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Zinc in PDB 6ael: Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp

Protein crystallography data

The structure of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp, PDB code: 6ael was solved by K.Kato, H.Nishimasu, S.Hirano, H.Hirano, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.169, 94.063, 74.274, 90.00, 95.93, 90.00
R / Rfree (%) 16.6 / 20.2

Other elements in 6ael:

The structure of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp (pdb code 6ael). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp, PDB code: 6ael:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ael

Go back to Zinc Binding Sites List in 6ael
Zinc binding site 1 out of 2 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1008

b:31.4
occ:1.00
OAE A:4BW1007 1.8 25.6 1.0
NE2 A:HIS362 2.0 32.1 1.0
NE2 A:HIS517 2.1 28.4 1.0
OD1 A:ASP358 2.2 33.3 1.0
OD2 A:ASP358 2.4 33.8 1.0
CG A:ASP358 2.6 30.9 1.0
CD2 A:HIS362 3.0 30.3 1.0
CE1 A:HIS517 3.0 23.8 1.0
CE1 A:HIS362 3.1 29.6 1.0
CD2 A:HIS517 3.1 26.1 1.0
PBS A:4BW1007 3.2 40.9 1.0
OAI A:4BW1007 3.8 35.2 1.0
CE1 A:HIS406 4.0 28.2 1.0
CBI A:4BW1007 4.0 66.5 1.0
ZN A:ZN1009 4.1 40.4 1.0
O5' A:4BW1007 4.1 38.1 1.0
C5' A:4BW1007 4.1 37.4 1.0
CB A:ASP358 4.1 28.9 1.0
CG A:HIS362 4.1 32.4 1.0
ND1 A:HIS517 4.1 23.4 1.0
ND1 A:HIS362 4.2 31.4 1.0
OAZ A:4BW1007 4.2 56.4 1.0
CBM A:4BW1007 4.2 64.8 1.0
NE2 A:HIS406 4.2 30.9 1.0
CG A:HIS517 4.2 25.4 1.0
OAG A:4BW1007 4.4 63.3 1.0
CE A:MET408 4.5 26.8 1.0
OD1 A:ASP200 4.5 31.5 1.0
O A:ASP358 4.9 29.9 1.0
CA A:ASP358 5.0 30.1 1.0

Zinc binding site 2 out of 2 in 6ael

Go back to Zinc Binding Sites List in 6ael
Zinc binding site 2 out of 2 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1009

b:40.4
occ:1.00
OD1 A:ASP200 1.9 31.5 1.0
NE2 A:HIS406 2.2 30.9 1.0
OD2 A:ASP405 2.2 21.2 1.0
CG A:ASP200 2.6 28.4 1.0
OD2 A:ASP200 2.7 29.8 1.0
CE1 A:HIS406 2.9 28.2 1.0
CG A:ASP405 3.0 26.5 1.0
OD1 A:ASP405 3.1 24.6 1.0
CB A:ALA238 3.2 20.5 1.0
CD2 A:HIS406 3.2 27.2 1.0
CA A:ALA238 3.7 22.2 1.0
OD1 A:ASP358 3.8 33.3 1.0
O5' A:4BW1007 3.9 38.1 1.0
OAI A:4BW1007 3.9 35.2 1.0
N A:GLY201 3.9 27.9 1.0
CG A:ASP358 4.0 30.9 1.0
ND1 A:HIS406 4.0 23.8 1.0
CB A:ASP200 4.0 28.6 1.0
ZN A:ZN1008 4.1 31.4 1.0
OAE A:4BW1007 4.1 25.6 1.0
N A:ALA238 4.1 25.1 1.0
PBS A:4BW1007 4.2 40.9 1.0
CG A:HIS406 4.2 23.9 1.0
OD2 A:ASP358 4.3 33.8 1.0
CE1 A:HIS517 4.3 23.8 1.0
NE2 A:HIS517 4.4 28.4 1.0
CB A:ASP405 4.4 24.5 1.0
CA A:ASP200 4.4 28.6 1.0
C A:ASP200 4.5 30.9 1.0
CA A:GLY201 4.5 24.6 1.0
CB A:ASP358 4.5 28.9 1.0
C5' A:4BW1007 4.6 37.4 1.0
CE1 A:HIS242 4.7 26.1 1.0
C A:LYS237 4.9 23.6 1.0

Reference:

K.Kato, H.Nishimasu, D.Oikawa, S.Hirano, H.Hirano, G.Kasuya, R.Ishitani, F.Tokunaga, O.Nureki. Structural Insights Into Cgamp Degradation By Ecto-Nucleotide Pyrophosphatase Phosphodiesterase 1. Nat Commun V. 9 4424 2018.
ISSN: ESSN 2041-1723
PubMed: 30356045
DOI: 10.1038/S41467-018-06922-7
Page generated: Wed Dec 16 11:29:34 2020

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