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Zinc in PDB 5kas: Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine

Protein crystallography data

The structure of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine, PDB code: 5kas 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) 31.99 / 1.62
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.892, 47.031, 93.861, 90.00, 98.07, 90.00
R / Rfree (%) 16.9 / 19.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine (pdb code 5kas). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine, PDB code: 5kas:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5kas

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Zinc binding site 1 out of 5 in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:18.3
occ:1.00
OD1 A:ASN134 2.0 23.7 1.0
O A:HOH604 2.0 33.9 1.0
NE2 A:HIS236 2.1 16.6 1.0
ND1 A:HIS277 2.1 16.3 1.0
O4 A:PC517 2.1 24.6 1.0
OD2 A:ASP93 2.2 19.6 1.0
CE1 A:HIS277 2.9 17.8 1.0
HE1 A:HIS277 2.9 21.4 1.0
HA A:HIS277 3.0 16.9 1.0
CG A:ASP93 3.0 18.3 1.0
CD2 A:HIS236 3.0 14.6 1.0
CE1 A:HIS236 3.1 18.3 1.0
CG A:ASN134 3.1 20.2 1.0
HD2 A:HIS236 3.2 17.5 1.0
P1 A:PC517 3.2 25.5 1.0
CG A:HIS277 3.3 14.2 1.0
HE1 A:HIS236 3.3 22.0 1.0
HD21 A:ASN134 3.3 24.3 1.0
OD1 A:ASP93 3.3 21.9 1.0
HD2 A:HIS135 3.5 27.6 1.0
O1 A:PC517 3.6 26.7 1.0
H A:ASN134 3.6 21.8 1.0
ND2 A:ASN134 3.6 20.3 1.0
ZN A:ZN502 3.6 19.1 1.0
O2 A:PC517 3.7 30.9 1.0
HB2 A:HIS277 3.7 16.4 1.0
CB A:HIS277 3.8 13.7 1.0
CA A:HIS277 3.8 14.1 1.0
OD1 A:ASP28 4.0 19.4 1.0
NE2 A:HIS277 4.1 21.4 1.0
ND1 A:HIS236 4.2 16.1 1.0
CG A:HIS236 4.2 13.6 1.0
HG22 A:VAL237 4.2 23.2 1.0
O A:HIS277 4.2 22.1 1.0
H11 A:PC517 4.3 45.8 1.0
CD2 A:HIS277 4.3 19.9 1.0
CB A:ASP93 4.3 20.1 1.0
HB2 A:ASP93 4.3 24.1 1.0
N A:ASN134 4.4 18.1 1.0
CB A:ASN134 4.4 18.1 1.0
CD2 A:HIS135 4.4 23.0 1.0
HD22 A:ASN134 4.5 24.3 1.0
O3 A:PC517 4.5 41.9 1.0
H A:HIS135 4.5 24.0 1.0
C1 A:PC517 4.5 38.1 1.0
C A:HIS277 4.5 21.4 1.0
HB3 A:ASN134 4.6 21.7 1.0
HE1 A:HIS30 4.7 20.2 1.0
HB3 A:ASP93 4.7 24.1 1.0
HB3 A:HIS277 4.7 16.4 1.0
HE2 A:HIS277 4.8 25.7 1.0
H A:HIS277 4.8 22.8 1.0
N A:HIS277 4.8 19.0 1.0
HA3 A:GLY133 4.9 19.9 1.0
HD1 A:HIS236 4.9 19.3 1.0
CA A:ASN134 4.9 17.2 1.0
HG23 A:VAL237 5.0 23.2 1.0

