Zinc in PDB 9grn: Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918)
Enzymatic activity of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918)
All present enzymatic activity of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, 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 (Apo, Loop Deletion Residues 848-918), PDB code: 9grn
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)
|
45.26 /
3.40
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
249.475,
90.516,
200.898,
90,
126.91,
90
|
|
R / Rfree (%)
|
24.4 /
29.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918)
(pdb code 9grn). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918), PDB code: 9grn:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 9grn
Go back to
Zinc Binding Sites List in 9grn
Zinc binding site 1 out
of 6 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, 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 (Apo, Loop Deletion Residues 848-918) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2011
b:58.2
occ:1.00
|
NE2
|
A:HIS651
|
2.0
|
55.3
|
1.0
|
|
ND1
|
A:HIS836
|
2.0
|
51.7
|
1.0
|
|
ND1
|
A:HIS997
|
2.0
|
82.9
|
1.0
|
|
SG
|
A:CYS793
|
2.3
|
54.1
|
1.0
|
|
HB2
|
A:HIS997
|
2.7
|
67.7
|
1.0
|
|
HB3
|
A:HIS836
|
2.9
|
64.9
|
1.0
|
|
CG
|
A:HIS997
|
2.9
|
66.4
|
1.0
|
|
CD2
|
A:HIS651
|
2.9
|
80.5
|
1.0
|
|
CG
|
A:HIS836
|
3.0
|
66.5
|
1.0
|
|
CE1
|
A:HIS836
|
3.0
|
53.2
|
1.0
|
|
CE1
|
A:HIS651
|
3.0
|
91.6
|
1.0
|
|
CE1
|
A:HIS997
|
3.0
|
72.7
|
1.0
|
|
HD2
|
A:HIS651
|
3.1
|
96.7
|
1.0
|
|
CB
|
A:HIS997
|
3.2
|
56.3
|
1.0
|
|
HE1
|
A:HIS836
|
3.2
|
63.4
|
1.0
|
|
HE1
|
A:HIS651
|
3.2
|
110.1
|
1.0
|
|
HA
|
A:HIS836
|
3.3
|
61.5
|
1.0
|
|
HE1
|
A:HIS997
|
3.3
|
87.3
|
1.0
|
|
CB
|
A:HIS836
|
3.3
|
54.0
|
1.0
|
|
HB3
|
A:CYS793
|
3.3
|
68.7
|
1.0
|
|
HB3
|
A:HIS997
|
3.3
|
67.7
|
1.0
|
|
HH12
|
A:ARG791
|
3.3
|
99.8
|
1.0
|
|
CB
|
A:CYS793
|
3.4
|
57.6
|
1.0
|
|
HB2
|
A:CYS793
|
3.5
|
68.7
|
1.0
|
|
CA
|
A:HIS836
|
3.8
|
51.1
|
1.0
|
|
HH11
|
A:ARG791
|
3.9
|
99.8
|
1.0
|
|
NH1
|
A:ARG791
|
3.9
|
83.1
|
1.0
|
|
CD2
|
A:HIS997
|
4.1
|
63.5
|
1.0
|
|
NE2
|
A:HIS836
|
4.1
|
51.9
|
1.0
|
|
ND1
|
A:HIS651
|
4.1
|
85.7
|
1.0
|
|
CG
|
A:HIS651
|
4.1
|
60.8
|
1.0
|
|
NE2
|
A:HIS997
|
4.1
|
76.8
|
