Calcium in PDB 7l9f: Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
Enzymatic activity of Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
All present enzymatic activity of Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose:
3.2.1.143;
Protein crystallography data
The structure of Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose, PDB code: 7l9f
was solved by
Y.Pourfarjam,
I.Kurinov,
J.Moss,
I.K.Kim,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
67.88 /
1.75
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.93,
71.473,
115.595,
93.97,
94.33,
107.41
|
|
R / Rfree (%)
|
14.9 /
18.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
(pdb code 7l9f). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose, PDB code: 7l9f:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 1 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 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 Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:19.7
occ:1.00
|
O
|
C:HOH501
|
2.0
|
27.2
|
1.0
|
|
OG1
|
C:THR317
|
2.4
|
12.0
|
1.0
|
|
OD1
|
C:ASP314
|
2.4
|
21.2
|
1.0
|
|
O3D
|
C:AR6401
|
2.4
|
15.7
|
1.0
|
|
OD1
|
C:ASP316
|
2.5
|
22.6
|
1.0
|
|
O1D
|
C:AR6401
|
2.5
|
24.8
|
1.0
|
|
HO3D
|
C:AR6401
|
2.6
|
18.9
|
1.0
|
|
O
|
C:HOH524
|
2.6
|
29.5
|
1.0
|
|
O2D
|
C:AR6401
|
2.7
|
26.6
|
1.0
|
|
OD2
|
C:ASP314
|
2.9
|
16.1
|
1.0
|
|
CG
|
C:ASP314
|
3.0
|
21.7
|
1.0
|
|
HD1
|
C:AR6401
|
3.0
|
29.8
|
1.0
|
|
HO2D
|
C:AR6401
|
3.0
|
31.9
|
1.0
|
|
CG
|
C:ASP316
|
3.4
|
21.1
|
1.0
|
|
C3D
|
C:AR6401
|
3.5
|
15.4
|
1.0
|
|
C2D
|
C:AR6401
|
3.5
|
20.2
|
1.0
|
|
CB
|
C:THR317
|
3.5
|
14.3
|
1.0
|
|
HB
|
C:THR317
|
3.5
|
17.2
|
1.0
|
|
H
|
C:THR317
|
3.6
|
13.7
|
1.0
|
|
C1D
|
C:AR6401
|
3.6
|
26.8
|
1.0
|
|
OD2
|
C:ASP316
|
3.6
|
34.0
|
1.0
|
|
CA
|
C:CA403
|
3.6
|
30.4
|
1.0
|
|
H4D
|
C:AR6401
|
4.0
|
26.3
|
1.0
|
|
OE2
|
C:GLU41
|
4.0
|
30.0
|
1.0
|
|
N
|
C:THR317
|
4.1
|
11.4
|
1.0
|
|
C4D
|
C:AR6401
|
4.2
|
21.9
|
1.0
|
|
OD1
|
C:ASP78
|
4.2
|
38.2
|
1.0
|
|
HD21
|
C:ASN151
|
4.3
|
17.4
|
1.0
|
|
H3D
|
C:AR6401
|
4.3
|
18.5
|
1.0
|
|
H1D
|
C:AR6401
|
4.3
|
32.1
|
1.0
|
|
HG21
|
C:THR317
|
4.4
