Zinc in PDB 7mw8: Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

The structure of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase, PDB code: 7mw8 was solved by D.Fernandez, L.Li, J.A.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.04 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	130.42, 66.719, 134.961, 90, 116.25, 90
R / Rfree (%)	24.3 / 30.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase (pdb code 7mw8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase, PDB code: 7mw8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:29.8 occ:1.00 OD1 D:ASP54 1.8 27.7 1.0 OP3 K:A1 2.0 23.9 1.0 OD2 D:ASP257 2.2 28.1 1.0 NE2 D:HIS258 2.3 36.3 1.0 CG D:ASP54 2.6 29.5 1.0 OD2 D:ASP54 2.7 26.9 1.0 CD2 D:HIS258 2.9 32.1 1.0 CG D:ASP257 3.0 28.4 1.0 OD1 D:ASP257 3.1 31.8 1.0 CE1 D:HIS258 3.3 35.1 1.0 P K:A1 3.4 27.9 1.0 CB D:ALA90 3.6 29.2 1.0 OD1 D:ASP210 3.7 34.2 1.0 CA D:ALA90 3.9 28.2 1.0 OP1 K:A1 3.9 21.1 1.0 CB D:ASP54 4.0 31.7 1.0 CG D:ASP210 4.0 34.5 1.0 ZN D:ZN502 4.0 32.6 1.0 O5' K:A1 4.1 28.9 1.0 NE2 D:HIS363 4.1 36.3 1.0 CG D:HIS258 4.1 35.5 1.0 N D:GLY55 4.2 32.1 1.0 N D:ALA90 4.2 30.6 1.0 CE1 D:HIS363 4.2 33.1 1.0 ND1 D:HIS258 4.2 37.8 1.0 OP2 K:A1 4.3 22.2 1.0 CB D:ASP257 4.4 27.6 1.0 CA D:ASP54 4.4 31.8 1.0 C5' K:A1 4.4 34.6 1.0 OD2 D:ASP210 4.5 38.0 1.0 CB D:ASP210 4.5 34.1 1.0 C D:ASP54 4.5 30.9 1.0 CE1 D:HIS94 4.6 27.4 1.0 CD2 D:HIS363 4.8 35.2 1.0 CA D:GLY55 4.8 34.0 1.0 C D:LEU89 4.9 32.4 1.0 ND1 D:HIS363 4.9 36.7 1.0

Zinc binding site 2 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:32.6 occ:1.00 OP2 K:A1 1.8 22.2 1.0 OD1 D:ASP210 1.9 34.2 1.0 NE2 D:HIS214 2.3 39.7 1.0 OD2 D:ASP210 2.3 38.0 1.0 NE2 D:HIS363 2.4 36.3 1.0 CG D:ASP210 2.4 34.5 1.0 OP3 K:A1 2.7 23.9 1.0 P K:A1 2.8 27.9 1.0 CE1 D:HIS214 3.0 41.4 1.0 CD2 D:HIS363 3.1 35.2 1.0 CD2 D:HIS214 3.4 39.3 1.0 CE1 D:HIS363 3.4 33.1 1.0 O5' K:A1 3.9 28.9 1.0 OP1 K:A1 3.9 21.1 1.0 CB D:ASP210 3.9 34.1 1.0 C5' K:A1 4.0 34.6 1.0 NE2 D:HIS258 4.0 36.3 1.0 ZN D:ZN501 4.0 29.8 1.0 ND1 D:HIS214 4.2 41.6 1.0 CE1 D:HIS258 4.3 35.1 1.0 CG D:HIS363 4.4 35.1 1.0 CG D:HIS214 4.4 39.1 1.0 OD1 D:ASP54 4.4 27.7 1.0 ND1 D:HIS363 4.5 36.7 1.0 O D:ASP210 4.6 33.1 1.0 O D:HOH620 4.8 35.5 1.0 CA D:ASP210 4.8 34.0 1.0 C D:ASP210 4.8 37.0 1.0