1.0
|
|
CD2
|
A:HIS836
|
4.1
|
57.2
|
1.0
|
|
HB2
|
A:HIS836
|
4.2
|
64.9
|
1.0
|
|
HG23
|
A:THR794
|
4.4
|
70.9
|
1.0
|
|
O
|
A:HIS836
|
4.5
|
69.0
|
1.0
|
|
O
|
A:ARG996
|
4.5
|
70.6
|
1.0
|
|
OG
|
A:SER652
|
4.5
|
65.1
|
1.0
|
|
H
|
A:CYS793
|
4.6
|
88.6
|
1.0
|
|
HG
|
A:SER652
|
4.6
|
78.2
|
1.0
|
|
CA
|
A:HIS997
|
4.6
|
51.5
|
1.0
|
|
C
|
A:HIS836
|
4.7
|
47.5
|
1.0
|
|
CA
|
A:CYS793
|
4.7
|
58.5
|
1.0
|
|
O
|
A:LEU835
|
4.8
|
63.9
|
1.0
|
|
HE2
|
A:HIS836
|
4.9
|
61.8
|
1.0
|
|
HD1
|
A:HIS651
|
4.9
|
102.9
|
1.0
|
|
N
|
A:HIS836
|
4.9
|
49.5
|
1.0
|
|
HD2
|
A:HIS997
|
4.9
|
76.2
|
1.0
|
|
HE2
|
A:HIS997
|
4.9
|
92.2
|
1.0
|
|
C
|
A:ARG996
|
4.9
|
64.3
|
1.0
|
|
HD2
|
A:HIS836
|
4.9
|
68.7
|
1.0
|
|
N
|
A:HIS997
|
5.0
|
54.3
|
1.0
|
|
Zinc binding site 2 out
of 6 in 9grn
Go back to
Zinc Binding Sites List in 9grn
Zinc binding site 2 out
of 6 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, 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 (Apo, Loop Deletion Residues 848-918) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2012
b:108.9
occ:1.00
|
OE2
|
D:GLU575
|
1.9
|
96.0
|
1.0
|
|
OE2
|
A:GLU575
|
2.0
|
120.5
|
1.0
|
|
ND1
|
D:HIS573
|
2.3
|
91.5
|
1.0
|
|
ND1
|
A:HIS573
|
2.3
|
96.6
|
1.0
|
|
CD
|
D:GLU575
|
2.6
|
100.1
|
1.0
|
|
CD
|
A:GLU575
|
2.6
|
110.3
|
1.0
|
|
OE1
|
D:GLU575
|
2.7
|
97.2
|
1.0
|
|
OE1
|
A:GLU575
|
2.7
|
111.3
|
1.0
|
|
HB3
|
A:HIS573
|
2.9
|
121.7
|
1.0
|
|
HA
|
A:HIS573
|
3.1
|
105.6
|
1.0
|
|
CE1
|
D:HIS573
|
3.2
|
96.8
|
1.0
|
|
CG
|
A:HIS573
|
3.2
|
108.8
|
1.0
|
|
HB3
|
D:HIS573
|
3.2
|
157.0
|
1.0
|
|
HE1
|
D:HIS573
|
3.3
|
116.2
|
1.0
|
|
CE1
|
A:HIS573
|
3.3
|
112.0
|
1.0
|
|
CG
|
D:HIS573
|
3.3
|
90.8
|
1.0
|
|
CB
|
A:HIS573
|
3.4
|
101.4
|
1.0
|
|
HA
|
D:HIS573
|
3.5
|
123.8
|
1.0
|
|
H
|
A:LYS574
|
3.5
|
113.1
|
1.0
|
|
HE1
|
A:HIS573
|
3.5
|
134.5
|
1.0
|
|
CB
|
D:HIS573
|
3.7
|
130.8
|
1.0
|
|
CA
|
A:HIS573
|
3.7
|
88.4
|
1.0
|
|
H
|
D:LYS574
|
3.8
|
116.3
|
1.0
|
|
CG
|
A:GLU575
|
4.1
|
100.3
|
1.0
|
|
CG
|
D:GLU575
|
4.1
|
108.8
|
1.0
|
|
CA
|
D:HIS573
|
4.1
|
103.0
|
1.0
|
|
N
|
A:LYS574
|
4.2
|
94.2
|
1.0
|
|
H
|
A:GLU575
|
4.2
|
125.2
|
1.0
|
|
HG2
|
A:GLU575
|
4.3
|
120.4
|
1.0
|
|
HB2
|
A:HIS573
|
4.3
|
121.7
|
1.0
|
|
NE2
|
D:HIS573
|
4.3
|