Zinc binding site 2 out of 5 in 5kas

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Zinc binding site 2 out of 5 in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:19.1
occ:1.00
O A:HOH604 1.9 33.9 1.0
OD1 A:ASP28 2.0 19.4 1.0
NE2 A:HIS30 2.0 13.9 1.0
NE2 A:HIS279 2.1 16.5 1.0
O1 A:PC517 2.1 26.7 1.0
OD2 A:ASP93 2.3 19.6 1.0
CE1 A:HIS30 3.0 16.9 1.0
CE1 A:HIS279 3.0 20.0 1.0
CG A:ASP28 3.1 19.2 1.0
CD2 A:HIS30 3.1 16.8 1.0
HB3 A:ASP93 3.1 24.1 1.0
HE1 A:HIS279 3.1 24.0 1.0
HE1 A:HIS30 3.1 20.2 1.0
CD2 A:HIS279 3.1 17.6 1.0
HB3 A:ASP28 3.1 20.4 1.0
CG A:ASP93 3.3 18.3 1.0
P1 A:PC517 3.3 25.5 1.0
HD2 A:HIS30 3.3 20.2 1.0
HD2 A:HIS279 3.3 21.1 1.0
CB A:ASP93 3.6 20.1 1.0
CB A:ASP28 3.6 17.0 1.0
ZN A:ZN501 3.6 18.3 1.0
HE1 A:HIS236 3.6 22.0 1.0
HA A:HIS277 3.7 16.9 1.0
HB2 A:ASP93 3.7 24.1 1.0
O2 A:PC517 3.7 30.9 1.0
O4 A:PC517 3.8 24.6 1.0
HA A:ASP28 4.0 19.9 1.0
HE1 A:HIS97 4.1 30.2 1.0
O A:HIS277 4.1 22.1 1.0
ND1 A:HIS30 4.1 16.4 1.0
ND1 A:HIS279 4.1 20.0 1.0
OD2 A:ASP28 4.1 17.6 1.0
CG A:HIS30 4.2 16.1 1.0
CG A:HIS279 4.2 19.0 1.0
HD2 A:HIS135 4.3 27.6 1.0
CE1 A:HIS236 4.3 18.3 1.0
NE2 A:HIS97 4.3 19.7 1.0
OD1 A:ASP93 4.4 21.9 1.0
CA A:ASP28 4.4 16.6 1.0
HB2 A:ASP28 4.4 20.4 1.0
NE2 A:HIS236 4.5 16.6 1.0
O3 A:PC517 4.5 41.9 1.0
CA A:HIS277 4.5 14.1 1.0
CE1 A:HIS97 4.6 25.1 1.0
C A:HIS277 4.7 21.4 1.0
H53 A:PC517 4.7 56.5 1.0
H A:HIS277 4.7 22.8 1.0
HG21 A:THR304 4.8 19.4 1.0
HD1 A:HIS30 4.9 19.7 1.0
HD1 A:HIS279 4.9 24.0 1.0
ND1 A:HIS277 4.9 16.3 1.0
CD2 A:HIS135 4.9 23.0 1.0

Zinc binding site 3 out of 5 in 5kas

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Zinc binding site 3 out of 5 in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:22.1
occ:0.24
O3 A:PC517 1.8 41.9 1.0
NE2 A:HIS135 2.1 27.2 1.0
O A:HOH897 2.1 33.5 1.0
O A:HOH917 2.3 42.4 1.0
CE1 A:HIS135 2.9 24.6 1.0
HD2 A:HIS97 2.9 26.8 1.0
HE1 A:HIS135 3.0 29.5 1.0
P1 A:PC517 3.1 25.5 1.0
CD2 A:HIS135 3.2 23.0 1.0
HD21 A:ASN134 3.2 24.3 1.0
O4 A:PC517 3.3 24.6 1.0
HD2 A:HIS135 3.4 27.6 1.0
CD2 A:HIS97 3.7 22.3 1.0
HZ2 A:LYS140 3.8 77.6 1.0
H12 A:PC517 3.8 45.8 1.0
ND2 A:ASN134 3.9 20.3 1.0
O1 A:PC517 4.0 26.7 1.0
NE2 A:HIS97 4.0 19.7 1.0
HD22 A:ASN134 4.0 24.3 1.0
ND1 A:HIS135 4.1 27.1 1.0
O2 A:PC517 4.2 30.9 1.0
CG A:HIS135 4.2 22.4 1.0
HZ3 A:LYS140 4.3 77.6 1.0
HD2 A:LYS140 4.3 51.4 1.0
C1 A:PC517 4.3 38.1 1.0
H11 A:PC517 4.4 45.8 1.0
NZ A:LYS140 4.4 64.7 1.0
HH A:TYR198 4.5 67.0 1.0
HE1 A:HIS277 4.6 21.4 1.0
O A:HOH886 4.6 44.9 1.0
HD21 A:ASN141 4.7 40.9 1.0
HD1 A:HIS135 4.8 32.6 1.0
O A:HOH975 4.9 47.1 1.0
CG A:HIS97 4.9 22.8 1.0
HZ1 A:LYS140 5.0 77.6 1.0
H43 A:PC517 5.0 80.4 1.0

