Calcium in PDB 5ucq: The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
Enzymatic activity of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
All present enzymatic activity of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate:
3.6.1.1;
Protein crystallography data
The structure of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate, PDB code: 5ucq
was solved by
N.Inoguchi,
R.C.Hughes,
E.J.Meehan,
J.D.Ng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
43.37 /
1.40
|
|
Space group
|
P 32 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.161,
100.161,
97.801,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
10.9 /
14
|
Other elements in 5ucq:
The structure of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
(pdb code 5ucq). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the
The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate, PDB code: 5ucq:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Calcium binding site 1 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 1 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:8.2
occ:1.00
|
O2
|
A:POP208
|
2.2
|
6.7
|
0.7
|
|
OD2
|
A:ASP98
|
2.2
|
10.1
|
1.0
|
|
OD2
|
A:ASP103
|
2.3
|
10.7
|
1.0
|
|
O6
|
A:POP208
|
2.3
|
6.7
|
0.7
|
|
O
|
A:HOH343
|
2.3
|
12.9
|
1.0
|
|
O
|
A:HOH317
|
2.4
|
9.3
|
1.0
|
|
O2
|
A:POP208
|
2.6
|
8.4
|
0.3
|
|
O6
|
A:POP208
|
2.7
|
13.6
|
0.3
|
|
CG
|
A:ASP98
|
3.3
|
9.4
|
1.0
|
|
P2
|
A:POP208
|
3.3
|
7.4
|
0.7
|
|
O
|
A:POP208
|
3.4
|
7.8
|
0.3
|
|
P1
|
A:POP208
|
3.5
|
8.3
|
0.7
|
|
CG
|
A:ASP103
|
3.5
|
8.5
|
1.0
|
|
P2
|
A:POP208
|
3.6
|
12.6
|
0.3
|
|
P1
|
A:POP208
|
3.6
|
7.5
|
0.3
|
|
O5
|
A:POP208
|
3.6
|
8.5
|
0.7
|
|
O
|
A:POP208
|
3.7
|
5.7
|
0.7
|
|
CA
|
A:CA202
|
3.8
|
8.6
|
1.0
|
|
CB
|
A:ASP98
|
3.9
|
8.6
|
1.0
|
|
OD2
|
A:ASP66
|
4.0
|
10.0
|
1.0
|
|
NZ
|
A:LYS141
|
4.0
|
11.0
|
0.7
|
|
NZ
|
A:LYS141
|
4.0
|
6.5
|
0.3
|
|
O4
|
A:POP208
|
4.2
|
14.1
|
0.3
|
|
OH
|
A:TYR140
|
4.2
|
7.7
|
1.0
|
|
O3
|
A:POP208
|
4.3
|
6.5
|
0.7
|
|
NZ
|
A:LYS105
|
4.3
|
9.4
|
1.0
|
|
OD1
|
A:ASP98
|
4.3
|
10.8
|
1.0
|
|
OD1
|
A:ASP103
|
4.3
|
9.8
|
1.0
|
|
CB
|
A:ASP103
|