|
13.5
|
1.0
|
|
O4D
|
C:AR6401
|
4.4
|
24.9
|
1.0
|
|
O
|
C:HOH613
|
4.4
|
20.5
|
1.0
|
|
CA
|
C:THR317
|
4.4
|
14.5
|
1.0
|
|
HG22
|
C:ILE271
|
4.4
|
22.9
|
1.0
|
|
CB
|
C:ASP314
|
4.5
|
13.5
|
1.0
|
|
CD
|
C:GLU41
|
4.5
|
42.2
|
1.0
|
|
H2D
|
C:AR6401
|
4.5
|
24.3
|
1.0
|
|
CG2
|
C:THR317
|
4.6
|
11.4
|
1.0
|
|
OE1
|
C:GLU41
|
4.6
|
38.0
|
1.0
|
|
OD2
|
C:ASP78
|
4.6
|
17.4
|
1.0
|
|
CB
|
C:ASP316
|
4.8
|
12.5
|
1.0
|
|
OD1
|
C:ASN151
|
4.8
|
12.4
|
1.0
|
|
HA
|
C:THR317
|
4.8
|
17.4
|
1.0
|
|
HA
|
C:ASP314
|
4.8
|
13.3
|
1.0
|
|
H
|
C:ASP316
|
4.8
|
15.1
|
1.0
|
|
CG
|
C:ASP78
|
4.9
|
25.4
|
1.0
|
|
OD1
|
C:ASP77
|
4.9
|
12.8
|
1.0
|
|
HB2
|
C:ASP314
|
4.9
|
16.2
|
1.0
|
|
HB3
|
C:ASP314
|
4.9
|
16.2
|
1.0
|
|
C
|
C:ASP316
|
5.0
|
12.4
|
1.0
|
|
Calcium binding site 2 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 2 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 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 Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca403
b:30.4
occ:1.00
|
O
|
C:HOH501
|
2.1
|
27.2
|
1.0
|
|
OD1
|
C:ASP78
|
2.2
|
38.2
|
1.0
|
|
OD1
|
C:ASP77
|
2.2
|
12.8
|
1.0
|
|
OG1
|
C:THR76
|
2.4
|
13.9
|
1.0
|
|
O
|
C:HOH613
|
2.5
|
20.5
|
1.0
|
|
OD2
|
C:ASP316
|
2.6
|
34.0
|
1.0
|
|
HB
|
C:THR76
|
2.9
|
19.9
|
1.0
|
|
HO2D
|
C:AR6401
|
3.2
|
31.9
|
1.0
|
|
CB
|
C:THR76
|
3.2
|
16.5
|
1.0
|
|
H
|
C:ASP78
|
3.2
|
14.0
|
1.0
|
|
CG
|
C:ASP316
|
3.3
|
21.1
|
1.0
|
|
O
|
C:HOH524
|
3.3
|
29.5
|
1.0
|
|
O2D
|
C:AR6401
|
3.3
|
26.6
|
1.0
|
|
CG
|
C:ASP77
|
3.4
|
13.1
|
1.0
|
|
CG
|
C:ASP78
|
3.5
|
25.4
|
1.0
|
|
H
|
C:ASP77
|
3.5
|
14.0
|
1.0
|
|
HG21
|
C:THR76
|
3.5
|
24.8
|
1.0
|
|
CA
|
C:CA402
|
3.6
|
19.7
|
1.0
|
|
OD1
|
C:ASP316
|
3.7
|
22.6
|
1.0
|
|
CG2
|
C:THR76
|
3.9
|
20.6
|
1.0
|
|
HB2
|
C:ASP316
|
3.9
|
15.0
|
1.0
|
|
OD2
|
C:ASP77
|
3.9
|
12.8
|
1.0
|
|
N
|
C:ASP77
|
4.0
|
11.7
|
1.0
|
|
N
|
C:ASP78
|
4.0
|
11.7
|
1.0
|
|
OD1
|
C:ASP34
|
4.2
|
15.5
|
1.0
|
|
OD2
|
C:ASP78
|
4.2
|
17.4
|
1.0
|
|
CB
|
C:ASP316
|
4.2
|
12.5
|
1.0
|
|
OG1
|
C:THR317
|
4.3
|
12.0
|
1.0
|
|
HG23
|
C:THR76
|
4.3
|
24.8
|
1.0
|
|
HO3D
|
C:AR6401
|
4.4
|
18.9
|
1.0
|
|
HB2
|
C:ASP78
|