103.2
|
1.0
|
|
CD2
|
A:HIS573
|
4.4
|
111.3
|
1.0
|
|
H
|
D:GLU575
|
4.4
|
106.0
|
1.0
|
|
HG3
|
D:GLU575
|
4.4
|
130.7
|
1.0
|
|
NE2
|
A:HIS573
|
4.4
|
105.3
|
1.0
|
|
HG2
|
D:GLU575
|
4.4
|
130.7
|
1.0
|
|
CD2
|
D:HIS573
|
4.4
|
116.4
|
1.0
|
|
HG3
|
A:GLU575
|
4.5
|
120.4
|
1.0
|
|
N
|
D:LYS574
|
4.5
|
96.9
|
1.0
|
|
C
|
A:HIS573
|
4.5
|
88.2
|
1.0
|
|
HB2
|
D:HIS573
|
4.6
|
157.0
|
1.0
|
|
C
|
D:HIS573
|
4.8
|
91.9
|
1.0
|
|
N
|
A:GLU575
|
4.9
|
104.3
|
1.0
|
|
N
|
A:HIS573
|
4.9
|
88.6
|
1.0
|
|
HB3
|
D:GLU575
|
5.0
|
103.7
|
1.0
|
|
Zinc binding site 3 out
of 6 in 9grn
Go back to
Zinc Binding Sites List in 9grn
Zinc binding site 3 out
of 6 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, 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 3 of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2007
b:134.4
occ:1.00
|
HD1
|
B:HIS997
|
1.6
|
124.7
|
1.0
|
|
NE2
|
B:HIS651
|
2.0
|
63.2
|
1.0
|
|
ND1
|
B:HIS836
|
2.0
|
64.3
|
1.0
|
|
ND1
|
B:HIS997
|
2.0
|
103.8
|
1.0
|
|
SG
|
B:CYS793
|
2.3
|
59.9
|
1.0
|
|
HB2
|
B:HIS997
|
2.7
|
85.6
|
1.0
|
|
CG
|
B:HIS997
|
2.8
|
85.6
|
1.0
|
|
CE1
|
B:HIS997
|
2.9
|
97.9
|
1.0
|
|
CE1
|
B:HIS836
|
2.9
|
74.7
|
1.0
|
|
CE1
|
B:HIS651
|
3.0
|
102.5
|
1.0
|
|
CD2
|
B:HIS651
|
3.0
|
97.0
|
1.0
|
|
HB3
|
B:HIS836
|
3.0
|
92.6
|
1.0
|
|
CG
|
B:HIS836
|
3.1
|
76.8
|
1.0
|
|
HE1
|
B:HIS836
|
3.1
|
89.7
|
1.0
|
|
HE1
|
B:HIS997
|
3.2
|
117.6
|
1.0
|
|
HD2
|
B:HIS651
|
3.2
|
116.5
|
1.0
|
|
HE1
|
B:HIS651
|
3.2
|
123.1
|
1.0
|
|
CB
|
B:HIS997
|
3.2
|
71.3
|
1.0
|
|
HB3
|
B:CYS793
|
3.4
|
92.3
|
1.0
|
|
CB
|
B:CYS793
|
3.4
|
76.8
|
1.0
|
|
CB
|
B:HIS836
|
3.4
|
77.1
|
1.0
|
|
HA
|
B:HIS836
|
3.5
|
83.9
|
1.0
|
|
HB3
|
B:HIS997
|
3.5
|
85.6
|
1.0
|
|
HB2
|
B:CYS793
|
3.6
|
92.3
|
1.0
|
|
CD2
|
B:HIS997
|
3.7
|
94.7
|
1.0
|
|
NE2
|
B:HIS997
|
3.8
|
91.6
|
1.0
|
|
CA
|
B:HIS836
|
4.0
|
69.8
|
1.0
|
|
NE2
|
B:HIS836
|
4.1
|
68.4
|
1.0
|
|
ND1
|
B:HIS651
|
4.1
|
104.8
|
1.0
|
|
CG
|
B:HIS651
|
4.1
|
97.3
|
1.0
|
|
CD2
|
B:HIS836
|
4.1
|
62.8
|
1.0
|
|
O
|
B:ARG996
|
4.2
|
106.3
|
1.0
|
|
OG
|
B:SER652
|
4.3
|
91.0
|
1.0
|
|
HB2
|
B:HIS836
|
4.3
|
92.6
|
1.0
|
|
HG
|
B:SER652
|
4.4
|
109.3
|
1.0
|
|
CA
|
B:HIS997
|
4.5
|
66.8
|
1.0
|
|
HD2
|
B:HIS997
|
4.6
|
113.7
|
1.0
|
|
