.8 52.0 1.0
HB3 B:HIS455 4.8 50.0 1.0
NE2 B:HIS206 4.8 49.3 1.0
CG B:HIS317 4.8 54.7 1.0
H B:HIS455 4.9 45.4 1.0
HB2 B:ASN316 4.9 54.8 1.0
N B:HIS455 4.9 37.8 1.0
CE1 B:HIS206 4.9 58.7 1.0
N B:HIS317 5.0 65.5 1.0

Zinc binding site 5 out of 8 in 5fic

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Zinc binding site 5 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
C:Zn701

b:26.3
occ:1.00
 O4 C:PO4706 1.9 25.0 1.0
OD1 C:ASP204 2.0 30.2 1.0
NE2 C:HIS457 2.0 25.4 1.0
NE2 C:HIS206 2.1 51.2 1.0
OD1 C:ASP276 2.3 33.9 1.0
HB3 C:ASP204 2.9 46.2 1.0
CG C:ASP204 3.0 29.5 1.0
CE1 C:HIS457 3.0 33.7 1.0
CD2 C:HIS457 3.0 28.4 1.0
CE1 C:HIS206 3.0 27.7 1.0
CD2 C:HIS206 3.1 48.5 1.0
P C:PO4706 3.2 40.2 1.0
HE1 C:HIS457 3.2 40.4 1.0
HE1 C:HIS206 3.2 33.2 1.0
HD2 C:HIS457 3.2 34.1 1.0
HD2 C:HIS206 3.3 58.2 1.0
CG C:ASP276 3.4 41.5 1.0
CB C:ASP204 3.4 38.5 1.0
O1 C:PO4706 3.5 32.6 1.0
HB3 C:ASP276 3.5 42.7 1.0
ZN C:ZN702 3.5 44.0 1.0
HD2 C:HIS317 3.7 41.0 1.0
O2 C:PO4706 3.8 39.7 1.0
HE2 C:HIS280 3.8 39.8 1.0
HA C:HIS455 3.8 29.4 1.0
CB C:ASP276 3.9 35.6 1.0
O C:HIS455 3.9 20.4 1.0
OD2 C:ASP204 4.0 34.4 1.0
HA C:ASP204 4.0 37.3 1.0
HE1 C:HIS423 4.0 32.0 1.0
ND1 C:HIS457 4.1 37.9 1.0
HB2 C:ASP276 4.1 42.7 1.0
HE1 C:HIS280 4.1 43.7 1.0
CG C:HIS457 4.1 27.3 1.0
ND1 C:HIS206 4.1 27.6 1.0
HB2 C:ASP204 4.2 46.2 1.0
CG C:HIS206 4.2 31.0 1.0
CA C:ASP204 4.4 31.1 1.0
O3 C:PO4706 4.4 32.9 1.0
NE2 C:HIS280 4.4 33.2 1.0
OD2 C:ASP276 4.4 24.9 1.0
CD2 C:HIS317 4.5 34.1 1.0
CE1 C:HIS280 4.5 36.4 1.0
NE2 C:HIS423 4.5 23.4 1.0
C C:HIS455 4.6 22.5 1.0
CA C:HIS455 4.6 24.5 1.0
CE1 C:HIS423 4.6 26.7 1.0
HG21 C:THR484 4.6 36.1 1.0
HD1 C:HIS457 4.8 45.5 1.0
NE2 C:HIS317 4.9 42.5 1.0
HD1 C:HIS206 4.9 33.2 1.0
ND1 C:HIS455 4.9 34.7 1.0
H C:HIS455 5.0 24.7 1.0
HB3 C:SER482 5.0 61.5 1.0