4.4
|
17.1
|
1.0
|
|
CB
|
C:ASP78
|
4.5
|
14.3
|
1.0
|
|
CA
|
C:THR76
|
4.5
|
14.8
|
1.0
|
|
CB
|
C:ASP77
|
4.5
|
12.1
|
1.0
|
|
C
|
C:THR76
|
4.6
|
12.8
|
1.0
|
|
O
|
C:HOH621
|
4.6
|
36.2
|
1.0
|
|
O
|
C:GLY115
|
4.7
|
16.9
|
1.0
|
|
CA
|
C:ASP77
|
4.7
|
11.8
|
1.0
|
|
HB3
|
C:ASP316
|
4.7
|
15.0
|
1.0
|
|
HG22
|
C:THR76
|
4.7
|
24.8
|
1.0
|
|
C2D
|
C:AR6401
|
4.7
|
20.2
|
1.0
|
|
O
|
C:ARG114
|
4.8
|
26.0
|
1.0
|
|
O3D
|
C:AR6401
|
4.8
|
15.7
|
1.0
|
|
HA3
|
C:GLY115
|
4.8
|
26.8
|
1.0
|
|
C
|
C:ASP77
|
4.8
|
11.8
|
1.0
|
|
CA
|
C:ASP78
|
4.8
|
15.9
|
1.0
|
|
HB3
|
C:ASP77
|
4.9
|
14.5
|
1.0
|
|
Calcium binding site 3 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 3 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 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 Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca402
b:19.0
occ:1.00
|
O3D
|
D:AR6401
|
2.3
|
16.3
|
1.0
|
|
OD1
|
D:ASP314
|
2.4
|
21.4
|
1.0
|
|
OG1
|
D:THR317
|
2.5
|
13.9
|
1.0
|
|
OD1
|
D:ASP316
|
2.5
|
19.4
|
1.0
|
|
O
|
D:HOH528
|
2.5
|
20.9
|
1.0
|
|
O1D
|
D:AR6401
|
2.6
|
23.1
|
1.0
|
|
HO3D
|
D:AR6401
|
2.6
|
19.6
|
1.0
|
|
O2D
|
D:AR6401
|
2.7
|
22.0
|
1.0
|
|
OD2
|
D:ASP314
|
3.0
|
19.4
|
1.0
|
|
CG
|
D:ASP314
|
3.1
|
16.3
|
1.0
|
|
HD1
|
D:AR6401
|
3.2
|
27.7
|
1.0
|
|
CA
|
D:CA403
|
3.3
|
34.6
|
1.0
|
|
HO2D
|
D:AR6401
|
3.4
|
26.4
|
1.0
|
|
C2D
|
D:AR6401
|
3.4
|
15.5
|
1.0
|
|
C3D
|
D:AR6401
|
3.4
|
14.5
|
1.0
|
|
CG
|
D:ASP316
|
3.4
|
26.5
|
1.0
|
|
HB
|
D:THR317
|
3.5
|
17.4
|
1.0
|
|
C1D
|
D:AR6401
|
3.6
|
20.9
|
1.0
|
|
CB
|
D:THR317
|
3.6
|
14.5
|
1.0
|
|
H
|
D:THR317
|
3.6
|
14.6
|
1.0
|
|
OD2
|
D:ASP316
|
3.7
|
29.2
|
1.0
|
|
O
|
D:HOH507
|
3.8
|
15.5
|
1.0
|
|
H4D
|
D:AR6401
|
4.1
|
24.8
|
1.0
|
|
O
|
D:HOH512
|
4.1
|
29.6
|
1.0
|
|
OD1
|
D:ASP78
|
4.1
|
38.6
|
1.0
|
|
N
|
D:THR317
|
4.1
|
12.2
|
1.0
|
|
C4D
|
D:AR6401
|
4.2
|
20.6
|
1.0
|
|
H3D
|
D:AR6401
|
4.2
|
17.4
|
1.0
|
|
O4D
|
D:AR6401
|
4.3
|
22.6
|
1.0
|
|
H1D
|
D:AR6401
|
4.4
|
25.1
|
1.0
|
|
H2D
|
D:AR6401
|
4.4
|
18.7
|
1.0
|
|
HD21
|
D:ASN151
|
4.4
|
18.3
|
1.0
|
|
CA
|
D:THR317
|
4.5
|
12.8
|
1.0
|
|
HG21
|
D:THR317
|
4.5
|
18.2
|
1.0
