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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

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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

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