4.4
|
8.4
|
1.0
|
|
O3
|
A:POP208
|
4.5
|
8.0
|
0.3
|
|
O1
|
A:POP208
|
4.6
|
8.1
|
0.7
|
|
O
|
A:HOH420
|
4.6
|
53.3
|
1.0
|
|
O
|
A:HOH367
|
4.6
|
15.8
|
1.0
|
|
O4
|
A:POP208
|
4.7
|
11.0
|
0.7
|
|
OD1
|
A:ASP71
|
4.7
|
9.8
|
1.0
|
|
O1
|
A:POP208
|
4.8
|
6.3
|
0.3
|
|
CE
|
A:LYS141
|
4.8
|
10.7
|
0.7
|
|
O
|
A:HOH301
|
4.9
|
12.0
|
0.8
|
|
O5
|
A:POP208
|
4.9
|
9.5
|
0.3
|
|
OD1
|
A:ASP66
|
5.0
|
11.9
|
0.0
|
|
Calcium binding site 2 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 2 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:8.6
occ:1.00
|
O6
|
A:POP208
|
2.3
|
13.6
|
0.3
|
|
OD1
|
A:ASP71
|
2.4
|
9.8
|
1.0
|
|
O
|
A:HOH329
|
2.4
|
13.6
|
1.0
|
|
OD2
|
A:ASP66
|
2.4
|
10.0
|
1.0
|
|
O
|
A:HOH301
|
2.4
|
12.0
|
0.8
|
|
OD1
|
A:ASP103
|
2.4
|
9.8
|
1.0
|
|
O6
|
A:POP208
|
2.4
|
6.7
|
0.7
|
|
OD2
|
A:ASP68
|
2.5
|
9.9
|
0.4
|
|
OD2
|
A:ASP103
|
2.7
|
10.7
|
1.0
|
|
OD1
|
A:ASP66
|
2.8
|
11.9
|
0.0
|
|
CG
|
A:ASP103
|
2.9
|
8.5
|
1.0
|
|
CG
|
A:ASP71
|
3.0
|
8.9
|
1.0
|
|
OD2
|
A:ASP71
|
3.0
|
10.9
|
1.0
|
|
CG
|
A:ASP66
|
3.4
|
12.2
|
1.0
|
|
CG
|
A:ASP66
|
3.4
|
12.0
|
0.0
|
|
OD2
|
A:ASP66
|
3.5
|
11.9
|
0.0
|
|
P2
|
A:POP208
|
3.6
|
7.4
|
0.7
|
|
CG
|
A:ASP68
|
3.7
|
12.9
|
0.4
|
|
P2
|
A:POP208
|
3.7
|
12.6
|
0.3
|
|
OD1
|
A:ASP66
|
3.7
|
13.9
|
1.0
|
|
O4
|
A:POP208
|
3.7
|
11.0
|
0.7
|
|
CA
|
A:CA201
|
3.8
|
8.2
|
1.0
|
|
CA
|
A:CA203
|
3.9
|
11.8
|
1.0
|
|
O
|
A:HOH366
|
3.9
|
9.6
|
1.0
|
|
O
|
A:HOH343
|
3.9
|
12.9
|
1.0
|
|
O5
|
A:POP208
|
4.1
|
9.5
|
0.3
|
|
CB
|
A:ASP68
|
4.2
|
13.9
|
0.4
|
|
NZ
|
A:LYS105
|
4.2
|
9.4
|
1.0
|
|
O5
|
A:POP208
|
4.3
|
8.5
|
0.7
|
|
O4
|
A:POP208
|
4.3
|
14.1
|
0.3
|
|
CB
|
A:ASP103
|
4.4
|
8.4
|
1.0
|
|
CB
|
A:ASP71
|
4.4
|
8.1
|
1.0
|
|
O
|
A:PRO69
|
4.5
|
11.6
|
1.0
|
|
O
|
A:HOH337
|
4.6
|
14.9
|
0.3
|
|
CB
|
A:ASP66
|
4.6
|
12.2
|
0.0
|
|
CB
|
A:ASP68
|
4.6
|
20.4
|
0.6
|
|
O
|
A:HOH310
|
4.6
|
17.6
|
0.6
|
|
OD1
|
A:ASP68
|
4.7
|
11.6
|
0.4
|
|
OH
|
A:TYR56
|
4.7
|
10.1
|
0.3
|
|
CB
|
A:ASP66
|
4.7
|
11.8
|
1.0
|
|
O
|
A:HOH317
|
4.7
|
9.3
|
1.0
|
|
O
|
A:POP208
|
4.8
|
7.8
|
0.3
|
|
O
|
A:HOH310
|
4.8
|
10.2
|
0.4
|
|
O
|
A:POP208