|
|
HG22
|
D:ILE271
|
4.5
|
23.8
|
1.0
|
|
CB
|
D:ASP314
|
4.6
|
11.3
|
1.0
|
|
OD2
|
D:ASP78
|
4.6
|
17.1
|
1.0
|
|
CG2
|
D:THR317
|
4.7
|
15.2
|
1.0
|
|
CB
|
D:ASP316
|
4.8
|
12.3
|
1.0
|
|
HA
|
D:THR317
|
4.8
|
15.4
|
1.0
|
|
CG
|
D:ASP78
|
4.8
|
25.6
|
1.0
|
|
HA
|
D:ASP314
|
4.8
|
15.7
|
1.0
|
|
OD1
|
D:ASP77
|
4.8
|
16.1
|
1.0
|
|
OD1
|
D:ASN151
|
4.9
|
13.5
|
1.0
|
|
O
|
D:HOH707
|
4.9
|
41.5
|
1.0
|
|
O
|
D:HOH754
|
4.9
|
32.4
|
1.0
|
|
H
|
D:ASP316
|
4.9
|
14.0
|
1.0
|
|
HB2
|
D:ASP316
|
5.0
|
14.8
|
1.0
|
|
O
|
D:ASP314
|
5.0
|
13.9
|
1.0
|
|
C
|
D:ASP316
|
5.0
|
14.1
|
1.0
|
|
Calcium binding site 4 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 4 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 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 Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca403
b:34.6
occ:1.00
|
OD1
|
D:ASP78
|
2.2
|
38.6
|
1.0
|
|
OD1
|
D:ASP77
|
2.4
|
16.1
|
1.0
|
|
OG1
|
D:THR76
|
2.6
|
14.2
|
1.0
|
|
O
|
D:HOH507
|
2.7
|
15.5
|
1.0
|
|
OD2
|
D:ASP316
|
2.8
|
29.2
|
1.0
|
|
O
|
D:HOH757
|
2.9
|
31.3
|
1.0
|
|
HB
|
D:THR76
|
3.0
|
14.5
|
1.0
|
|
O
|
D:HOH528
|
3.0
|
20.9
|
1.0
|
|
HO2D
|
D:AR6401
|
3.0
|
26.4
|
1.0
|
|
O2D
|
D:AR6401
|
3.1
|
22.0
|
1.0
|
|
CG
|
D:ASP316
|
3.2
|
26.5
|
1.0
|
|
CA
|
D:CA402
|
3.3
|
19.0
|
1.0
|
|
CB
|
D:THR76
|
3.3
|
12.1
|
1.0
|
|
H
|
D:ASP78
|
3.3
|
14.5
|
1.0
|
|
CG
|
D:ASP78
|
3.4
|
25.6
|
1.0
|
|
OD1
|
D:ASP316
|
3.4
|
19.4
|
1.0
|
|
CG
|
D:ASP77
|
3.5
|
14.5
|
1.0
|
|
HG21
|
D:THR76
|
3.6
|
26.8
|
1.0
|
|
H
|
D:ASP77
|
3.7
|
15.3
|
1.0
|
|
HB2
|
D:ASP316
|
3.8
|
14.8
|
1.0
|
|
CG2
|
D:THR76
|
4.0
|
22.3
|
1.0
|
|
OD2
|
D:ASP77
|
4.0
|
15.5
|
1.0
|
|
OG1
|
D:THR317
|
4.0
|
13.9
|
1.0
|
|
OD2
|
D:ASP78
|
4.1
|
17.1
|
1.0
|
|
N
|
D:ASP78
|
4.1
|
12.1
|
1.0
|
|
N
|
D:ASP77
|
4.1
|
12.7
|
1.0
|
|
CB
|
D:ASP316
|
4.1
|
12.3
|
1.0
|
|
HO3D
|
D:AR6401
|
4.3
|
19.6
|
1.0
|
|
OD1
|
D:ASP34
|
4.3
|
13.3
|
1.0
|
|
HB2
|
D:ASP78
|
4.4
|
15.1
|
1.0
|
|
HG23
|
D:THR76
|
4.4
|
26.8
|
1.0
|
|
CB
|
D:ASP78
|
4.5
|
12.6
|
1.0
|
|
C2D
|
D:AR6401
|
4.5
|
15.5
|
1.0
|
|
O3D
|
D:AR6401
|
4.6
|
16.3
|
1.0
|
|
O
|
D:GLY115
|
4.6
|
15.7
|
1.0