Zinc binding site 6 out of 8 in 5fic

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Zinc binding site 6 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:44.0
occ:1.00
 O1 C:PO4706 2.0 32.6 1.0
NE2 C:HIS423 2.0 23.4 1.0
ND1 C:HIS455 2.1 34.7 1.0
OD1 C:ASN316 2.1 53.0 1.0
OD1 C:ASP276 2.1 33.9 1.0
CG C:ASP276 2.7 41.5 1.0
CE1 C:HIS455 2.8 41.2 1.0
HE1 C:HIS455 2.8 49.5 1.0
HA C:HIS455 2.9 29.4 1.0
CD2 C:HIS423 3.0 22.4 1.0
OD2 C:ASP276 3.0 24.9 1.0
HD2 C:HIS423 3.1 26.9 1.0
HD21 C:ASN316 3.1 48.1 1.0
CE1 C:HIS423 3.1 26.7 1.0
CG C:ASN316 3.1 33.0 1.0
P C:PO4706 3.2 40.2 1.0
CG C:HIS455 3.3 31.0 1.0
HE1 C:HIS423 3.3 32.0 1.0
OD1 C:ASP204 3.4 30.2 1.0
HD2 C:HIS317 3.4 41.0 1.0
ND2 C:ASN316 3.5 40.1 1.0
ZN C:ZN701 3.5 26.3 1.0
O2 C:PO4706 3.6 39.7 1.0
O4 C:PO4706 3.6 25.0 1.0
H C:ASN316 3.7 50.7 1.0
CA C:HIS455 3.7 24.5 1.0
CB C:HIS455 3.8 40.4 1.0
HB2 C:HIS455 3.9 48.4 1.0
HB2 C:ASP276 4.0 42.7 1.0
NE2 C:HIS455 4.0 39.3 1.0
CB C:ASP276 4.0 35.6 1.0
O C:HIS455 4.1 20.4 1.0
CG C:HIS423 4.1 22.5 1.0
ND1 C:HIS423 4.2 25.9 1.0
CD2 C:HIS317 4.2 34.1 1.0
CD2 C:HIS455 4.2 26.5 1.0
HD22 C:ASN316 4.3 48.1 1.0
C C:HIS455 4.4 22.5 1.0
H C:HIS317 4.4 65.7 1.0
HB3 C:ASP276 4.4 42.7 1.0
O3 C:PO4706 4.4 32.9 1.0
CB C:ASN316 4.5 26.8 1.0
HE1 C:HIS206 4.5 33.2 1.0
N C:ASN316 4.5 42.3 1.0
CG C:ASP204 4.5 29.5 1.0
HB3 C:ASN316 4.6 32.1 1.0
HE2 C:HIS455 4.7 47.2 1.0
HG12 C:ILE424 4.8 51.3 1.0
HB3 C:HIS455 4.8 48.4 1.0
H C:HIS455 4.8 24.7 1.0
N C:HIS455 4.8 20.6 1.0
NE2 C:HIS317 4.9 42.5 1.0
NE2 C:HIS206 4.9 51.2 1.0
OD2 C:ASP204 4.9 34.4 1.0
HD1 C:HIS423 5.0 31.1 1.0

Zinc binding site 7 out of 8 in 5fic

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Zinc binding site 7 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:42.1
occ:1.00
 OD1 D:ASP204 2.0 47.8 1.0
NE2 D:HIS206 2.1 68.7 1.0
NE2 D:HIS457 2.1 45.5 1.0
O2 D:PO4709 2.1 45.5 1.0
OD1 D:ASP276 2.3 69.5 1.0
O1 D:PO4709 2.4 56.3 1.0
HE1 D:HIS457 2.7 48.8 1.0
CE1 D:HIS457 2.7 40.7 1.0
P D:PO4709 2.8 50.0 1.0
CE1 D:HIS206 3.0 46.0 1.0
HE1 D:HIS206 3.1 55.2 1.0
HB3 D:ASP204 3.1 58.0 1.0
CG D:ASP204 3.1 56.7 1.0
CD2 D:HIS206 3.2 48.8 1.0
HB3 D:ASP276 3.2 69.0 1.0
CG D:ASP276 3.3 47.9 1.0
HD2 D:HIS317 3.4 55.7 1.0
CD2 D:HIS457 3.4 53.6 1.0
HD2 D:HIS206 3.4 58.5 1.0
ZN D:ZN702 3.5 35.8 1.0
CB D:ASP204 3.6 48.3 1.0
CB D:ASP276 3.7 57.5 1.0
HE1 D:HIS423 3.7 47.1 1.0
O4 D:PO4709 3.7 36.2 1.0
HD2 D:HIS457 3.8 64.4 1.0
HA D:HIS455 3.9 39.2 1.0
O3 D:PO4709 3.9 56.9 1.0
HB2 D:ASP276 4.0 69.0 1.0
HE2 D:HIS280 4.0 67.4 1.0
ND1 D:HIS457 4.0 37.4 1.0
CD2 D:HIS317 4.0 46.4 1.0
HA D:ASP204 4.0 53.5 1.0
HE1 D:HIS280 4.1 66.5 1.0
ND1 D:HIS206 4.1 55.3 1.0
OD2 D:ASP204 4.2 48.9 1.0
NE2 D:HIS423 4.3 34.0 1.0
CG D:HIS206 4.3 45.4 1.0
CE1 D:HIS423 4.3 39.3 1.0
CG D:HIS457 4.3 39.9 1.0
OD2 D:ASP276 4.4 33.2 1.0
O D:HIS455 4.4 38.9 1.0
NE2 D:HIS317 4.4 51.0 1.0
HB2 D:ASP204 4.4 58.0 1.0
CA D:ASP204 4.4 44.6 1.0
NE2 D:HIS280 4.5 56.2 1.0
CE1 D:HIS280 4.6 55.4 1.0
HD1 D:HIS457 4.7 44.9 1.0
CA D:HIS455 4.8 32.6 1.0
HG21 D:THR484 4.9 52.0 1.0
HD1 D:HIS206 4.9 66.4 1.0
ND1 D:HIS455 5.0 57.1 1.0
C D:HIS455 5.0 30.4 1.0