HG23
|
B:THR794
|
4.6
|
90.8
|
1.0
|
|
C
|
B:ARG996
|
4.6
|
96.6
|
1.0
|
|
O
|
B:HIS836
|
4.6
|
82.6
|
1.0
|
|
H
|
B:CYS793
|
4.7
|
119.3
|
1.0
|
|
N
|
B:HIS997
|
4.8
|
80.2
|
1.0
|
|
O
|
B:ASP995
|
4.8
|
82.7
|
1.0
|
|
HE2
|
B:HIS836
|
4.8
|
82.2
|
1.0
|
|
CA
|
B:CYS793
|
4.8
|
79.9
|
1.0
|
|
C
|
B:HIS836
|
4.9
|
72.6
|
1.0
|
|
HD1
|
B:HIS651
|
4.9
|
125.8
|
1.0
|
|
O
|
B:LEU835
|
5.0
|
71.2
|
1.0
|
|
Zinc binding site 4 out
of 6 in 9grn
Go back to
Zinc Binding Sites List in 9grn
Zinc binding site 4 out
of 6 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, 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 4 of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2008
b:115.3
occ:1.00
|
OE2
|
C:GLU575
|
1.9
|
85.2
|
1.0
|
|
OE2
|
B:GLU575
|
2.1
|
102.6
|
1.0
|
|
ND1
|
B:HIS573
|
2.3
|
95.0
|
1.0
|
|
ND1
|
C:HIS573
|
2.3
|
83.7
|
1.0
|
|
OE1
|
C:GLU575
|
2.4
|
102.0
|
1.0
|
|
CD
|
C:GLU575
|
2.5
|
78.7
|
1.0
|
|
OE1
|
B:GLU575
|
2.6
|
86.3
|
1.0
|
|
CD
|
B:GLU575
|
2.6
|
101.8
|
1.0
|
|
HB3
|
B:HIS573
|
2.9
|
97.2
|
1.0
|
|
HA
|
B:HIS573
|
3.0
|
111.7
|
1.0
|
|
CG
|
B:HIS573
|
3.2
|
88.2
|
1.0
|
|
CE1
|
C:HIS573
|
3.2
|
80.0
|
1.0
|
|
HB3
|
C:HIS573
|
3.3
|
123.2
|
1.0
|
|
HE1
|
C:HIS573
|
3.3
|
96.1
|
1.0
|
|
CB
|
B:HIS573
|
3.3
|
81.0
|
1.0
|
|
CE1
|
B:HIS573
|
3.3
|
103.2
|
1.0
|
|
CG
|
C:HIS573
|
3.3
|
100.8
|
1.0
|
|
H
|
B:LYS574
|
3.4
|
110.9
|
1.0
|
|
HA
|
C:HIS573
|
3.4
|
117.4
|
1.0
|
|
HE1
|
B:HIS573
|
3.6
|
123.9
|
1.0
|
|
H
|
C:LYS574
|
3.6
|
122.7
|
1.0
|
|
CA
|
B:HIS573
|
3.6
|
93.0
|
1.0
|
|
CB
|
C:HIS573
|
3.7
|
102.6
|
1.0
|
|
CG
|
C:GLU575
|
4.0
|
101.2
|
1.0
|
|
CA
|
C:HIS573
|
4.0
|
97.8
|
1.0
|
|
CG
|
B:GLU575
|
4.1
|
102.2
|
1.0
|
|
N
|
B:LYS574
|
4.1
|
92.3
|
1.0
|
|
H
|
B:GLU575
|
4.1
|
106.5
|
1.0
|
|
HG2
|
B:GLU575
|
4.3
|
122.8
|
1.0
|
|
HB2
|
B:HIS573
|
4.3
|
97.2
|
1.0
|
|
H
|
C:GLU575
|
4.3
|
99.2
|
1.0
|
|
HG3
|
C:GLU575
|
4.3
|
121.5
|
1.0
|
|
N
|
C:LYS574
|
4.3
|
102.2
|
1.0
|
|
HG2
|
C:GLU575
|
4.3
|
121.5
|
1.0
|
|
NE2
|
C:HIS573
|
4.3
|
103.4
|
1.0
|
|
CD2
|
B:HIS573
|
4.4
|
90.0
|
1.0
|
|
C
|
B:HIS573
|
4.4
|
89.9
|
1.0
|
|
NE2
|
B:HIS573
|
4.4
|
103.7
|
1.0
|
|
CD2
|
C:HIS573
|
4.4
|
107.5
|
1.0
|
|
HG3
|
B:GLU575
|
4.5
|
122.8
|
1.0
|
|
HB2
|
C:HIS573
|
4.6
|
123.2
