Calcium in PDB 3g5i: Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor
Enzymatic activity of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor
All present enzymatic activity of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor:
3.2.2.8;
Protein crystallography data
The structure of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor, PDB code: 3g5i
was solved by
G.Garau,
L.Muzzolini,
P.Tornaghi,
M.Degano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.50 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.350,
82.910,
93.870,
90.00,
112.15,
90.00
|
R / Rfree (%)
|
20.3 /
24.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor
(pdb code 3g5i). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor, PDB code: 3g5i:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 3g5i
Go back to
Calcium Binding Sites List in 3g5i
Calcium binding site 1 out
of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:16.3
occ:1.00
|
O
|
A:HOH312
|
2.4
|
15.8
|
1.0
|
O
|
A:THR124
|
2.4
|
24.5
|
1.0
|
OD1
|
A:ASP10
|
2.4
|
30.5
|
1.0
|
OD2
|
A:ASP241
|
2.4
|
27.4
|
1.0
|
OD1
|
A:ASP15
|
2.5
|
22.9
|
1.0
|
O2'
|
A:DNB502
|
2.5
|
28.3
|
1.0
|
OD2
|
A:ASP15
|
2.5
|
24.5
|
1.0
|
O3'
|
A:DNB502
|
2.8
|
16.2
|
1.0
|
CG
|
A:ASP15
|
2.9
|
26.7
|
1.0
|
ND2
|
A:ASN39
|
3.3
|
38.4
|
1.0
|
CG
|
A:ASP241
|
3.4
|
28.2
|
1.0
|
C
|
A:THR124
|
3.5
|
24.8
|
1.0
|
CG
|
A:ASP10
|
3.5
|
29.2
|
1.0
|
C2'
|
A:DNB502
|
3.7
|
29.1
|
1.0
|
C3'
|
A:DNB502
|
3.7
|
27.0
|
1.0
|
OD1
|
A:ASP241
|
3.7
|
28.8
|
1.0
|
OD2
|
A:ASP10
|
3.9
|
28.9
|
1.0
|
N
|
A:GLY125
|
4.2
|
23.6
|
1.0
|
CA
|
A:GLY125
|
4.2
|
24.3
|
1.0
|
OG1
|
A:THR124
|
4.3
|
24.4
|
1.0
|
CB
|
A:ASP15
|
4.4
|
26.6
|
1.0
|
CG
|
A:ASN39
|
4.4
|
40.7
|
1.0
|
C1'
|
A:DNB502
|
4.4
|
32.6
|
1.0
|
OD1
|
A:ASP14
|
4.4
|
37.1
|
1.0
|
CB
|
A:THR124
|
4.4
|
25.4
|
1.0
|
N
|
A:ASP10
|
4.5
|
25.0
|
1.0
|
ND2
|
A:ASN166
|
4.5
|
24.1
|
1.0
|
O
|
A:ASP10
|
4.5
|
26.1
|
1.0
|
OD1
|
A:ASN166
|
4.5
|
22.8
|
1.0
|
CA
|
A:THR124
|
4.5
|
24.9
|
1.0
|
N4'
|
A:DNB502
|
4.6
|
26.1
|
1.0
|
C4'
|
A:DNB502
|
4.8
|
28.6
|
1.0
|
CB
|
A:ASP10
|
4.8
|
25.9
|
1.0
|
C
|
A:ASP10
|
4.8
|
26.3
|
1.0
|
OD2
|
A:ASP14
|
4.8
|
39.5
|
1.0
|
CB
|
A:ASP241
|
4.8
|
25.7
|
1.0
|
N
|
A:ASP15
|
4.8
|
27.2
|
1.0
|
OD1
|
A:ASN39
|
4.9
|
41.0
|
1.0
|
CA
|
A:ASP10
|
4.9
|
26.0
|
1.0
|
CG
|
A:ASP14
|
4.9
|
32.9
|
1.0
|
CG
|
A:ASN166
|
5.0
|
25.0
|
1.0
|
CA
|
A:ASP15
|
5.0
|
27.2
|
1.0
|
|
Calcium binding site 2 out
of 4 in 3g5i
Go back to
Calcium Binding Sites List in 3g5i
