Calcium in PDB 3fz0: Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)
Enzymatic activity of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)
All present enzymatic activity of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh):
3.2.2.1;
Protein crystallography data
The structure of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh), PDB code: 3fz0
was solved by
A.Vandemeulebroucke,
C.Minici,
I.Bruno,
L.Muzzolini,
P.Tornaghi,
D.W.Parkin,
V.L.Schramm,
W.Versees,
J.Steyaert,
M.Degano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.93 /
2.50
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.690,
116.040,
204.760,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.9 /
22.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)
(pdb code 3fz0). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh), PDB code: 3fz0:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 3fz0
Go back to
Calcium Binding Sites List in 3fz0
Calcium binding site 1 out
of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca400
b:63.8
occ:1.00
|
O
|
A:HOH402
|
2.3
|
43.7
|
1.0
|
O
|
A:LEU131
|
2.4
|
61.9
|
1.0
|
OD2
|
A:ASP280
|
2.5
|
64.9
|
1.0
|
O
|
A:HOH386
|
2.5
|
38.5
|
1.0
|
OD1
|
A:ASP11
|
2.5
|
66.5
|
1.0
|
OD2
|
A:ASP16
|
2.6
|
62.6
|
1.0
|
OD1
|
A:ASP16
|
2.6
|
65.9
|
1.0
|
CG
|
A:ASP16
|
2.9
|
63.0
|
1.0
|
CG
|
A:ASP280
|
3.4
|
65.4
|
1.0
|
C
|
A:LEU131
|
3.6
|
61.5
|
1.0
|
OD1
|
A:ASP280
|
3.6
|
67.3
|
1.0
|
CG
|
A:ASP11
|
3.6
|
65.9
|
1.0
|
OD2
|
A:ASP11
|
4.1
|
65.6
|
1.0
|
O4
|
A:BTB401
|
4.3
|
50.3
|
1.0
|
CB
|
A:LEU131
|
4.3
|
60.4
|
1.0
|
OD1
|
A:ASP15
|
4.4
|
64.7
|
1.0
|
CB
|
A:ASP16
|
4.4
|
61.5
|
1.0
|
CA
|
A:GLY132
|
4.5
|
62.0
|
1.0
|
C4
|
A:BTB401
|
4.5
|
55.4
|
1.0
|
CA
|
A:LEU131
|
4.5
|
61.1
|
1.0
|
N
|
A:GLY132
|
4.5
|
61.5
|
1.0
|
O3
|
A:BTB401
|
4.5
|
52.0
|
1.0
|
ND2
|
A:ASN179
|
4.6
|
58.4
|
1.0
|
OD1
|
A:ASN179
|
4.6
|
63.2
|
1.0
|
OD2
|
A:ASP15
|
4.6
|
63.1
|
1.0
|
N
|
A:ASP11
|
4.6
|
64.8
|
1.0
|
CB
|
A:ASP280
|
4.8
|
63.9
|
1.0
|
CG
|
A:ASP15
|
4.8
|
64.4
|
1.0
|
CB
|
A:ASP11
|
4.9
|
65.5
|
1.0
|
N
|
A:ASP16
|
4.9
|
62.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 3fz0