Zinc binding site 3 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:22.0 occ:1.00 OD1 B:ASP54 1.8 18.9 1.0 OP3 L:A1 1.9 15.9 1.0 OD2 B:ASP257 2.1 17.9 1.0 NE2 B:HIS258 2.1 21.7 1.0 CG B:ASP54 2.6 22.9 1.0 OD2 B:ASP54 2.8 22.4 1.0 CE1 B:HIS258 2.9 21.9 1.0 CG B:ASP257 3.0 19.4 1.0 OD1 B:ASP257 3.2 18.7 1.0 CD2 B:HIS258 3.2 20.6 1.0 P L:A1 3.3 19.3 1.0 CB B:ALA90 3.4 20.5 1.0 OD1 B:ASP210 3.6 20.2 1.0 CA B:ALA90 3.9 18.6 1.0 CB B:ASP54 4.0 22.8 1.0 OP1 L:A1 4.0 15.9 1.0 NE2 B:HIS363 4.0 20.8 1.0 CG B:ASP210 4.0 21.2 1.0 N B:GLY55 4.1 23.6 1.0 ND1 B:HIS258 4.1 20.8 1.0 ZN B:ZN502 4.1 24.1 1.0 O5' L:A1 4.1 21.1 1.0 CE1 B:HIS363 4.1 19.4 1.0 N B:ALA90 4.2 18.9 1.0 CG B:HIS258 4.2 21.2 1.0 C5' L:A1 4.3 22.3 1.0 CB B:ASP257 4.3 17.2 1.0 OP2 L:A1 4.4 17.9 1.0 CA B:ASP54 4.5 23.0 1.0 CB B:ASP210 4.5 20.5 1.0 C B:ASP54 4.5 24.5 1.0 OD2 B:ASP210 4.5 24.1 1.0 CA B:GLY55 4.7 23.6 1.0 CD2 B:HIS363 4.8 20.3 1.0 CE1 B:HIS94 4.8 20.8 1.0 ND1 B:HIS363 4.8 22.9 1.0 C B:LEU89 4.9 20.6 1.0

Zinc binding site 4 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:24.1 occ:1.00 OD1 B:ASP210 1.8 20.2 1.0 NE2 B:HIS363 2.0 20.8 1.0 OP2 L:A1 2.1 17.9 1.0 NE2 B:HIS214 2.3 25.3 1.0 CG B:ASP210 2.5 21.2 1.0 OD2 B:ASP210 2.5 24.1 1.0 OP3 L:A1 2.7 15.9 1.0 P L:A1 2.9 19.3 1.0 CD2 B:HIS363 3.0 20.3 1.0 CE1 B:HIS363 3.0 19.4 1.0 CD2 B:HIS214 3.0 27.2 1.0 CE1 B:HIS214 3.4 28.9 1.0 OP1 L:A1 3.9 15.9 1.0 CB B:ASP210 4.0 20.5 1.0 O5' L:A1 4.0 21.1 1.0 ZN B:ZN501 4.1 22.0 1.0 C5' L:A1 4.1 22.3 1.0 ND1 B:HIS363 4.1 22.9 1.0 CG B:HIS363 4.2 21.3 1.0 CG B:HIS214 4.3 25.1 1.0 CE1 B:HIS258 4.3 21.9 1.0 ND1 B:HIS214 4.4 26.7 1.0 NE2 B:HIS258 4.5 21.7 1.0 OD1 B:ASP54 4.6 18.9 1.0 O B:ASP210 4.6 22.1 1.0 CE B:MET260 4.8 25.2 1.0 CA B:ASP210 4.8 21.6 1.0 C B:ASP210 4.9 23.6 1.0 O B:HOH645 4.9 19.0 1.0

Zinc binding site 5 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:24.5 occ:1.00 OP3 M:A1 1.9 23.5 1.0 OD1 C:ASP54 1.9 21.6 1.0 OD2 C:ASP257 2.0 18.6 1.0 NE2 C:HIS258 2.1 20.5 1.0 CG C:ASP54 2.7 24.6 1.0 CG C:ASP257 2.8 23.6 1.0 CE1 C:HIS258 2.8 21.0 1.0 OD2 C:ASP54 2.9 26.8 1.0 OD1 C:ASP257 3.0 27.4 1.0 CD2 C:HIS258 3.1 19.5 1.0 P M:A1 3.3 23.1 1.0 CB C:ALA90 3.7 19.0 1.0 OD1 C:ASP210 3.7 27.0 1.0 CG C:ASP210 3.9 26.2 1.0 OP1 M:A1 4.0 21.9 1.0 ND1 C:HIS258 4.0 20.2 1.0 CA C:ALA90 4.0 18.6 1.0 ZN C:ZN502 4.0 25.0 1.0 N C:GLY55 4.0 24.1 1.0 NE2 C:HIS363 4.0 28.0 1.0 CB C:ASP54 4.1 25.3 1.0 CE1 C:HIS363 4.1 25.7 1.0 O5' M:A1 4.1 23.0 1.0 CG C:HIS258 4.1 21.5 1.0 N C:ALA90 4.2 19.2 1.0 CB C:ASP257 4.2 22.6 1.0 OD2 C:ASP210 4.2 29.4 1.0 OP2 M:A1 4.3 22.1 1.0 C5' M:A1 4.3 22.9 1.0 CA C:ASP54 4.5 25.2 1.0 CB C:ASP210 4.5 23.8 1.0 C C:ASP54 4.5 25.1 1.0 CA C:GLY55 4.7 23.8 1.0 ND1 C:HIS363 4.8 25.0 1.0 CD2 C:HIS363 4.8 25.5 1.0 CE1 C:HIS94 4.8 21.1 1.0 C C:LEU89 4.9 22.5 1.0

Zinc binding site 6 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:25.0 occ:1.00 OP2 M:A1 2.0 22.1 1.0 NE2 C:HIS363 2.2 28.0 1.0 NE2 C:HIS214 2.2 31.0 1.0 OD1 C:ASP210 2.2 27.0 1.0 OD2 C:ASP210 2.2 29.4 1.0 CG C:ASP210 2.5 26.2 1.0 OP3 M:A1 2.8 23.5 1.0 P M:A1 2.9 23.1 1.0 CD2 C:HIS363 3.1 25.5 1.0 CE1 C:HIS214 3.1 33.1 1.0 CD2 C:HIS214 3.2 30.7 1.0 CE1 C:HIS363 3.2 25.7 1.0 OP1 M:A1 3.9 21.9 1.0 O M:HOH102 3.9 26.2 1.0 CB C:ASP210 4.0 23.8 1.0 O5' M:A1 4.0 23.0 1.0 ZN C:ZN501 4.0 24.5 1.0 C5' M:A1 4.2 22.9 1.0 ND1 C:HIS214 4.2 32.8 1.0 CE1 C:HIS258 4.2 21.0 1.0 CG C:HIS363 4.2 25.9 1.0 CG C:HIS214 4.3 32.0 1.0 ND1 C:HIS363 4.3 25.0 1.0 NE2 C:HIS258 4.4 20.5 1.0 OD1 C:ASP54 4.6 21.6 1.0 O C:ASP210 4.7 23.9 1.0 CE C:MET260 4.8 27.6 1.0 O C:HOH641 4.8 23.0 1.0 CA C:ASP210 4.8 25.3 1.0 C C:ASP210 4.9 27.0 1.0

Zinc binding site 7 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:27.0 occ:1.00 OP1 J:A1 1.8 24.5 1.0 OD2 A:ASP257 2.0 31.3 1.0 OD1 A:ASP54 2.1 23.6 1.0 NE2 A:HIS258 2.2 33.0 1.0 OD2 A:ASP54 2.6 34.6 1.0 CG A:ASP54 2.7 27.8 1.0 CE1 A:HIS258 3.0 32.9 1.0 CG A:ASP257 3.0 30.5 1.0 CD2 A:HIS258 3.1 31.4 1.0 P J:A1 3.3 24.1 1.0 OD1 A:ASP257 3.4 28.1 1.0 OD1 A:ASP210 3.6 28.1 1.0 CB A:ALA90 3.6 24.6 1.0 CA A:ALA90 3.9 25.0 1.0 CG A:ASP210 3.9 24.8 1.0 OP3 J:A1 3.9 27.2 1.0 ZN A:ZN502 4.0 26.6 1.0 O5' J:A1 4.0 29.0 1.0 NE2 A:HIS363 4.0 39.0 1.0 N A:ALA90 4.1 24.9 1.0 ND1 A:HIS258 4.1 34.5 1.0 CE1 A:HIS363 4.1 34.8 1.0 CB A:ASP54 4.1 31.0 1.0 CG A:HIS258 4.2 31.2 1.0 N A:GLY55 4.2 29.8 1.0 OD2 A:ASP210 4.3 24.1 1.0 C5' J:A1 4.3 29.8 1.0 CB A:ASP257 4.3 28.6 1.0 OP2 J:A1 4.4 25.3 1.0 CB A:ASP210 4.6 26.1 1.0 CA A:ASP54 4.7 30.8 1.0 C A:ASP54 4.7 31.8 1.0 C A:LEU89 4.7 24.6 1.0 CD2 A:HIS363 4.8 34.4 1.0 CA A:GLY55 4.8 28.5 1.0 ND1 A:HIS363 4.8 34.3 1.0 CE1 A:HIS94 5.0 25.2 1.0

Zinc binding site 8 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:26.6 occ:1.00 OD2 A:ASP210 2.1 24.1 1.0 NE2 A:HIS214 2.1 35.3 1.0 NE2 A:HIS363 2.2 39.0 1.0 OP2 J:A1 2.2 25.3 1.0 OD1 A:ASP210 2.3 28.1 1.0 CG A:ASP210 2.5 24.8 1.0 OP1 J:A1 2.7 24.5 1.0 P J:A1 2.9 24.1 1.0 CD2 A:HIS363 3.0 34.4 1.0 CE1 A:HIS214 3.0 37.4 1.0 CD2 A:HIS214 3.1 33.6 1.0 CE1 A:HIS363 3.3 34.8 1.0 ZN A:ZN501 4.0 27.0 1.0 O5' J:A1 4.0 29.0 1.0 OP3 J:A1 4.0 27.2 1.0 CB A:ASP210 4.1 26.1 1.0 ND1 A:HIS214 4.2 36.7 1.0 C4' J:G2 4.2 63.4 1.0 C5' J:A1 4.2 29.8 1.0 CG A:HIS363 4.2 32.9 1.0 CG A:HIS214 4.2 35.9 1.0 NE2 A:HIS258 4.3 33.0 1.0 ND1 A:HIS363 4.3 34.3 1.0 CE1 A:HIS258 4.4 32.9 1.0 OD1 A:ASP54 4.5 23.6 1.0 C5' J:G2 4.5 64.0 1.0 O A:HOH637 4.5 17.6 1.0 O4' J:G2 4.6 65.7 1.0 O A:ASP210 4.7 24.3 1.0 CE A:MET260 4.9 32.3 1.0 CA A:ASP210 4.9 27.0 1.0 C A:ASP210 5.0 27.2 1.0

Zinc binding site 9 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:37.5 occ:1.00 OP3 N:A1 1.8 32.6 1.0 OD1 E:ASP54 1.9 28.5 1.0 OD2 E:ASP257 1.9 34.7 1.0 NE2 E:HIS258 2.2 45.7 1.0 CG E:ASP54 2.8 33.1 1.0 CE1 E:HIS258 2.8 43.5 1.0 CG E:ASP257 2.9 36.7 1.0 OD2 E:ASP54 3.0 29.0 1.0 P N:A1 3.3 30.3 1.0 CD2 E:HIS258 3.3 38.8 1.0 OD1 E:ASP210 3.3 42.4 1.0 OD1 E:ASP257 3.4 35.7 1.0 CB E:ALA90 3.6 25.6 1.0 OP1 N:A1 3.9 27.5 1.0 CG E:ASP210 4.0 38.6 1.0 ND1 E:HIS258 4.0 42.3 1.0 CA E:ALA90 4.0 25.2 1.0 NE2 E:HIS363 4.0 37.9 1.0 CE1 E:HIS363 4.0 36.0 1.0 ZN E:ZN502 4.0 33.6 1.0 O5' N:A1 4.1 32.7 1.0 N E:ALA90 4.1 24.9 1.0 CB E:ASP54 4.2 35.4 1.0 CG E:HIS258 4.2 38.6 1.0 N E:GLY55 4.2 34.2 1.0 CB E:ASP257 4.2 33.6 1.0 OP2 N:A1 4.3 32.4 1.0 C5' N:A1 4.4 34.1 1.0 CB E:ASP210 4.6 36.8 1.0 OD2 E:ASP210 4.6 39.1 1.0 CA E:ASP54 4.6 33.9 1.0 C E:ASP54 4.7 37.1 1.0 ND1 E:HIS363 4.8 34.8 1.0 CD2 E:HIS363 4.8 34.9 1.0 CA E:GLY55 4.8 33.5 1.0 C E:LEU89 4.9 27.2 1.0 CE1 E:HIS94 4.9 25.4 1.0

Zinc binding site 10 out of 12 in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:33.6 occ:1.00 OD1 E:ASP210 2.1 42.4 1.0 OP2 N:A1 2.2 32.4 1.0 NE2 E:HIS363 2.3 37.9 1.0 OD2 E:ASP210 2.3 39.1 1.0 NE2 E:HIS214 2.5 39.8 1.0 CG E:ASP210 2.6 38.6 1.0 OP3 N:A1 2.8 32.6 1.0 CD2 E:HIS214 2.8 40.1 1.0 P N:A1 3.0 30.3 1.0 CD2 E:HIS363 3.1 34.9 1.0 CE1 E:HIS363 3.4 36.0 1.0 CE1 E:HIS214 3.7 42.8 1.0 O N:HOH101 3.8 23.1 1.0 ZN E:ZN501 4.0 37.5 1.0 OP1 N:A1 4.1 27.5 1.0 O5' N:A1 4.1 32.7 1.0 CB E:ASP210 4.1 36.8 1.0 CG E:HIS214 4.1 41.7 1.0 C5' N:A1 4.2 34.1 1.0 CG E:HIS363 4.3 36.2 1.0 CE1 E:HIS258 4.3 43.5 1.0 OD1 E:ASP54 4.4 28.5 1.0 ND1 E:HIS363 4.4 34.8 1.0 NE2 E:HIS258 4.5 45.7 1.0 ND1 E:HIS214 4.5 43.0 1.0 O E:ASP210 4.6 33.1 1.0 CE E:MET260 4.7 39.1 1.0 C E:ASP210 5.0 36.2 1.0 CA E:ASP210 5.0 35.7 1.0

J.A.Carozza, A.F.Cordova, J.A.Brown, Y.Alsaif, V.Bohnert, X.Cao, R.E.Mardjuki, G.Skariah, D.Fernandez, L.Li. ENPP1'S Regulation of Extracellular Cgamp Is A Ubiquitous Mechanism of Attenuating Sting Signaling. Proc.Natl.Acad.Sci.Usa V. 119 89119 2022.
ISSN: ESSN 1091-6490
PubMed: 35588451
DOI: 10.1073/PNAS.2119189119