Calcium binding site 2 out
of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:19.8
occ:1.00
|
O2'
|
B:DNB502
|
2.4
|
27.1
|
0.7
|
OD1
|
B:ASP10
|
2.4
|
30.3
|
1.0
|
OD2
|
B:ASP241
|
2.5
|
26.8
|
1.0
|
OD2
|
B:ASP15
|
2.5
|
25.4
|
1.0
|
OD1
|
B:ASP15
|
2.5
|
22.1
|
1.0
|
O
|
B:THR124
|
2.5
|
24.1
|
1.0
|
O
|
B:HOH455
|
2.5
|
24.4
|
1.0
|
O3'
|
B:DNB502
|
2.6
|
16.9
|
0.7
|
CG
|
B:ASP15
|
2.8
|
26.6
|
1.0
|
ND2
|
B:ASN39
|
3.2
|
38.8
|
1.0
|
CG
|
B:ASP241
|
3.5
|
28.6
|
1.0
|
CG
|
B:ASP10
|
3.5
|
28.8
|
1.0
|
C
|
B:THR124
|
3.6
|
24.8
|
1.0
|
C2'
|
B:DNB502
|
3.6
|
26.7
|
0.7
|
C3'
|
B:DNB502
|
3.6
|
25.2
|
0.7
|
OD1
|
B:ASP241
|
3.8
|
28.2
|
1.0
|
OD2
|
B:ASP10
|
4.0
|
28.8
|
1.0
|
N
|
B:GLY125
|
4.2
|
24.1
|
1.0
|
CA
|
B:GLY125
|
4.2
|
24.0
|
1.0
|
CG
|
B:ASN39
|
4.3
|
41.1
|
1.0
|
CB
|
B:ASP15
|
4.3
|
26.3
|
1.0
|
O
|
B:ASP10
|
4.3
|
26.9
|
1.0
|
OG1
|
B:THR124
|
4.4
|
24.5
|
1.0
|
C1'
|
B:DNB502
|
4.4
|
30.0
|
0.7
|
OD1
|
B:ASP14
|
4.5
|
37.2
|
1.0
|
CB
|
B:THR124
|
4.5
|
25.1
|
1.0
|
N
|
B:ASP10
|
4.5
|
25.2
|
1.0
|
OD2
|
B:ASP14
|
4.6
|
39.6
|
1.0
|
OD1
|
B:ASN166
|
4.6
|
23.0
|
1.0
|
ND2
|
B:ASN166
|
4.6
|
22.9
|
1.0
|
CA
|
B:THR124
|
4.7
|
24.5
|
1.0
|
C4'
|
B:DNB502
|
4.7
|
26.6
|
0.7
|
N4'
|
B:DNB502
|
4.7
|
27.2
|
0.7
|
C
|
B:ASP10
|
4.7
|
26.8
|
1.0
|
OD1
|
B:ASN39
|
4.7
|
41.6
|
1.0
|
N
|
B:ASP15
|
4.8
|
27.6
|
1.0
|
CB
|
B:ASP10
|
4.8
|
26.0
|
1.0
|
CB
|
B:ASP241
|
4.8
|
25.9
|
1.0
|
CG
|
B:ASP14
|
4.8
|
33.2
|
1.0
|
CA
|
B:ASP10
|
4.9
|
26.0
|
1.0
|
CA
|
B:ASP15
|
4.9
|
27.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 3g5i
Go back to
Calcium Binding Sites List in 3g5i
Calcium binding site 3 out
of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca501
b:19.5
occ:1.00
|
O
|
C:THR124
|
2.4
|
24.6
|
1.0
|
O
|
C:HOH573
|
2.4
|
22.5
|
1.0
|
OD2
|
C:ASP241
|
2.4
|
27.1
|
1.0
|
OD1
|
C:ASP15
|
2.4
|
22.9
|
1.0
|
OD2
|
C:ASP15
|
2.5
|
25.2
|
1.0
|
OD1
|
C:ASP10
|
2.5
|
31.1
|
1.0
|
O3'
|
C:DNB502
|
2.6
|
25.0
|
0.7
|
O2'
|
C:DNB502
|
2.6
|
32.1
|
0.7
|
CG
|
C:ASP15
|
2.8
|
26.7
|
1.0
|
CG
|
C:ASP241
|
3.4
|
28.1
|
1.0
|
ND2
|
C:ASN39
|
3.4
|
39.2
|
1.0
|
C
|
C:THR124
|
3.5
|
25.2
|
1.0
|
CG
|
C:ASP10
|
3.6
|
28.6
|
1.0
|
OD1
|
C:ASP241
|
3.7
|
27.7
|
1.0
|
C2'
|
C:DNB502
|
3.7
|
34.8
|
0.7
|
C3'
|
C:DNB502
|
3.7
|
32.6
|
0.7
|
OD2
|
C:ASP10
|
4.1
|
28.5
|
1.0
|
OG1
|
C:THR124
|
4.2
|
25.0
|
1.0
|
CB
|
C:ASP15
|
4.2
|
26.9
|
1.0
|
N
|
C:GLY125
|
4.3
|
24.2
|
1.0
|
CA
|
C:GLY125
|
4.3
|
24.2
|
1.0
|
O
|
C:ASP10
|
4.3
|