Go back to
Calcium Binding Sites List in 3fz0
Calcium binding site 2 out
of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca400
b:62.4
occ:1.00
|
O
|
B:LEU131
|
2.3
|
62.3
|
1.0
|
O
|
B:HOH410
|
2.3
|
33.9
|
1.0
|
OD2
|
B:ASP280
|
2.4
|
65.5
|
1.0
|
OD1
|
B:ASP11
|
2.4
|
66.2
|
1.0
|
O
|
B:HOH409
|
2.4
|
28.7
|
1.0
|
OD2
|
B:ASP16
|
2.5
|
63.3
|
1.0
|
OD1
|
B:ASP16
|
2.6
|
65.6
|
1.0
|
O
|
B:HOH408
|
2.7
|
45.1
|
1.0
|
CG
|
B:ASP16
|
2.9
|
62.9
|
1.0
|
CG
|
B:ASP280
|
3.4
|
65.4
|
1.0
|
C
|
B:LEU131
|
3.5
|
61.5
|
1.0
|
OD1
|
B:ASP280
|
3.6
|
66.7
|
1.0
|
CG
|
B:ASP11
|
3.6
|
65.6
|
1.0
|
O4
|
B:BTB401
|
3.9
|
51.3
|
1.0
|
OD2
|
B:ASP11
|
4.1
|
65.1
|
1.0
|
O
|
B:HOH364
|
4.1
|
54.5
|
1.0
|
CB
|
B:LEU131
|
4.2
|
60.4
|
1.0
|
O3
|
B:BTB401
|
4.2
|
50.7
|
1.0
|
CB
|
B:ASP16
|
4.4
|
61.4
|
1.0
|
CA
|
B:GLY132
|
4.4
|
61.7
|
1.0
|
N
|
B:GLY132
|
4.4
|
61.3
|
1.0
|
CA
|
B:LEU131
|
4.4
|
60.8
|
1.0
|
OD1
|
B:ASP15
|
4.5
|
64.4
|
1.0
|
N
|
B:ASP11
|
4.6
|
64.7
|
1.0
|
ND2
|
B:ASN179
|
4.6
|
59.0
|
1.0
|
OD1
|
B:ASN179
|
4.7
|
63.4
|
1.0
|
CB
|
B:ASP280
|
4.7
|
63.9
|
1.0
|
OD2
|
B:ASP15
|
4.8
|
63.8
|
1.0
|
CB
|
B:ASP11
|
4.8
|
65.2
|
1.0
|
N
|
B:ASP16
|
4.9
|
62.0
|
1.0
|
CG
|
B:ASP15
|
5.0
|
64.6
|
1.0
|
CA
|
B:ASP16
|
5.0
|
61.5
|
1.0
|
OG1
|
B:THR10
|
5.0
|
63.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 3fz0
Go back to
Calcium Binding Sites List in 3fz0
Calcium binding site 3 out
of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca400
b:61.1
occ:1.00
|
O
|
C:HOH410
|
2.3
|
43.2
|
1.0
|
OD1
|
C:ASP11
|
2.3
|
66.2
|
1.0
|
O
|
C:LEU131
|
2.4
|
61.8
|
1.0
|
O
|
C:HOH411
|
2.5
|
42.4
|
1.0
|
OD2
|
C:ASP16
|
2.5
|
63.2
|
1.0
|
OD2
|
C:ASP280
|
2.5
|
64.9
|
1.0
|
OD1
|
C:ASP16
|
2.6
|
65.7
|
1.0
|
O
|
C:HOH407
|
2.6
|
45.1
|
1.0
|
CG
|
C:ASP16
|
2.9
|
62.8
|
1.0
|
CG
|
C:ASP11
|
3.5
|
65.9
|
1.0
|
CG
|
C:ASP280
|
3.5
|
65.2
|
1.0
|
C
|
C:LEU131
|
3.6
|
61.5
|
1.0
|
OD1
|
C:ASP280
|
3.7
|
67.1
|
1.0
|
OD2
|
C:ASP11
|
3.9
|
65.5
|
1.0
|
O4
|
C:BTB401
|
4.0
|
47.6
|
1.0
|
O3
|
C:BTB401
|
4.3
|
48.0
|
1.0
|
CB
|
C:ASP16
|
4.3
|
61.7
|
1.0
|
CB
|
C:LEU131
|
4.3
|
60.6
|
1.0
|
OD1