Zinc binding site 4 out of 5 in 5kas

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Zinc binding site 4 out of 5 in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:31.4
occ:0.16
OE2 A:GLU356 2.2 36.7 1.0
OE1 A:GLU356 2.3 44.7 1.0
CD A:GLU356 2.6 39.2 1.0
O A:HOH805 2.6 42.9 1.0
O A:HOH830 3.4 49.1 1.0
HD22 A:ASN343 4.0 38.3 1.0
HZ A:PHE341 4.0 25.5 1.0
CG A:GLU356 4.1 34.9 1.0
HB2 A:ASN343 4.4 27.3 1.0
HG2 A:GLU356 4.4 41.8 1.0
HG3 A:GLU356 4.5 41.8 1.0
CZ A:PHE341 4.6 21.3 1.0
HB3 A:GLU356 4.8 30.0 1.0
HB3 A:ASN343 4.8 27.3 1.0
O A:HOH820 4.8 29.2 1.0
ND2 A:ASN343 4.8 31.9 1.0
HE1 A:PHE341 4.9 28.6 1.0
CB A:GLU356 4.9 25.0 1.0
HB2 A:GLU356 4.9 30.0 1.0
CB A:ASN343 5.0 22.7 1.0

Zinc binding site 5 out of 5 in 5kas

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Zinc binding site 5 out of 5 in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:40.9
occ:0.36
NE2 A:HIS267 2.1 26.0 1.0
HH22 A:ARG268 2.2 71.2 1.0
O A:HOH658 2.4 42.2 1.0
HH12 A:ARG268 2.6 55.2 1.0
NH2 A:ARG268 2.6 59.3 1.0
O A:HOH686 2.8 42.6 1.0
NH1 A:ARG268 3.0 46.0 1.0
CE1 A:HIS267 3.0 28.2 1.0
CZ A:ARG268 3.0 54.9 1.0
CD2 A:HIS267 3.1 30.3 1.0
HH21 A:ARG268 3.2 71.2 1.0
HE1 A:HIS267 3.2 33.9 1.0
HD2 A:HIS267 3.3 36.4 1.0
HH11 A:ARG268 3.7 55.2 1.0
O A:GLN264 4.1 25.1 1.0
O A:HOH931 4.1 39.1 1.0
NE A:ARG268 4.2 53.5 1.0
ND1 A:HIS267 4.2 24.6 1.0
OD2 A:ASP288 4.2 32.1 1.0
HG21 A:ILE294 4.2 26.2 1.0
CG A:HIS267 4.2 24.5 1.0
HG3 A:ARG268 4.4 46.4 1.0
HB3 A:ASP288 4.4 32.1 1.0
HE A:ARG268 4.5 64.2 1.0
HG22 A:ILE294 4.7 26.2 1.0
HB2 A:ASP288 4.7 32.1 1.0
O A:HOH633 4.8 32.2 1.0
CG2 A:ILE294 4.9 21.9 1.0
HD1 A:HIS267 4.9 29.5 1.0
CB A:ASP288 4.9 26.7 1.0

Reference:

A.Gorelik, L.X.Heinz, K.Illes, G.Superti-Furga, B.Nagar. Crystal Structure of the Acid Sphingomyelinase-Like Phosphodiesterase SMPDL3B Provides Insights Into Determinants of Substrate Specificity. J.Biol.Chem. V. 291 24054 2016.
ISSN: ESSN 1083-351X
PubMed: 27687724
DOI: 10.1074/JBC.M116.755801
Page generated: Wed Dec 16 06:26:39 2020

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