Zinc binding site 8 out of 8 in 5fic

Go back to Zinc Binding Sites List in 5fic
Zinc binding site 8 out of 8 in the Open Form of Murine Acid Sphingomyelinase in Presence of Lipid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Open Form of Murine Acid Sphingomyelinase in Presence of Lipid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn702

b:35.8
occ:1.00
 NE2 D:HIS423 2.0 34.0 1.0
ND1 D:HIS455 2.1 57.1 1.0
OD1 D:ASN316 2.1 44.2 1.0
OD1 D:ASP276 2.2 69.5 1.0
O2 D:PO4709 2.3 45.5 1.0
O4 D:PO4709 2.5 36.2 1.0
CD2 D:HIS423 2.8 34.6 1.0
P D:PO4709 2.9 50.0 1.0
CE1 D:HIS455 2.9 51.7 1.0
HD2 D:HIS423 2.9 41.5 1.0
HE1 D:HIS455 3.0 62.0 1.0
HA D:HIS455 3.0 39.2 1.0
CE1 D:HIS423 3.1 39.3 1.0
CG D:ASN316 3.1 37.5 1.0
HD21 D:ASN316 3.1 47.1 1.0
CG D:ASP276 3.1 47.9 1.0
CG D:HIS455 3.2 31.1 1.0
HD2 D:HIS317 3.3 55.7 1.0
HE1 D:HIS423 3.4 47.1 1.0
ND2 D:ASN316 3.5 39.2 1.0
HB2 D:HIS455 3.5 52.4 1.0
OD2 D:ASP276 3.5 33.2 1.0
ZN D:ZN701 3.5 42.1 1.0
H D:ASN316 3.7 51.6 1.0
CB D:HIS455 3.7 43.6 1.0
CA D:HIS455 3.8 32.6 1.0
OD1 D:ASP204 3.8 47.8 1.0
O1 D:PO4709 3.9 56.3 1.0
O3 D:PO4709 3.9 56.9 1.0
CD2 D:HIS317 4.0 46.4 1.0
CG D:HIS423 4.0 32.4 1.0
NE2 D:HIS455 4.1 47.6 1.0
ND1 D:HIS423 4.1 33.5 1.0
HG12 D:ILE424 4.2 37.1 1.0
CD2 D:HIS455 4.3 25.5 1.0
O D:HIS455 4.3 38.9 1.0
HD22 D:ASN316 4.3 47.1 1.0
CB D:ASP276 4.4 57.5 1.0
HB2 D:ASP276 4.4 69.0 1.0
CB D:ASN316 4.5 37.2 1.0
N D:ASN316 4.5 43.0 1.0
C D:HIS455 4.6 30.4 1.0
NE2 D:HIS317 4.6 51.0 1.0
HG13 D:ILE424 4.6 37.1 1.0
H D:HIS317 4.6 61.7 1.0
HB3 D:ASN316 4.6 44.6 1.0
HB3 D:HIS455 4.6 52.4 1.0
HB3 D:ASP276 4.7 69.0 1.0
CG1 D:ILE424 4.8 30.9 1.0
N D:HIS455 4.8 31.2 1.0
H D:HIS455 4.8 37.4 1.0
HD11 D:ILE424 4.8 37.6 1.0
HE2 D:HIS455 4.8 57.1 1.0
NE2 D:HIS457 4.8 45.5 1.0
CG D:ASP204 4.9 56.7 1.0
HD1 D:HIS423 4.9 40.2 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: Thu Aug 21 02:26:27 2025

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