|
C:ASP15
|
4.4
|
64.5
|
1.0
|
CA
|
C:GLY132
|
4.5
|
62.0
|
1.0
|
N
|
C:ASP11
|
4.5
|
64.9
|
1.0
|
N
|
C:GLY132
|
4.5
|
61.5
|
1.0
|
CA
|
C:LEU131
|
4.6
|
61.1
|
1.0
|
ND2
|
C:ASN179
|
4.6
|
58.8
|
1.0
|
CB
|
C:ASP11
|
4.7
|
65.5
|
1.0
|
OD1
|
C:ASN179
|
4.8
|
63.7
|
1.0
|
OD2
|
C:ASP15
|
4.8
|
63.2
|
1.0
|
CB
|
C:ASP280
|
4.9
|
63.7
|
1.0
|
N
|
C:ASP16
|
4.9
|
61.9
|
1.0
|
CA
|
C:ASP16
|
4.9
|
61.6
|
1.0
|
CG
|
C:ASP15
|
4.9
|
64.3
|
1.0
|
CA
|
C:ASP11
|
4.9
|
65.7
|
1.0
|
OG1
|
C:THR10
|
5.0
|
63.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 3fz0
Go back to
Calcium Binding Sites List in 3fz0
Calcium binding site 4 out
of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca400
b:60.2
occ:1.00
|
O
|
D:HOH385
|
2.3
|
41.2
|
1.0
|
O
|
D:LEU131
|
2.4
|
62.0
|
1.0
|
O
|
D:HOH384
|
2.4
|
45.1
|
1.0
|
OD2
|
D:ASP280
|
2.4
|
65.0
|
1.0
|
OD2
|
D:ASP16
|
2.4
|
62.6
|
1.0
|
OD1
|
D:ASP11
|
2.5
|
66.5
|
1.0
|
OD1
|
D:ASP16
|
2.5
|
65.9
|
1.0
|
CG
|
D:ASP16
|
2.8
|
62.8
|
1.0
|
CG
|
D:ASP280
|
3.4
|
65.3
|
1.0
|
CG
|
D:ASP11
|
3.6
|
65.8
|
1.0
|
C
|
D:LEU131
|
3.6
|
61.6
|
1.0
|
OD1
|
D:ASP280
|
3.7
|
67.5
|
1.0
|
O3
|
D:BTB401
|
3.8
|
61.1
|
1.0
|
OD2
|
D:ASP11
|
4.0
|
65.8
|
1.0
|
CB
|
D:LEU131
|
4.2
|
60.5
|
1.0
|
CB
|
D:ASP16
|
4.3
|
61.6
|
1.0
|
OD1
|
D:ASP15
|
4.3
|
64.7
|
1.0
|
CA
|
D:GLY132
|
4.5
|
61.9
|
1.0
|
CA
|
D:LEU131
|
4.5
|
61.1
|
1.0
|
N
|
D:GLY132
|
4.5
|
61.8
|
1.0
|
O1
|
D:BTB401
|
4.5
|
57.3
|
1.0
|
N
|
D:ASP11
|
4.6
|
65.1
|
1.0
|
OD2
|
D:ASP15
|
4.7
|
63.4
|
1.0
|
OD1
|
D:ASN179
|
4.7
|
63.4
|
1.0
|
ND2
|
D:ASN179
|
4.8
|
59.0
|
1.0
|
CB
|
D:ASP280
|
4.8
|
63.8
|
1.0
|
N
|
D:ASP16
|
4.8
|
61.9
|
1.0
|
CB
|
D:ASP11
|
4.8
|
65.2
|
1.0
|
CA
|
D:ASP16
|
4.9
|
61.5
|
1.0
|
CG
|
D:ASP15
|
4.9
|
64.4
|
1.0
|
OG1
|
D:THR10
|
5.0
|
63.2
|
1.0
|
|
Reference:
A.Vandemeulebroucke,
C.Minici,
I.Bruno,
L.Muzzolini,
P.Tornaghi,
D.W.Parkin,
W.Versees,
J.Steyaert,
M.Degano.
Structure and Mechanism of the 6-Oxopurine Nucleosidase From Trypanosoma Brucei Brucei Biochemistry V. 49 8999 2010.
ISSN: ISSN 0006-2960
PubMed: 20825170
DOI: 10.1021/BI100697D
Page generated: Sat Jul 13 10:27:50 2024
|