26.8
|
1.0
|
CB
|
C:THR124
|
4.3
|
25.2
|
1.0
|
OD1
|
C:ASP14
|
4.4
|
37.8
|
1.0
|
C1'
|
C:DNB502
|
4.5
|
37.7
|
0.7
|
CG
|
C:ASN39
|
4.5
|
40.9
|
1.0
|
N
|
C:ASP10
|
4.6
|
25.5
|
1.0
|
CA
|
C:THR124
|
4.6
|
25.1
|
1.0
|
OD2
|
C:ASP14
|
4.6
|
39.7
|
1.0
|
ND2
|
C:ASN166
|
4.6
|
22.9
|
1.0
|
C4'
|
C:DNB502
|
4.7
|
33.8
|
0.7
|
C
|
C:ASP10
|
4.7
|
26.6
|
1.0
|
N4'
|
C:DNB502
|
4.7
|
35.8
|
0.7
|
CB
|
C:ASP241
|
4.7
|
26.0
|
1.0
|
N
|
C:ASP15
|
4.7
|
27.2
|
1.0
|
OD1
|
C:ASN166
|
4.8
|
23.4
|
1.0
|
CG
|
C:ASP14
|
4.8
|
33.5
|
1.0
|
CA
|
C:ASP15
|
4.9
|
27.1
|
1.0
|
CB
|
C:ASP10
|
4.9
|
25.8
|
1.0
|
OD1
|
C:ASN39
|
4.9
|
41.6
|
1.0
|
CA
|
C:ASP10
|
4.9
|
25.9
|
1.0
|
|
Calcium binding site 4 out
of 4 in 3g5i
Go back to
Calcium Binding Sites List in 3g5i
Calcium binding site 4 out
of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca501
b:20.2
occ:1.00
|
O
|
D:HOH390
|
2.4
|
17.9
|
1.0
|
OD1
|
D:ASP10
|
2.4
|
30.8
|
1.0
|
O
|
D:THR124
|
2.5
|
24.9
|
1.0
|
OD2
|
D:ASP15
|
2.5
|
25.1
|
1.0
|
OD2
|
D:ASP241
|
2.5
|
27.2
|
1.0
|
OD1
|
D:ASP15
|
2.5
|
22.2
|
1.0
|
O2'
|
D:DNB502
|
2.5
|
40.5
|
1.0
|
CG
|
D:ASP15
|
2.8
|
26.5
|
1.0
|
O3'
|
D:DNB502
|
2.9
|
30.7
|
1.0
|
ND2
|
D:ASN39
|
3.3
|
39.0
|
1.0
|
CG
|
D:ASP10
|
3.5
|
28.6
|
1.0
|
CG
|
D:ASP241
|
3.5
|
28.5
|
1.0
|
C
|
D:THR124
|
3.6
|
24.9
|
1.0
|
C2'
|
D:DNB502
|
3.7
|
39.0
|
1.0
|
OD1
|
D:ASP241
|
3.8
|
28.9
|
1.0
|
C3'
|
D:DNB502
|
3.8
|
37.2
|
1.0
|
OD2
|
D:ASP10
|
3.9
|
28.8
|
1.0
|
CA
|
D:GLY125
|
4.2
|
24.1
|
1.0
|
N
|
D:GLY125
|
4.2
|
24.4
|
1.0
|
CG
|
D:ASN39
|
4.3
|
40.9
|
1.0
|
CB
|
D:ASP15
|
4.3
|
26.5
|
1.0
|
C1'
|
D:DNB502
|
4.4
|
42.6
|
1.0
|
O
|
D:ASP10
|
4.4
|
26.6
|
1.0
|
N
|
D:ASP10
|
4.4
|
24.9
|
1.0
|
OG1
|
D:THR124
|
4.4
|
25.0
|
1.0
|
OD1
|
D:ASP14
|
4.5
|
37.5
|
1.0
|
CB
|
D:THR124
|
4.5
|
25.1
|
1.0
|
N4'
|
D:DNB502
|
4.6
|
39.2
|
1.0
|
OD1
|
D:ASN166
|
4.6
|
22.7
|
1.0
|
CA
|
D:THR124
|
4.6
|
24.7
|
1.0
|
ND2
|
D:ASN166
|
4.7
|
23.3
|
1.0
|
C
|
D:ASP10
|
4.7
|
26.4
|
1.0
|
OD2
|
D:ASP14
|
4.7
|
39.5
|
1.0
|
CB
|
D:ASP10
|
4.7
|
25.9
|
1.0
|
C4'
|
D:DNB502
|
4.8
|
38.2
|
1.0
|
OD1
|
D:ASN39
|
4.8
|
41.4
|
1.0
|
CA
|
D:ASP10
|
4.8
|
25.8
|
1.0
|
N
|
D:ASP15
|
4.8
|
27.3
|
1.0
|
CB
|
D:ASP241
|
4.9
|
26.1
|
1.0
|
CG
|
D:ASP14
|
4.9
|
33.3
|
1.0
|
CA
|
D:ASP15
|
5.0
|
26.8
|
1.0
|
|
Reference:
G.Garau,
L.Muzzolini,
P.Tornaghi,
M.Degano.
Crystal Structure of the Riha Nucleoside Hydrolase Bound to A Competitive Inhibitor To Be Published.
Page generated: Sat Jul 13 10:29:19 2024
|