Zinc in PDB 9grh: Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo)

All present enzymatic activity of Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo):
2.7.4.24;

The structure of Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo), PDB code: 9grh was solved by P.Raia, K.Lee, M.Hothorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.71 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.473, 194.857, 84.441, 90, 112.16, 90
R / Rfree (%)	21.8 / 27.6

The binding sites of Zinc atom in the Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo) (pdb code 9grh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo), PDB code: 9grh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo)


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 the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:343.9 occ:1.00 ND1 A:HIS1064 2.0 104.3 1.0 ND1 A:HIS836 2.0 124.2 1.0 NE2 A:HIS651 2.0 88.7 1.0 SG A:CYS793 2.3 111.9 1.0 HB3 A:HIS836 2.8 138.5 1.0 HB2 A:HIS1064 2.9 137.6 1.0 CE1 A:HIS1064 3.0 157.0 1.0 CG A:HIS836 3.0 121.2 1.0 CD2 A:HIS651 3.0 85.6 1.0 CE1 A:HIS836 3.0 119.2 1.0 CE1 A:HIS651 3.0 115.8 1.0 CG A:HIS1064 3.0 101.5 1.0 HB3 A:CYS793 3.0 127.0 1.0 CB A:CYS793 3.1 105.8 1.0 HE1 A:HIS1064 3.1 188.5 1.0 HD2 A:HIS651 3.2 102.8 1.0 HE1 A:HIS836 3.2 143.0 1.0 HE1 A:HIS651 3.2 139.1 1.0 CB A:HIS836 3.3 115.3 1.0 HB2 A:CYS793 3.3 127.0 1.0 CB A:HIS1064 3.3 114.6 1.0 HA A:HIS836 3.4 136.2 1.0 HB3 A:HIS1064 3.5 137.6 1.0 CA A:HIS836 3.9 113.5 1.0 NE2 A:HIS1064 4.1 163.1 1.0 NE2 A:HIS836 4.1 92.3 1.0 ND1 A:HIS651 4.1 110.0 1.0 CD2 A:HIS836 4.1 110.2 1.0 CD2 A:HIS1064 4.1 148.7 1.0 CG A:HIS651 4.1 105.8 1.0 HB2 A:HIS836 4.1 138.5 1.0 HG23 A:THR794 4.2 122.3 1.0 O A:HIS836 4.5 125.8 1.0 CA A:CYS793 4.6 87.8 1.0 H A:CYS793 4.6 117.2 1.0 HH11 A:ARG791 4.6 212.6 1.0 O A:ARG1063 4.7 147.7 1.0 HH12 A:ARG791 4.7 212.6 1.0 C A:HIS836 4.8 105.6 1.0 NH1 A:ARG791 4.8 177.1 1.0 CA A:HIS1064 4.8 132.9 1.0 OG A:SER652 4.9 190.9 1.0 HE2 A:HIS1064 4.9 195.8 1.0 HE2 A:HIS836 4.9 110.8 1.0 HD1 A:HIS651 4.9 132.0 1.0 HB A:THR650 4.9 123.0 1.0 HD2 A:HIS836 5.0 132.2 1.0 HD2 A:HIS1064 5.0 178.5 1.0 HG A:SER652 5.0 229.1 1.0 N A:HIS836 5.0 120.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo)


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 the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:112.8 occ:1.00 ND1 B:HIS836 2.0 134.5 1.0 ND1 B:HIS1064 2.0 133.8 1.0 NE2 B:HIS651 2.0 137.4 1.0 SG B:CYS793 2.3 161.6 1.0 HB3 B:HIS836 2.8 133.3 1.0 HB2 B:HIS1064 2.9 172.7 1.0 CE1 B:HIS1064 3.0 149.9 1.0 CG B:HIS836 3.0 119.8 1.0 CD2 B:HIS651 3.0 104.0 1.0 CE1 B:HIS836 3.0 131.4 1.0 CG B:HIS1064 3.0 135.4 1.0 CE1 B:HIS651 3.0 153.4 1.0 HB3 B:CYS793 3.0 140.9 1.0 HD2 B:HIS651 3.1 124.9 1.0 HE1 B:HIS1064 3.1 179.9 1.0 CB B:CYS793 3.2 117.3 1.0 HE1 B:HIS836 3.2 157.7 1.0 HE1 B:HIS651 3.2 184.2 1.0 CB B:HIS836 3.3 111.1 1.0 CB B:HIS1064 3.4 143.8 1.0 HB2 B:CYS793 3.4 140.9 1.0 HA B:HIS836 3.5 118.4 1.0 HB3 B:HIS1064 3.5 172.7 1.0 CA B:HIS836 3.9 98.6 1.0 NE2 B:HIS1064 4.1 159.4 1.0 NE2 B:HIS836 4.1 96.7 1.0 CD2 B:HIS836 4.1 105.2 1.0 ND1 B:HIS651 4.1 122.0 1.0 CD2 B:HIS1064 4.1 163.8 1.0 CG B:HIS651 4.1 91.7 1.0 HB2 B:HIS836 4.1 133.3 1.0 HH11 B:ARG791 4.4 326.2 1.0 HG23 B:THR794 4.5 177.7 1.0 HH12 B:ARG791 4.5 326.2 1.0 H B:CYS793 4.5 184.7 1.0 NH1 B:ARG791 4.5 271.8 1.0 O B:HIS836 4.5 88.6 1.0 CA B:CYS793 4.6 127.5 1.0 O B:ARG1063 4.7 251.9 1.0 C B:HIS836 4.8 98.6 1.0 OG B:SER652 4.8 143.4 1.0 CA B:HIS1064 4.8 151.8 1.0 HE2 B:HIS1064 4.9 191.3 1.0 HE2 B:HIS836 4.9 116.1 1.0 HD1 B:HIS651 4.9 146.5 1.0 HB B:THR650 4.9 96.0 1.0 HG B:SER652 4.9 172.2 1.0 N B:CYS793 4.9 153.9 1.0 HD3 B:ARG791 5.0 331.6 1.0 HD2 B:HIS836 5.0 126.4 1.0 HD2 B:HIS1064 5.0 196.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2000 b:129.9 occ:1.00 ND1 C:HIS1064 2.0 177.8 1.0 ND1 C:HIS836 2.0 195.1 1.0 NE2 C:HIS651 2.0 131.8 1.0 SG C:CYS793 2.3 143.1 1.0 HB3 C:HIS836 2.8 211.8 1.0 HB2 C:HIS1064 2.9 230.9 1.0 CE1 C:HIS1064 3.0 186.3 1.0 CD2 C:HIS651 3.0 121.6 1.0 CG C:HIS836 3.0 187.9 1.0 CE1 C:HIS836 3.0 176.2 1.0 CG C:HIS1064 3.0 195.8 1.0 CE1 C:HIS651 3.0 156.0 1.0 HB3 C:CYS793 3.1 136.4 1.0 HD2 C:HIS651 3.1 146.0 1.0 HE1 C:HIS1064 3.1 223.7 1.0 HE1 C:HIS836 3.2 211.5 1.0 CB C:CYS793 3.2 113.6 1.0 HE1 C:HIS651 3.2 187.3 1.0 CB C:HIS836 3.3 176.5 1.0 CB C:HIS1064 3.4 192.4 1.0 HB2 C:CYS793 3.4 136.4 1.0 HA C:HIS836 3.5 205.2 1.0 HB3 C:HIS1064 3.5 230.9 1.0 CA C:HIS836 3.9 171.0 1.0 NE2 C:HIS1064 4.1 210.6 1.0 NE2 C:HIS836 4.1 154.2 1.0 ND1 C:HIS651 4.1 134.3 1.0 CD2 C:HIS836 4.1 163.7 1.0 CG C:HIS651 4.1 128.2 1.0 CD2 C:HIS1064 4.1 221.0 1.0 HB2 C:HIS836 4.2 211.8 1.0 HG23 C:THR794 4.3 119.0 1.0 O C:HIS836 4.5 172.5 1.0 CA C:CYS793 4.6 106.3 1.0 H C:CYS793 4.6 140.1 1.0 HH11 C:ARG791 4.7 200.1 1.0 O C:ARG1063 4.7 336.8 1.0 OG C:SER652 4.7 172.3 1.0 C C:HIS836 4.8 165.6 1.0 CA C:HIS1064 4.8 191.4 1.0 HH12 C:ARG791 4.8 200.1 1.0 NH1 C:ARG791 4.8 166.7 1.0 HE2 C:HIS1064 4.9 252.7 1.0 HE2 C:HIS836 4.9 185.0 1.0 HG C:SER652 4.9 206.9 1.0 HB C:THR650 4.9 123.0 1.0 HD1 C:HIS651 4.9 161.2 1.0 HD2 C:HIS836 5.0 196.5 1.0 HD2 C:HIS1064 5.0 265.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2000 b:155.0 occ:1.00 ND1 D:HIS836 2.0 116.8 1.0 ND1 D:HIS1064 2.0 120.8 1.0 NE2 D:HIS651 2.0 123.5 1.0 SG D:CYS793 2.3 153.5 1.0 HB3 D:HIS836 2.8 126.6 1.0 HB2 D:HIS1064 2.9 150.0 1.0 CE1 D:HIS1064 3.0 147.4 1.0 CE1 D:HIS836 3.0 114.7 1.0 CD2 D:HIS651 3.0 95.2 1.0 CG D:HIS836 3.0 108.2 1.0 CG D:HIS1064 3.0 118.5 1.0 CE1 D:HIS651 3.0 143.4 1.0 HB3 D:CYS793 3.1 140.5 1.0 HE1 D:HIS1064 3.1 176.9 1.0 HD2 D:HIS651 3.2 114.3 1.0 HE1 D:HIS836 3.2 137.7 1.0 CB D:CYS793 3.2 117.0 1.0 HE1 D:HIS651 3.2 172.1 1.0 CB D:HIS836 3.3 105.5 1.0 HB2 D:CYS793 3.4 140.5 1.0 CB D:HIS1064 3.4 125.0 1.0 HA D:HIS836 3.5 109.1 1.0 HB3 D:HIS1064 3.5 150.0 1.0 CA D:HIS836 3.9 90.9 1.0 NE2 D:HIS1064 4.1 150.1 1.0 NE2 D:HIS836 4.1 100.6 1.0 ND1 D:HIS651 4.1 132.3 1.0 CD2 D:HIS836 4.1 91.6 1.0 CD2 D:HIS1064 4.1 145.9 1.0 CG D:HIS651 4.1 108.7 1.0 HB2 D:HIS836 4.2 126.6 1.0 HG23 D:THR794 4.3 137.7 1.0 O D:HIS836 4.5 111.9 1.0 H D:CYS793 4.6 118.9 1.0 CA D:CYS793 4.6 95.2 1.0 HH11 D:ARG791 4.7 215.0 1.0 O D:ARG1063 4.7 244.6 1.0 OG D:SER652 4.8 143.3 1.0 C D:HIS836 4.8 95.8 1.0 CA D:HIS1064 4.8 149.2 1.0 HH12 D:ARG791 4.8 215.0 1.0 NH1 D:ARG791 4.8 179.1 1.0 HE2 D:HIS1064 4.9 180.1 1.0 HE2 D:HIS836 4.9 120.8 1.0 HG D:SER652 4.9 172.0 1.0 HD1 D:HIS651 4.9 158.9 1.0 HB D:THR650 5.0 96.9 1.0 HD2 D:HIS836 5.0 110.0 1.0 HD2 D:HIS1064 5.0 175.1 1.0

P.Raia, K.Lee, S.M.Bartsch, F.Rico-Resendiz, D.Portugal-Calisto, O.Vadas, V.G.Panse, D.Fiedler, M.Hothorn. A Small Signaling Domain Controls PPIP5K Phosphatase Activity in Phosphate Homeostasis. Nat Commun V. 16 1753 2025.
ISSN: ESSN 2041-1723
PubMed: 39966396
DOI: 10.1038/S41467-025-56937-0