Atomistry » Zinc » PDB 5e8c-5ehe » 5ege
Atomistry »
  Zinc »
    PDB 5e8c-5ehe »
      5ege »

Zinc in PDB 5ege: Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase

Enzymatic activity of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase

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

Protein crystallography data

The structure of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase, PDB code: 5ege 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) 41.90 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.290, 78.240, 103.640, 90.04, 89.98, 114.61
R / Rfree (%) 16.7 / 20.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase (pdb code 5ege). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase, PDB code: 5ege:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 1 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:23.8
occ:1.00
 O A:HOH910 1.9 21.4 1.0
NE2 A:HIS197 2.0 13.2 1.0
NE2 A:HIS354 2.1 15.3 1.0
OD2 A:ASP193 2.2 20.0 1.0
O A:HOH610 2.3 23.4 1.0
OD1 A:ASP193 2.6 17.0 1.0
CG A:ASP193 2.7 14.7 1.0
CD2 A:HIS197 3.0 11.8 1.0
CE1 A:HIS197 3.1 12.2 1.0
CD2 A:HIS354 3.1 12.0 1.0
CE1 A:HIS354 3.1 14.9 1.0
O A:HOH1017 3.5 29.0 1.0
O A:HOH655 3.9 15.1 1.0
CE1 A:HIS241 4.0 15.4 1.0
CG A:HIS197 4.1 17.5 1.0
ND1 A:HIS197 4.1 14.7 1.0
O A:HOH928 4.2 30.7 1.0
CB A:ASP193 4.2 13.7 1.0
ND1 A:HIS354 4.2 11.3 1.0
CG A:HIS354 4.2 13.3 1.0
NE2 A:HIS241 4.2 14.1 1.0
ZN A:ZN509 4.4 32.6 1.0
O A:HOH621 4.4 17.8 1.0
OD1 A:ASP32 4.4 16.6 1.0
CE A:MET243 4.5 12.3 1.0
OG A:SER71 4.5 17.6 1.0
O A:ASP193 4.9 11.5 1.0
O1 A:EDO511 5.0 34.9 1.0

Zinc binding site 2 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 2 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:32.6
occ:1.00
 OG A:SER71 2.1 17.6 1.0
OD2 A:ASP240 2.1 11.2 1.0
OD1 A:ASP32 2.1 16.6 1.0
NE2 A:HIS241 2.3 14.1 1.0
OD2 A:ASP32 2.4 19.1 1.0
O A:HOH610 2.5 23.4 1.0
CG A:ASP32 2.5 16.6 1.0
CG A:ASP240 3.0 12.8 1.0
CB A:SER71 3.1 15.8 1.0
CD2 A:HIS241 3.2 12.0 1.0
CE1 A:HIS241 3.2 15.4 1.0
OD1 A:ASP240 3.2 9.4 1.0
CA A:SER71 3.6 14.5 1.0
O A:HOH928 4.0 30.7 1.0
CB A:ASP32 4.0 14.2 1.0
N A:SER71 4.1 10.6 1.0
O A:HOH655 4.1 15.1 1.0
OD1 A:ASP193 4.2 17.0 1.0
CE1 A:HIS354 4.2 14.9 1.0
OH A:TYR75 4.2 13.6 1.0
ND1 A:HIS241 4.2 11.4 1.0
CG A:HIS241 4.3 10.8 1.0
N A:GLY33 4.3 10.3 1.0
CB A:ASP240 4.4 14.4 1.0
ZN A:ZN508 4.4 23.8 1.0
NE2 A:HIS354 4.4 15.3 1.0
CG A:ASP193 4.4 14.7 1.0
CE1 A:TYR75 4.4 16.8 1.0
OD2 A:ASP193 4.4 20.0 1.0
CA A:ASP32 4.6 13.4 1.0
O A:HOH910 4.6 21.4 1.0
CZ A:TYR75 4.7 15.0 1.0
C A:ASP32 4.8 13.9 1.0
C A:SER71 4.9 11.5 1.0
C A:LEU70 4.9 12.2 1.0

Zinc binding site 3 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 3 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn508

b:22.6
occ:1.00
 O B:HOH975 2.0 24.7 1.0
NE2 B:HIS197 2.0 13.7 1.0
NE2 B:HIS354 2.1 13.4 1.0
OD2 B:ASP193 2.2 18.9 1.0
O B:HOH631 2.3 24.1 1.0
OD1 B:ASP193 2.6 13.2 1.0
CG B:ASP193 2.8 14.2 1.0
CD2 B:HIS197 3.0 13.1 1.0
CD2 B:HIS354 3.0 13.0 1.0
CE1 B:HIS197 3.1 11.9 1.0
CE1 B:HIS354 3.2 14.9 1.0
O B:HOH657 3.6 16.9 1.0
CE1 B:HIS241 4.0 15.7 1.0
ND1 B:HIS197 4.1 15.1 1.0
CG B:HIS197 4.2 13.2 1.0
NE2 B:HIS241 4.2 14.5 1.0
CG B:HIS354 4.2 12.8 1.0
ND1 B:HIS354 4.2 12.9 1.0
CB B:ASP193 4.3 12.1 1.0
O B:HOH636 4.3 18.8 1.0
O B:HOH944 4.4 27.0 1.0
ZN B:ZN509 4.4 29.1 1.0
OD1 B:ASP32 4.4 12.2 1.0
CE B:MET243 4.4 12.5 1.0
OG B:SER71 4.5 19.2 1.0
O B:ASP193 4.9 12.2 1.0