|
|
CA
|
D:THR76
|
4.6
|
11.4
|
1.0
|
|
HB3
|
D:ASP316
|
4.7
|
14.8
|
1.0
|
|
CB
|
D:ASP77
|
4.7
|
11.3
|
1.0
|
|
C
|
D:THR76
|
4.7
|
11.3
|
1.0
|
|
O1D
|
D:AR6401
|
4.8
|
23.1
|
1.0
|
|
HG22
|
D:THR76
|
4.8
|
26.8
|
1.0
|
|
CA
|
D:ASP77
|
4.8
|
11.3
|
1.0
|
|
CA
|
D:ASP78
|
4.9
|
11.5
|
1.0
|
|
C
|
D:ASP77
|
4.9
|
12.6
|
1.0
|
|
H2D
|
D:AR6401
|
4.9
|
18.7
|
1.0
|
|
HA3
|
D:GLY115
|
4.9
|
20.2
|
1.0
|
|
Calcium binding site 5 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 5 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:22.0
occ:1.00
|
OG1
|
A:THR317
|
2.3
|
13.3
|
1.0
|
|
O3D
|
A:AR6401
|
2.4
|
15.5
|
1.0
|
|
OD1
|
A:ASP314
|
2.4
|
24.3
|
1.0
|
|
O2D
|
A:AR6401
|
2.5
|
31.8
|
1.0
|
|
OD1
|
A:ASP316
|
2.5
|
20.0
|
1.0
|
|
O1D
|
A:AR6401
|
2.5
|
27.1
|
1.0
|
|
HO3D
|
A:AR6401
|
2.7
|
18.7
|
1.0
|
|
HO2D
|
A:AR6401
|
2.8
|
38.2
|
1.0
|
|
O
|
A:HOH519
|
2.9
|
34.6
|
1.0
|
|
OD2
|
A:ASP314
|
2.9
|
20.6
|
1.0
|
|
CG
|
A:ASP314
|
3.0
|
19.3
|
1.0
|
|
HD1
|
A:AR6401
|
3.2
|
32.5
|
1.0
|
|
C2D
|
A:AR6401
|
3.3
|
30.1
|
1.0
|
|
C3D
|
A:AR6401
|
3.4
|
22.8
|
1.0
|
|
HB
|
A:THR317
|
3.4
|
15.9
|
1.0
|
|
CB
|
A:THR317
|
3.5
|
13.2
|
1.0
|
|
CG
|
A:ASP316
|
3.5
|
26.9
|
1.0
|
|
H
|
A:THR317
|
3.6
|
15.5
|
1.0
|
|
C1D
|
A:AR6401
|
3.6
|
30.2
|
1.0
|
|
CA
|
A:CA403
|
3.7
|
26.6
|
1.0
|
|
OD2
|
A:ASP316
|
3.9
|
36.6
|
1.0
|
|
OE1
|
A:GLU41
|
3.9
|
30.5
|
1.0
|
|
H4D
|
A:AR6401
|
4.0
|
38.5
|
1.0
|
|
N
|
A:THR317
|
4.1
|
13.1
|
1.0
|
|
C4D
|
A:AR6401
|
4.1
|
32.1
|
1.0
|
|
OD1
|
A:ASP78
|
4.2
|
25.8
|
1.0
|
|
HD21
|
A:ASN151
|
4.2
|
16.7
|
1.0
|
|
H3D
|
A:AR6401
|
4.3
|
27.4
|
1.0
|
|
O
|
A:HOH544
|
4.3
|
20.3
|
1.0
|
|
HG21
|
A:THR317
|
4.3
|
21.8
|
1.0
|
|
H2D
|
A:AR6401
|
4.3
|
36.2
|
1.0
|
|
O4D
|
A:AR6401
|
4.3
|
28.3
|
1.0
|
|
CA
|
A:THR317
|
4.4
|
15.3
|
1.0
|
|
O
|
A:HOH539
|
4.4
|
42.9
|
1.0
|
|
HG22
|
A:ILE271
|
4.4
|
33.2
|
1.0
|
|
H1D
|
A:AR6401
|
4.4
|
36.3
|
1.0
|
|
CG2
|
A:THR317
|
4.5
|
18.1
|
1.0
|
|
CB
|
A:ASP314
|
4.5
|
13.1
|
1.0
|
|
OD2
|
A:ASP78
|
4.6
|
17.0
|
1.0
|
|
CD
|
A:GLU41
|
4.6
|
41.8
|
1.0
|
|
OD1
|
A:ASN151
|
4.7
|
16.3
|
1.0
|
|
HA
|
A:THR317
|
4.7
|
18.4
|
1.0
|
|
OE2
|
A:GLU41
|
4.8
|
32.8
|
1.0
|
|
HA
|
A:ASP314
|
4.8
|
16.8
|
1.0
|
|
CG
|
A:ASP78
|
4.8
|
23.0
|
1.0
|
|
CB
|
A:ASP316
|
4.8
|
19.0
|
1.0
|
|
H
|
A:ASP316
|
4.9
|
17.0
|
1.0
|
|
HB3
|
A:ASP314
|
4.9
|
15.8
|
1.0
|
|
HG23
|
A:THR317
|
5.0
|
21.8
|
1.0
|
|
HB2
|
A:ASP314
|
5.0
|
15.8
|
1.0
|
|
C
|
A:ASP316
|
5.0
|
14.5
|
1.0
|
|
ND2
|
A:ASN151
|
5.0
|
13.9
|
1.0
|
|
OD1
|
A:ASP77
|
5.0
|
13.9
|
1.0
|
|
Calcium binding site 6 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 6 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:26.6
occ:1.00
|
OD1
|
A:ASP77
|
2.2
|
13.9
|
1.0
|
|
OD1
|
A:ASP78
|
2.3
|
25.8
|
1.0
|
|
O
|
A:HOH544
|
2.3
|
20.3
|
1.0
|
|
OG1
|
A:THR76
|
2.4
|
15.2
|
1.0
|
|
HO2D
|
A:AR6401
|
2.7
|
38.2
|
1.0
|
|
OD2
|
A:ASP316
|
2.9
|
36.6
|
1.0
|
|
HB
|
A:THR76
|
2.9
|
19.0
|
1.0
|
|
O
|
A:HOH519
|
3.1
|
34.6
|
1.0
|
|
O2D
|
A:AR6401
|
3.1
|
31.8
|
1.0
|
|
CB
|
A:THR76
|
3.2
|
15.8
|
1.0
|
|
H
|
A:ASP78
|
3.3
|
16.0
|
1.0
|
|
CG
|
A:ASP316
|
3.4
|
26.9
|
1.0
|
|
CG
|
A:ASP77
|
3.4
|
15.7
|
1.0
|
|
CG
|
A:ASP78
|
3.6
|
23.0
|
1.0
|
|
HG21
|
A:THR76
|
3.6
|
33.3
|
1.0
|
|
H
|
A:ASP77
|
3.6
|
16.4
|
1.0
|
|
OD1
|
A:ASP316
|
3.6
|
20.0
|
1.0
|
|
CA
|
A:CA402
|
3.7
|
22.0
|
1.0
|
|
CG2
|
A:THR76
|
3.9
|
27.7
|
1.0
|
|
OD2
|
A:ASP77
|
3.9
|
14.7
|
1.0
|
|
HB2
|
A:ASP316
|
4.0
|
22.9
|
1.0
|
|
N
|
A:ASP77
|
4.0
|
13.8
|
1.0
|
|
N
|
A:ASP78
|
4.1
|
13.5
|
1.0
|
|
OD1
|
A:ASP34
|
4.2
|
15.1
|
1.0
|
|
OD2
|
A:ASP78
|
4.3
|
17.0
|
1.0
|
|
CB
|
A:ASP316
|
4.3
|
19.0
|
1.0
|
|
OG1
|
A:THR317
|
4.3
|
13.3
|
1.0
|
|
HG23
|
A:THR76
|
4.4
|
33.3
|
1.0
|
|
C2D
|
A:AR6401
|
4.4
|
30.1
|
1.0
|
|
CA
|
A:THR76
|
4.5
|
13.8
|
1.0
|
|
O
|
A:HOH744
|
4.5
|
33.5
|
1.0
|
|
O
|
A:GLY115
|
4.5
|
17.0
|
1.0
|
|
HB2
|
A:ASP78
|
4.6
|
16.3
|
1.0
|
|
C
|
A:THR76
|
4.6
|
13.8
|
1.0
|
|
CB
|
A:ASP77
|
4.6
|
13.8
|
1.0
|
|
CB
|
A:ASP78
|
4.6
|
13.6
|
1.0
|
|
O
|
A:ARG114
|
4.6
|
25.4
|
1.0
|
|
H2D
|
A:AR6401
|
4.7
|
36.2
|
1.0
|
|
HG22
|
A:THR76
|
4.7
|
33.3
|
1.0
|
|
CA
|
A:ASP77
|
4.7
|
13.7
|
1.0
|
|
HO3D
|
A:AR6401
|
4.7
|
18.7
|
1.0
|
|
O1D
|
A:AR6401
|
4.8
|
27.1
|
1.0
|
|
HB3
|
A:ASP316
|
4.8
|
22.9
|
1.0
|
|
C
|
A:ASP77
|
4.9
|
13.6
|
1.0
|
|
HB3
|
A:ASP77
|
4.9
|
16.4
|
1.0
|
|
O3D
|
A:AR6401
|
4.9
|
15.5
|
1.0
|
|
CA
|
A:ASP78
|
4.9
|
13.4
|
1.0
|
|
HA3
|
A:GLY115
|
4.9
|
23.7
|
1.0
|
|
Calcium binding site 7 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 7 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:31.9
occ:1.00
|
OD1
|
B:ASP314
|
2.4
|
30.9
|
1.0
|
|
O3D
|
B:AR6401
|
2.4
|
22.3
|
1.0
|
|
OG1
|
B:THR317
|
2.5
|
19.4
|
1.0
|
|
OD1
|
B:ASP316
|
2.5
|
23.4
|
1.0
|
|
O1D
|
B:AR6401
|
2.6
|
33.0
|
1.0
|
|
O2D
|
B:AR6401
|
2.6
|
33.2
|
1.0
|
|
HO3D
|
B:AR6401
|
2.7
|
26.8
|
1.0
|
|
O
|
B:HOH527
|
2.9
|
35.2
|
1.0
|
|
HO2D
|
B:AR6401
|
3.1
|
39.9
|
1.0
|
|
CG
|
B:ASP314
|
3.1
|
26.9
|
1.0
|
|
OD2
|
B:ASP314
|
3.2
|
23.7
|
1.0
|
|
HD1
|
B:AR6401
|
3.3
|
39.6
|
1.0
|
|
C2D
|
B:AR6401
|
3.3
|
30.0
|
1.0
|
|
CA
|
B:CA403
|
3.3
|
35.1
|
1.0
|
|
C3D
|
B:AR6401
|
3.4
|
29.4
|
1.0
|
|
CG
|
B:ASP316
|
3.4
|
33.0
|
1.0
|
|
HB
|
B:THR317
|
3.5
|
17.8
|
1.0
|
|
C1D
|
B:AR6401
|
3.5
|
36.1
|
1.0
|
|
CB
|
B:THR317
|
3.6
|
14.8
|
1.0
|
|
H
|
B:THR317
|
3.6
|
20.6
|
1.0
|
|
OD2
|
B:ASP316
|
3.6
|
35.8
|
1.0
|
|
O
|
B:HOH501
|
3.7
|
33.9
|
1.0
|
|
O
|
B:HOH506
|
3.8
|
25.2
|
1.0
|
|
H4D
|
B:AR6401
|
4.0
|
44.1
|
1.0
|
|
N
|
B:THR317
|
4.1
|
17.1
|
1.0
|
|
C4D
|
B:AR6401
|
4.1
|
36.7
|
1.0
|
|
OD1
|
B:ASP78
|
4.2
|
35.0
|
1.0
|
|
H3D
|
B:AR6401
|
4.2
|
35.4
|
1.0
|
|
O4D
|
B:AR6401
|
4.3
|
32.9
|
1.0
|
|
H1D
|
B:AR6401
|
4.3
|
43.3
|
1.0
|
|
H2D
|
B:AR6401
|
4.3
|
36.0
|
1.0
|
|
HD21
|
B:ASN151
|
4.4
|
28.0
|
1.0
|
|
CA
|
B:THR317
|
4.4
|
17.6
|
1.0
|
|
HG21
|
B:THR317
|
4.5
|
20.7
|
1.0
|
|
CB
|
B:ASP314
|
4.6
|
20.0
|
1.0
|
|
OD2
|
B:ASP78
|
4.6
|
23.1
|
1.0
|
|
CG2
|
B:THR317
|
4.7
|
17.3
|
1.0
|
|
CB
|
B:ASP316
|
4.8
|
22.5
|
1.0
|
|
HA
|
B:ASP314
|
4.8
|
26.8
|
1.0
|
|
HG22
|
B:ILE271
|
4.8
|
32.4
|
1.0
|
|
HA
|
B:THR317
|
4.8
|
21.1
|
1.0
|
|
CG
|
B:ASP78
|
4.8
|
26.2
|
1.0
|
|
H
|
B:ASP316
|
4.8
|
19.3
|
1.0
|
|
OD1
|
B:ASN151
|
4.9
|
17.7
|
1.0
|
|
OD1
|
B:ASP77
|
4.9
|
16.1
|
1.0
|
|
C
|
B:ASP316
|
5.0
|
18.2
|
1.0
|
|
Calcium binding site 8 out
of 8 in 7l9f
Go back to
Calcium Binding Sites List in 7l9f
Calcium binding site 8 out
of 8 in the Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Human ARH3 Bound to Calcium and Adp-Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:35.1
occ:1.00
|
OD1
|
B:ASP78
|
2.2
|
35.0
|
1.0
|
|
OD1
|
B:ASP77
|
2.4
|
16.1
|
1.0
|
|
O
|
B:HOH506
|
2.5
|
25.2
|
1.0
|
|
OG1
|
B:THR76
|
2.5
|
14.7
|
1.0
|
|
HO2D
|
B:AR6401
|
2.6
|
39.9
|
1.0
|
|
OD2
|
B:ASP316
|
2.6
|
35.8
|
1.0
|
|
O2D
|
B:AR6401
|
2.9
|
33.2
|
1.0
|
|
HB
|
B:THR76
|
3.1
|
24.0
|
1.0
|
|
CG
|
B:ASP316
|
3.2
|
33.0
|
1.0
|
|
O
|
B:HOH527
|
3.3
|
35.2
|
1.0
|
|
H
|
B:ASP78
|
3.3
|
16.5
|
1.0
|
|
CB
|
B:THR76
|
3.3
|
20.0
|
1.0
|
|
CA
|
B:CA402
|
3.3
|
31.9
|
1.0
|
|
CG
|
B:ASP78
|
3.4
|
26.2
|
1.0
|
|
CG
|
B:ASP77
|
3.5
|
16.6
|
1.0
|
|
OD1
|
B:ASP316
|
3.5
|
23.4
|
1.0
|
|
HG21
|
B:THR76
|
3.7
|
29.6
|
1.0
|
|
H
|
B:ASP77
|
3.7
|
15.9
|
1.0
|
|
HB2
|
B:ASP316
|
3.9
|
27.1
|
1.0
|
|
OD2
|
B:ASP77
|
3.9
|
19.1
|
1.0
|
|
CG2
|
B:THR76
|
4.0
|
24.7
|
1.0
|
|
OG1
|
B:THR317
|
4.1
|
19.4
|
1.0
|
|
OD2
|
B:ASP78
|
4.1
|
23.1
|
1.0
|
|
N
|
B:ASP78
|
4.1
|
13.7
|
1.0
|
|
N
|
B:ASP77
|
4.1
|
13.2
|
1.0
|
|
CB
|
B:ASP316
|
4.2
|
22.5
|
1.0
|
|
C2D
|
B:AR6401
|
4.3
|
30.0
|
1.0
|
|
OD1
|
B:ASP34
|
4.3
|
15.7
|
1.0
|
|
HO3D
|
B:AR6401
|
4.4
|
26.8
|
1.0
|
|
HB2
|
B:ASP78
|
4.4
|
17.1
|
1.0
|
|
CB
|
B:ASP78
|
4.5
|
14.2
|
1.0
|
|
O
|
B:GLY115
|
4.5
|
18.9
|
1.0
|
|
HG23
|
B:THR76
|
4.5
|
29.6
|
1.0
|
|
O1D
|
B:AR6401
|
4.6
|
33.0
|
1.0
|
|
H2D
|
B:AR6401
|
4.7
|
36.0
|
1.0
|
|
CA
|
B:THR76
|
4.7
|
12.6
|
1.0
|
|
O3D
|
B:AR6401
|
4.7
|
22.3
|
1.0
|
|
HB3
|
B:ASP316
|
4.7
|
27.1
|
1.0
|
|
CB
|
B:ASP77
|
4.7
|
16.9
|
1.0
|
|
C
|
B:THR76
|
4.7
|
11.4
|
1.0
|
|
CA
|
B:ASP77
|
4.8
|
11.9
|
1.0
|
|
HG22
|
B:THR76
|
4.8
|
29.6
|
1.0
|
|
CA
|
B:ASP78
|
4.9
|
16.3
|
1.0
|
|
HA3
|
B:GLY115
|
4.9
|
28.8
|
1.0
|
|
C
|
B:ASP77
|
4.9
|
15.6
|
1.0
|
|
Reference:
Y.Pourfarjam,
Z.Ma,
I.Kurinov,
J.Moss,
I.K.Kim.
Structural and Biochemical Analysis of Human Adp-Ribosyl-Acceptor Hydrolase 3 (ARH3) Reveals the Basis of Metal Selectivity and Different Roles For the Two Mg Ions J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Wed Jul 9 23:07:04 2025
|
