Atomistry » Zinc » PDB 5e9e-5ehh » 5egh
Atomistry »
  Zinc »
    PDB 5e9e-5ehh »
      5egh »

Zinc in PDB 5egh: Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine

Enzymatic activity of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine

All present enzymatic activity of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine:
3.1.4.38;

Protein crystallography data

The structure of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine, PDB code: 5egh was solved by J.Morita, K.Kano, K.Kato, H.Takita, R.Ishitani, H.Nishimasu, O.Nureki, J.Aoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.63 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.620, 68.849, 69.761, 60.59, 86.99, 68.10
R / Rfree (%) 17.5 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine (pdb code 5egh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine, PDB code: 5egh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5egh

Go back to Zinc Binding Sites List in 5egh
Zinc binding site 1 out of 4 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:26.5
occ:1.00
 NE2 A:HIS354 2.0 21.3 1.0
NE2 A:HIS197 2.1 21.5 1.0
O1 A:PC512 2.1 38.1 1.0
OD2 A:ASP193 2.3 22.8 1.0
OD1 A:ASP193 2.6 21.8 1.0
O3 A:PC512 2.7 27.9 1.0
CG A:ASP193 2.8 19.9 1.0
CD2 A:HIS354 3.0 19.8 1.0
CE1 A:HIS354 3.0 17.8 1.0
CD2 A:HIS197 3.0 21.9 1.0
P1 A:PC512 3.0 33.0 1.0
CE1 A:HIS197 3.1 26.3 1.0
CE1 A:HIS241 4.0 20.8 1.0
O4 A:PC512 4.0 24.1 1.0
ND1 A:HIS354 4.1 18.2 1.0
CG A:HIS354 4.1 20.0 1.0
ZN A:ZN509 4.1 27.1 1.0
O2 A:PC512 4.1 25.2 1.0
ND1 A:HIS197 4.1 22.5 1.0
CG A:HIS197 4.2 22.4 1.0
NE2 A:HIS241 4.2 18.2 1.0
C1 A:PC512 4.3 38.7 1.0
O A:HOH666 4.3 32.8 1.0
CB A:ASP193 4.3 19.2 1.0
CE A:MET243 4.4 16.9 1.0
OD1 A:ASP32 4.5 19.5 1.0

Zinc binding site 2 out of 4 in 5egh

Go back to Zinc Binding Sites List in 5egh
Zinc binding site 2 out of 4 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:27.1
occ:1.00
 O3 A:PC512 2.0 27.9 1.0
OD1 A:ASP32 2.0 19.5 1.0
NE2 A:HIS241 2.1 18.2 1.0
OD2 A:ASP240 2.1 18.9 1.0
OG A:SER71 2.4 33.2 1.0
CG A:ASP32 2.7 19.1 1.0
OD2 A:ASP32 2.9 25.9 1.0
CE1 A:HIS241 3.0 20.8 1.0
CG A:ASP240 3.0 19.9 1.0
CD2 A:HIS241 3.1 17.6 1.0
OD1 A:ASP240 3.2 19.1 1.0
P1 A:PC512 3.4 33.0 1.0
CB A:SER71 3.7 22.3 1.0
O4 A:PC512 3.9 24.1 1.0
OD1 A:ASP193 3.9 21.8 1.0
CA A:SER71 3.9 17.1 1.0
ND1 A:HIS241 4.0 17.9 1.0
CE1 A:HIS354 4.1 17.8 1.0
CG A:HIS241 4.1 14.5 1.0
CB A:ASP32 4.1 17.3 1.0
CG A:ASP193 4.1 19.9 1.0
ZN A:ZN508 4.1 26.5 1.0
N A:GLY33 4.2 17.4 1.0
O2 A:PC512 4.2 25.2 1.0
N A:SER71 4.2 19.3 1.0
OD2 A:ASP193 4.2 22.8 1.0
NE2 A:HIS354 4.2 21.3 1.0
O1 A:PC512 4.3 38.1 1.0
CB A:ASP240 4.4 15.5 1.0
C1 A:PC512 4.4 38.7 1.0
OH A:TYR75 4.5 21.9 1.0
CA A:ASP32 4.5 18.5 1.0
C A:ASP32 4.7 16.0 1.0
CA A:GLY33 4.8 16.9 1.0
CE1 A:TYR75 4.8 18.8 1.0
ND1 A:HIS354 4.9 18.2 1.0
CB A:ASP193 4.9 19.2 1.0
C2 A:PC512 4.9 36.2 1.0
C A:LEU70 4.9 19.1 1.0