Zinc binding site 4 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 4 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn509

b:29.1
occ:1.00
 OD2 B:ASP240 2.0 11.2 1.0
OD1 B:ASP32 2.1 12.2 1.0
OG B:SER71 2.2 19.2 1.0
NE2 B:HIS241 2.2 14.5 1.0
O B:HOH631 2.3 24.1 1.0
OD2 B:ASP32 2.5 20.0 1.0
CG B:ASP32 2.6 15.7 1.0
CG B:ASP240 2.9 13.0 1.0
CD2 B:HIS241 3.1 11.6 1.0
OD1 B:ASP240 3.1 10.6 1.0
CE1 B:HIS241 3.2 15.7 1.0
CB B:SER71 3.2 15.2 1.0
CA B:SER71 3.6 14.7 1.0
CB B:ASP32 4.0 14.3 1.0
O B:HOH657 4.0 16.9 1.0
N B:SER71 4.2 12.1 1.0
O B:HOH944 4.2 27.0 1.0
OD1 B:ASP193 4.2 13.2 1.0
CG B:HIS241 4.2 11.7 1.0
N B:GLY33 4.2 11.8 1.0
CE1 B:HIS354 4.2 14.9 1.0
ND1 B:HIS241 4.3 11.4 1.0
CB B:ASP240 4.3 12.4 1.0
OH B:TYR75 4.3 11.6 1.0
NE2 B:HIS354 4.3 13.4 1.0
ZN B:ZN508 4.4 22.6 1.0
CG B:ASP193 4.4 14.2 1.0
CE1 B:TYR75 4.4 14.4 1.0
OD2 B:ASP193 4.5 18.9 1.0
CA B:ASP32 4.5 15.2 1.0
O B:HOH975 4.6 24.7 1.0
CZ B:TYR75 4.7 11.7 1.0
C B:ASP32 4.8 15.2 1.0
C B:SER71 4.9 11.7 1.0
C B:LEU70 4.9 13.3 1.0
CA B:GLY33 5.0 12.9 1.0
OH B:TYR188 5.0 14.8 1.0

Zinc binding site 5 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 5 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn508

b:29.4
occ:1.00
 NE2 C:HIS354 2.0 23.8 1.0
NE2 C:HIS197 2.1 20.6 1.0
OD1 C:ASP193 2.4 22.3 1.0
OD2 C:ASP193 2.4 24.4 1.0
O C:HOH640 2.4 40.7 1.0
O C:HOH961 2.5 31.5 1.0
CG C:ASP193 2.7 22.0 1.0
CE1 C:HIS354 2.9 17.9 1.0
CD2 C:HIS354 3.0 16.3 1.0
CD2 C:HIS197 3.1 16.8 1.0
CE1 C:HIS197 3.1 20.2 1.0
O C:HOH957 3.2 32.9 1.0
O C:HOH744 3.7 14.5 1.0
O C:HOH616 3.9 24.2 1.0
CE1 C:HIS241 4.0 16.9 1.0
ND1 C:HIS354 4.0 15.3 1.0
CG C:HIS354 4.1 15.9 1.0
ND1 C:HIS197 4.2 21.9 1.0
CG C:HIS197 4.2 21.2 1.0
CB C:ASP193 4.2 19.6 1.0
NE2 C:HIS241 4.3 18.0 1.0
ZN C:ZN509 4.4 33.6 1.0
OD1 C:ASP32 4.4 15.9 1.0
OG C:SER71 4.5 17.2 1.0
CE C:MET243 4.5 20.4 1.0
O C:ASP193 4.9 19.7 1.0

Zinc binding site 6 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 6 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn509

b:33.6
occ:1.00
 OD2 C:ASP240 2.1 15.6 1.0
OG C:SER71 2.1 17.2 1.0
NE2 C:HIS241 2.1 18.0 1.0
OD1 C:ASP32 2.1 15.9 1.0
OD2 C:ASP32 2.5 21.9 1.0
CG C:ASP32 2.6 19.1 1.0
O C:HOH640 2.8 40.7 1.0
CG C:ASP240 2.9 13.6 1.0
CE1 C:HIS241 2.9 16.9 1.0
OD1 C:ASP240 3.1 16.3 1.0
CD2 C:HIS241 3.1 13.8 1.0
CB C:SER71 3.2 16.9 1.0
CA C:SER71 3.6 16.6 1.0
CB C:ASP32 4.0 15.2 1.0
ND1 C:HIS241 4.0 17.7 1.0
CG C:HIS241 4.2 17.1 1.0
CE1 C:HIS354 4.2 17.9 1.0
N C:SER71 4.2 15.9 1.0
N C:GLY33 4.2 15.5 1.0
O C:HOH744 4.2 14.5 1.0
OD1 C:ASP193 4.3 22.3 1.0
OH C:TYR75 4.3 21.8 1.0
CB C:ASP240 4.3 12.6 1.0
ZN C:ZN508 4.4 29.4 1.0
NE2 C:HIS354 4.4 23.8 1.0
CE1 C:TYR75 4.5 17.0 1.0
CG C:ASP193 4.5 22.0 1.0
CA C:ASP32 4.5 14.9 1.0
CZ C:TYR75 4.7 20.1 1.0
OD2 C:ASP193 4.7 24.4 1.0
C C:ASP32 4.8 13.2 1.0
C C:SER71 4.9 15.1 1.0
C C:LEU70 5.0 16.5 1.0
CA C:GLY33 5.0 15.3 1.0

Zinc binding site 7 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 7 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:28.4
occ:1.00
 O D:HOH939 2.0 26.2 1.0
NE2 D:HIS354 2.0 18.1 1.0
NE2 D:HIS197 2.2 21.2 1.0
OD2 D:ASP193 2.3 17.3 1.0
OD1 D:ASP193 2.5 17.0 1.0
CG D:ASP193 2.7 18.5 1.0
CD2 D:HIS354 3.0 16.9 1.0
CD2 D:HIS197 3.0 15.9 1.0
CE1 D:HIS354 3.0 16.8 1.0
O D:HOH975 3.1 25.3 1.0
CE1 D:HIS197 3.3 20.0 1.0
O D:HOH669 3.6 14.0 1.0
CE1 D:HIS241 4.0 14.1 1.0
ND1 D:HIS354 4.1 14.2 1.0
CG D:HIS354 4.2 14.1 1.0
NE2 D:HIS241 4.2 15.0 1.0
CB D:ASP193 4.2 17.2 1.0
CG D:HIS197 4.2 18.4 1.0
O D:HOH675 4.3 23.4 1.0
ND1 D:HIS197 4.3 18.5 1.0
OD1 D:ASP32 4.4 19.4 1.0
ZN D:ZN508 4.4 32.0 1.0
OG D:SER71 4.4 17.8 1.0
CE D:MET243 4.6 16.0 1.0
O D:ASP193 4.9 17.9 1.0

Zinc binding site 8 out of 8 in 5ege

Go back to Zinc Binding Sites List in 5ege
Zinc binding site 8 out of 8 in the Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of ENPP6, A Choline-Specific Glycerophosphodiester- Phosphodiesterase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:32.0
occ:1.00
 OG D:SER71 2.1 17.8 1.0
OD2 D:ASP240 2.1 16.7 1.0
OD1 D:ASP32 2.2 19.4 1.0
NE2 D:HIS241 2.2 15.0 1.0
OD2 D:ASP32 2.4 22.1 1.0
CG D:ASP32 2.6 17.7 1.0
CG D:ASP240 2.9 14.0 1.0
CD2 D:HIS241 3.0 16.0 1.0
CB D:SER71 3.1 17.4 1.0
OD1 D:ASP240 3.2 14.1 1.0
CE1 D:HIS241 3.2 14.1 1.0
CA D:SER71 3.6 18.1 1.0
CB D:ASP32 4.0 13.8 1.0
OH D:TYR75 4.1 23.6 1.0
O D:HOH669 4.1 14.0 1.0
CG D:HIS241 4.2 16.1 1.0
ND1 D:HIS241 4.2 14.4 1.0
N D:SER71 4.2 14.3 1.0
CE1 D:HIS354 4.3 16.8 1.0
OD1 D:ASP193 4.3 17.0 1.0
N D:GLY33 4.3 15.8 1.0
CB D:ASP240 4.3 12.0 1.0
CE1 D:TYR75 4.4 15.1 1.0
ZN D:ZN507 4.4 28.4 1.0
NE2 D:HIS354 4.5 18.1 1.0
CA D:ASP32 4.5 17.9 1.0
CG D:ASP193 4.5 18.5 1.0
O D:HOH939 4.6 26.2 1.0
CZ D:TYR75 4.6 19.4 1.0
OD2 D:ASP193 4.7 17.3 1.0
C D:ASP32 4.8 14.8 1.0
C D:SER71 4.9 15.0 1.0
C D:LEU70 5.0 17.3 1.0
OH D:TYR188 5.0 17.7 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 15:16:04 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy