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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

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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

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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

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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

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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

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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

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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

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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

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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

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