|
1.0
|
|
HB3
|
C:GLU575
|
4.7
|
106.4
|
1.0
|
|
C
|
C:HIS573
|
4.7
|
76.9
|
1.0
|
|
N
|
B:GLU575
|
4.8
|
88.7
|
1.0
|
|
N
|
B:HIS573
|
4.8
|
94.3
|
1.0
|
|
N
|
C:GLU575
|
4.9
|
82.6
|
1.0
|
|
HB3
|
B:GLU575
|
4.9
|
130.6
|
1.0
|
|
CB
|
C:GLU575
|
4.9
|
88.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 9grn
Go back to
Zinc Binding Sites List in 9grn
Zinc binding site 5 out
of 6 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, 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 5 of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1112
b:121.5
occ:1.00
|
ND1
|
C:HIS997
|
2.0
|
76.8
|
1.0
|
|
NE2
|
C:HIS651
|
2.0
|
99.2
|
1.0
|
|
ND1
|
C:HIS836
|
2.0
|
78.7
|
1.0
|
|
SG
|
C:CYS793
|
2.3
|
72.8
|
1.0
|
|
HB3
|
C:HIS836
|
2.6
|
122.6
|
1.0
|
|
CE1
|
C:HIS997
|
2.9
|
122.0
|
1.0
|
|
CG
|
C:HIS836
|
2.9
|
91.1
|
1.0
|
|
CE1
|
C:HIS651
|
2.9
|
93.6
|
1.0
|
|
HE1
|
C:HIS651
|
3.0
|
112.4
|
1.0
|
|
HE1
|
C:HIS997
|
3.0
|
146.4
|
1.0
|
|
CE1
|
C:HIS836
|
3.0
|
111.9
|
1.0
|
|
CG
|
C:HIS997
|
3.1
|
87.9
|
1.0
|
|
CD2
|
C:HIS651
|
3.1
|
112.0
|
1.0
|
|
CB
|
C:HIS836
|
3.2
|
102.1
|
1.0
|
|
HB2
|
C:HIS997
|
3.2
|
90.3
|
1.0
|
|
HE1
|
C:HIS836
|
3.3
|
134.3
|
1.0
|
|
HD2
|
C:HIS651
|
3.3
|
134.5
|
1.0
|
|
HA
|
C:HIS836
|
3.3
|
105.8
|
1.0
|
|
HB3
|
C:HIS997
|
3.4
|
90.3
|
1.0
|
|
CB
|
C:HIS997
|
3.5
|
75.6
|
1.0
|
|
CB
|
C:CYS793
|
3.7
|
76.9
|
1.0
|
|
CA
|
C:HIS836
|
3.8
|
88.1
|
1.0
|
|
HB3
|
C:CYS793
|
3.9
|
92.4
|
1.0
|
|
HB2
|
C:CYS793
|
3.9
|
92.4
|
1.0
|
|
HB2
|
C:HIS836
|
4.0
|
122.6
|
1.0
|
|
NE2
|
C:HIS997
|
4.0
|
130.7
|
1.0
|
|
CD2
|
C:HIS836
|
4.0
|
76.6
|
1.0
|
|
ND1
|
C:HIS651
|
4.0
|
94.3
|
1.0
|
|
NE2
|
C:HIS836
|
4.1
|
88.3
|
1.0
|
|
CD2
|
C:HIS997
|
4.1
|
96.7
|
1.0
|
|
CG
|
C:HIS651
|
4.2
|
97.7
|
1.0
|
|
HG23
|
C:THR794
|
4.3
|
145.9
|
1.0
|
|
O
|
C:HIS836
|
4.4
|
57.0
|
1.0
|
|
HG
|
C:SER652
|
4.5
|
141.3
|
1.0
|
|
OG
|
C:SER652
|
4.6
|
117.7
|
1.0
|
|
C
|
C:HIS836
|
4.6
|
58.3
|
1.0
|
|
HH21
|
C:ARG791
|
4.6
|
168.3
|
1.0
|
|
HE2
|
C:HIS997
|
4.8
|
156.9
|
1.0
|
|
H
|
C:CYS793
|
4.8
|
146.1
|
1.0
|
|
HD1
|
C:HIS651
|
4.8
|
113.3
|
1.0
|
|
HD2
|
C:HIS836
|
4.9
|
92.0
|
1.0
|
|
HE2
|
C:HIS836
|
4.9
|
106.1
|
1.0
|
|
N
|
C:HIS836
|
4.9
|
76.2
|
1.0
|
|
NH2
|
C:ARG791
|
4.9
|
140.2
|
1.0
|
|
O
|
C:LEU835
|
5.0
|
82.1
|
1.0
|
|
CA
|
C:HIS997
|
5.0
|
91.1
|
1.0
|
|
Zinc binding site 6 out
of 6 in 9grn
Go back to
Zinc Binding Sites List in 9grn
Zinc binding site 6 out
of 6 in the Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, 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 6 of Crystal Structure of the Engineered C-Terminal Phosphatase Domain From Saccharomyces Cerevisiae VIP1 (Apo, Loop Deletion Residues 848-918) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1206
b:95.9
occ:1.00
|
ND1
|
D:HIS1064
|
2.0
|
92.8
|
1.0
|
|
NE2
|
D:HIS651
|
2.0
|
99.8
|
1.0
|
|
ND1
|
D:HIS836
|
2.0
|
111.9
|
1.0
|
|
SG
|
D:CYS793
|
2.3
|
79.4
|
1.0
|
|
HB3
|
D:HIS836
|
2.7
|
120.2
|
1.0
|
|
CE1
|
D:HIS1064
|
2.8
|
105.2
|
1.0
|
|
HE1
|
D:HIS1064
|
2.9
|
126.3
|
1.0
|
|
CE1
|
D:HIS651
|
2.9
|
94.5
|
1.0
|
|
CG
|
D:HIS836
|
2.9
|
108.7
|
1.0
|
|
CE1
|
D:HIS836
|
3.0
|
113.6
|
1.0
|
|
CD2
|
D:HIS651
|
3.0
|
119.8
|
1.0
|
|
HE1
|
D:HIS651
|
3.1
|
113.0
|
1.0
|
|
CG
|
D:HIS1064
|
3.1
|
90.6
|
1.0
|
|
CB
|
D:HIS836
|
3.2
|
100.1
|
1.0
|
|
HE1
|
D:HIS836
|
3.3
|
136.4
|
1.0
|
|
HD2
|
D:HIS651
|
3.3
|
143.8
|
1.0
|
|
HB2
|
D:HIS1064
|
3.3
|
97.0
|
1.0
|
|
HA
|
D:HIS836
|
3.5
|
109.2
|
1.0
|
|
CB
|
D:HIS1064
|
3.6
|
81.1
|
1.0
|
|
HB3
|
D:HIS1064
|
3.6
|
97.0
|
1.0
|
|
CB
|
D:CYS793
|
3.7
|
95.6
|
1.0
|
|
HB3
|
D:CYS793
|
3.8
|
114.8
|
1.0
|
|
HB2
|
D:CYS793
|
3.8
|
114.8
|
1.0
|
|
CA
|
D:HIS836
|
3.9
|
91.0
|
1.0
|
|
HG1
|
D:THR650
|
4.0
|
142.2
|
1.0
|
|
NE2
|
D:HIS1064
|
4.0
|
131.2
|
1.0
|
|
CD2
|
D:HIS836
|
4.1
|
104.7
|
1.0
|
|
ND1
|
D:HIS651
|
4.1
|
115.2
|
1.0
|
|
NE2
|
D:HIS836
|
4.1
|
112.5
|
1.0
|
|
HB2
|
D:HIS836
|
4.1
|
120.2
|
1.0
|
|
CG
|
D:HIS651
|
4.1
|
118.3
|
1.0
|
|
CD2
|
D:HIS1064
|
4.2
|
119.9
|
1.0
|
|
HG23
|
D:THR794
|
4.2
|
153.1
|
1.0
|
|
O
|
D:HIS836
|
4.4
|
75.9
|
1.0
|
|
OG1
|
D:THR650
|
4.5
|
118.4
|
1.0
|
|
HD23
|
D:LEU835
|
4.6
|
124.6
|
1.0
|
|
HB2
|
D:SER652
|
4.7
|
147.3
|
1.0
|
|
C
|
D:HIS836
|
4.7
|
79.4
|
1.0
|
|
HE2
|
D:HIS1064
|
4.8
|
157.6
|
1.0
|
|
HD1
|
D:HIS651
|
4.8
|
138.3
|
1.0
|
|
HE2
|
D:HIS836
|
4.8
|
135.0
|
1.0
|
|
HD2
|
D:HIS836
|
4.9
|
125.8
|
1.0
|
|
H
|
D:CYS793
|
4.9
|
165.2
|
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 17:58:28 2025
|