Zinc binding site 3 out of 4 in 5egh

Go back to Zinc Binding Sites List in 5egh
Zinc binding site 3 out of 4 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn507

b:31.4
occ:1.00
 OD1 B:ASP32 1.9 23.0 1.0
O4 B:PC510 2.0 31.1 1.0
OD2 B:ASP240 2.1 24.4 1.0
NE2 B:HIS241 2.1 24.2 1.0
OG B:SER71 2.3 36.5 1.0
CG B:ASP32 2.7 24.4 1.0
OD2 B:ASP32 2.8 29.1 1.0
CE1 B:HIS241 2.9 21.9 1.0
CG B:ASP240 3.0 22.5 1.0
CD2 B:HIS241 3.1 20.5 1.0
OD1 B:ASP240 3.1 21.2 1.0
P1 B:PC510 3.4 37.0 1.0
CB B:SER71 3.6 25.4 1.0
O1 B:PC510 3.8 27.3 1.0
CA B:SER71 3.9 22.0 1.0
OD1 B:ASP193 4.0 26.3 1.0
ND1 B:HIS241 4.0 22.5 1.0
CB B:ASP32 4.1 19.1 1.0
CE1 B:HIS354 4.1 27.6 1.0
CG B:HIS241 4.1 21.3 1.0
ZN B:ZN508 4.1 33.3 1.0
O2 B:PC510 4.1 32.2 1.0
N B:SER71 4.1 24.5 1.0
NE2 B:HIS354 4.1 29.2 1.0
N B:GLY33 4.2 24.9 1.0
CG B:ASP193 4.2 27.9 1.0
OD2 B:ASP193 4.3 27.4 1.0
CB B:ASP240 4.4 18.6 1.0
O3 B:PC510 4.4 36.1 1.0
OH B:TYR75 4.4 23.3 1.0
C1 B:PC510 4.5 33.3 1.0
CA B:ASP32 4.5 18.3 1.0
C B:ASP32 4.7 17.8 1.0
CE1 B:TYR75 4.8 23.4 1.0
CA B:GLY33 4.8 20.9 1.0
C B:LEU70 4.9 23.9 1.0
CB B:ASP193 4.9 22.4 1.0
ND1 B:HIS354 4.9 24.1 1.0
CZ B:TYR75 4.9 23.5 1.0

Zinc binding site 4 out of 4 in 5egh

Go back to Zinc Binding Sites List in 5egh
Zinc binding site 4 out of 4 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase in Complex with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn508

b:33.3
occ:1.00
 NE2 B:HIS354 2.1 29.2 1.0
O3 B:PC510 2.1 36.1 1.0
NE2 B:HIS197 2.1 23.1 1.0
OD2 B:ASP193 2.3 27.4 1.0
OD1 B:ASP193 2.5 26.3 1.0
CG B:ASP193 2.7 27.9 1.0
O4 B:PC510 2.7 31.1 1.0
CD2 B:HIS354 2.9 26.4 1.0
P1 B:PC510 3.0 37.0 1.0
CD2 B:HIS197 3.0 25.5 1.0
CE1 B:HIS354 3.2 27.6 1.0
CE1 B:HIS197 3.2 28.7 1.0
O1 B:PC510 3.9 27.3 1.0
CE1 B:HIS241 4.0 21.9 1.0
CG B:HIS354 4.1 27.3 1.0
ZN B:ZN507 4.1 31.4 1.0
O2 B:PC510 4.2 32.2 1.0
CG B:HIS197 4.2 28.1 1.0
ND1 B:HIS354 4.2 24.1 1.0
CB B:ASP193 4.2 22.4 1.0
ND1 B:HIS197 4.2 26.5 1.0
NE2 B:HIS241 4.3 24.2 1.0
C1 B:PC510 4.3 33.3 1.0
O B:HOH683 4.4 42.6 1.0
OD1 B:ASP32 4.4 23.0 1.0
CE B:MET243 4.6 23.9 1.0
O B:ASP193 4.9 24.5 1.0

Reference:

J.Morita, K.Kano, K.Kato, H.Takita, H.Sakagami, Y.Yamamoto, E.Mihara, H.Ueda, T.Sato, H.Tokuyama, H.Arai, H.Asou, J.Takagi, R.Ishitani, H.Nishimasu, O.Nureki, J.Aoki. Structure and Biological Function of ENPP6, A Choline-Specific Glycerophosphodiester-Phosphodiesterase Sci Rep V. 6 20995 2016.
ISSN: ESSN 2045-2322
PubMed: 26888014
DOI: 10.1038/SREP20995
Page generated: Sun Oct 27 15:16:59 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy