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Zinc in PDB 9gro: Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918)

Enzymatic activity of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918)

All present enzymatic activity of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918):
2.7.4.24;

Protein crystallography data

The structure of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918), PDB code: 9gro was solved by P.Raia, M.Hothorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.68 / 2.36
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.586, 114.586, 172.179, 90, 90, 120
R / Rfree (%) 22.8 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918) (pdb code 9gro). 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 the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918), PDB code: 9gro:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 9gro

Go back to Zinc Binding Sites List in 9gro
Zinc binding site 1 out of 2 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918)


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 Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:61.2
occ:1.00
 OE2 A:GLU796 1.9 56.0 1.0
ND1 A:HIS836 2.3 52.4 1.0
NE2 A:HIS651 2.3 57.7 1.0
ND1 A:HIS1064 2.3 65.1 1.0
HB3 A:HIS836 2.9 67.2 1.0
CD A:GLU796 3.0 58.3 1.0
HB2 A:HIS1064 3.0 66.7 1.0
CD2 A:HIS651 3.2 58.3 1.0
CG A:HIS836 3.2 52.6 1.0
HA A:HIS836 3.2 69.2 1.0
HD2 A:HIS651 3.2 70.2 1.0
CG A:HIS1064 3.3 59.6 1.0
CE1 A:HIS1064 3.3 57.2 1.0
CE1 A:HIS836 3.3 47.2 1.0
CE1 A:HIS651 3.3 61.8 1.0
CB A:HIS836 3.4 55.8 1.0
HE1 A:HIS1064 3.4 68.9 1.0
OE1 A:GLU796 3.4 72.2 1.0
HE1 A:HIS836 3.5 56.9 1.0
CB A:HIS1064 3.5 55.4 1.0
HE1 A:HIS651 3.6 74.4 1.0
HB3 A:HIS1064 3.6 66.7 1.0
CA A:HIS836 3.8 57.5 1.0
HH21 B:ARG791 3.9 93.3 1.0
O A:HOH1325 4.0 56.2 1.0
HH22 B:ARG791 4.1 93.3 1.0
NH2 B:ARG791 4.2 77.5 1.0
CG A:GLU796 4.2 72.7 1.0
HG2 A:GLU796 4.3 87.5 1.0
HB2 A:HIS836 4.3 67.2 1.0
O A:HIS836 4.3 58.8 1.0
CG A:HIS651 4.4 56.4 1.0
CD2 A:HIS836 4.4 62.8 1.0
NE2 A:HIS1064 4.4 69.9 1.0
CD2 A:HIS1064 4.4 73.1 1.0
NE2 A:HIS836 4.4 59.1 1.0
ND1 A:HIS651 4.4 66.8 1.0
OG A:SER652 4.5 55.5 1.0
HG3 A:GLU796 4.5 87.5 1.0
HO2 A:EDO1216 4.6 81.5 1.0
C A:HIS836 4.6 54.6 1.0
HG A:SER652 4.6 66.9 1.0
O2 A:EDO1216 4.7 67.7 1.0
O A:LEU835 4.8 61.4 1.0
O B:HOH1306 4.9 59.2 1.0
O A:ASP1062 4.9 63.6 1.0
N A:HIS836 4.9 56.3 1.0
HB A:THR650 4.9 58.4 1.0
O A:ARG1063 5.0 57.4 1.0
CA A:HIS1064 5.0 64.9 1.0

Zinc binding site 2 out of 2 in 9gro

Go back to Zinc Binding Sites List in 9gro
Zinc binding site 2 out of 2 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918)


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 Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 in Complex with 1,5-INSP8 (Phosphatase Dead Mutant, Loop Deletion Residues 848-918) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:58.8
occ:1.00
 OE2 B:GLU796 2.0 79.3 1.0
ND1 B:HIS1064 2.3 51.0 1.0
NE2 B:HIS651 2.3 57.2 1.0
ND1 B:HIS836 2.3 68.9 1.0
HB3 B:HIS836 2.6 77.3 1.0
CD B:GLU796 2.8 67.2 1.0
HB2 B:HIS1064 3.1 76.5 1.0
OE1 B:GLU796 3.1 64.3 1.0
CG B:HIS836 3.1 65.9 1.0
HA B:HIS836 3.1 73.4 1.0
CB B:HIS836 3.1 64.2 1.0
HH21 A:ARG791 3.2 74.8 1.0
CD2 B:HIS651 3.2 60.7 1.0
CE1 B:HIS1064 3.3 54.2 1.0
CG B:HIS1064 3.3 73.2 1.0
CE1 B:HIS651 3.3 59.5 1.0
HD2 B:HIS651 3.4 73.1 1.0
HE1 B:HIS1064 3.4 65.3 1.0
CE1 B:HIS836 3.4 58.4 1.0
HE1 B:HIS651 3.5 71.7 1.0
CB B:HIS1064 3.5 63.5 1.0
HH22 A:ARG791 3.6 74.8 1.0
CA B:HIS836 3.6 61.0 1.0
NH2 A:ARG791 3.6 62.1 1.0
HB3 B:HIS1064 3.7 76.5 1.0
HE1 B:HIS836 3.7 70.4 1.0
HB2 B:HIS836 4.0 77.3 1.0
CG B:GLU796 4.1 79.0 1.0
O B:HOH1313 4.2 62.8 1.0
HG2 B:GLU796 4.2 95.0 1.0
CD2 B:HIS836 4.3 65.8 1.0
O B:HIS836 4.3 72.0 1.0
NE2 B:HIS1064 4.4 61.6 1.0
ND1 B:HIS651 4.4 58.4 1.0
CD2 B:HIS1064 4.4 58.0 1.0
CG B:HIS651 4.4 49.1 1.0
NE2 B:HIS836 4.4 70.3 1.0
OG B:SER652 4.4 66.4 1.0
C B:HIS836 4.5 72.3 1.0
HG3 B:GLU796 4.6 95.0 1.0
N B:HIS836 4.7 61.6 1.0
HG B:SER652 4.7 79.9 1.0
CZ A:ARG791 4.8 70.2 1.0
O B:HOH1301 4.8 59.0 1.0
HB B:THR650 4.9 62.8 1.0
HE A:ARG791 4.9 95.0 1.0
H4 B:1JW1204 5.0 100.2 1.0
CA B:HIS1064 5.0 70.4 1.0

Reference:

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
Page generated: Fri Aug 22 17:58:57 2025

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