|
4.9
|
5.7
|
0.7
|
|
OH
|
A:TYR56
|
4.9
|
8.1
|
0.7
|
|
Calcium binding site 3 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 3 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:11.8
occ:1.00
|
O
|
A:HOH310
|
2.1
|
17.6
|
0.6
|
|
O4
|
A:POP208
|
2.2
|
11.0
|
0.7
|
|
O
|
A:HOH346
|
2.3
|
17.8
|
1.0
|
|
OD2
|
A:ASP71
|
2.3
|
10.9
|
1.0
|
|
O
|
A:HOH330
|
2.4
|
10.4
|
1.0
|
|
O
|
A:HOH301
|
2.4
|
12.0
|
0.8
|
|
O5
|
A:POP208
|
2.4
|
9.5
|
0.3
|
|
O
|
A:HOH310
|
2.6
|
10.2
|
0.4
|
|
OD2
|
A:ASP68
|
2.7
|
9.9
|
0.4
|
|
OD1
|
A:ASP68
|
3.1
|
11.6
|
0.4
|
|
CG
|
A:ASP68
|
3.3
|
12.9
|
0.4
|
|
P2
|
A:POP208
|
3.5
|
12.6
|
0.3
|
|
CG
|
A:ASP71
|
3.5
|
8.9
|
1.0
|
|
P2
|
A:POP208
|
3.6
|
7.4
|
0.7
|
|
O6
|
A:POP208
|
3.7
|
13.6
|
0.3
|
|
CA
|
A:CA202
|
3.9
|
8.6
|
1.0
|
|
O4
|
A:POP208
|
3.9
|
14.1
|
0.3
|
|
O6
|
A:POP208
|
4.1
|
6.7
|
0.7
|
|
OD1
|
A:ASP71
|
4.1
|
9.8
|
1.0
|
|
OD2
|
A:ASP68
|
4.1
|
28.9
|
0.6
|
|
O
|
A:HOH337
|
4.2
|
14.9
|
0.3
|
|
OH
|
A:TYR56
|
4.2
|
10.1
|
0.3
|
|
OE2
|
A:GLU32
|
4.2
|
9.0
|
0.2
|
|
OE1
|
A:GLU22
|
4.3
|
10.4
|
1.0
|
|
O
|
A:PRO69
|
4.3
|
11.6
|
1.0
|
|
CE2
|
A:TYR56
|
4.3
|
4.0
|
0.3
|
|
CG2
|
A:ILE58
|
4.4
|
12.9
|
1.0
|
|
NZ
|
A:LYS30
|
4.4
|
10.2
|
1.0
|
|
O5
|
A:POP208
|
4.5
|
8.5
|
0.7
|
|
O
|
A:HOH393
|
4.6
|
36.1
|
1.0
|
|
O
|
A:HOH329
|
4.6
|
13.6
|
1.0
|
|
CB
|
A:ASP71
|
4.6
|
8.1
|
1.0
|
|
CE2
|
A:TYR56
|
4.6
|
9.6
|
0.7
|
|
O
|
A:POP208
|
4.6
|
5.7
|
0.7
|
|
CZ
|
A:TYR56
|
4.7
|
6.4
|
0.3
|
|
CB
|
A:ASP68
|
4.7
|
20.4
|
0.6
|
|
O
|
A:HOH336
|
4.7
|
12.0
|
1.0
|
|
CG
|
A:ASP68
|
4.7
|
25.8
|
0.6
|
|
CB
|
A:ASP68
|
4.8
|
13.9
|
0.4
|
|
OH
|
A:TYR56
|
4.8
|
8.1
|
0.7
|
|
O
|
A:POP208
|
4.8
|
7.8
|
0.3
|
|
CA
|
A:ASP71
|
4.9
|
7.4
|
1.0
|
|
O
|
A:GLY57
|
4.9
|
7.2
|
1.0
|
|
CD
|
A:GLU32
|
4.9
|
11.4
|
0.2
|
|
OE2
|
A:GLU22
|
5.0
|
12.0
|
1.0
|
|
Calcium binding site 4 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 4 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:12.0
occ:1.00
|
O3
|
B:POP208
|
2.1
|
14.3
|
0.4
|
|
O
|
B:HOH304
|
2.2
|
19.3
|
1.0
|
|
O
|
B:HOH336
|
2.3
|
12.5
|
1.0
|
|
OD2
|
B:ASP71
|
2.3
|
12.2
|
1.0
|
|
O3
|
B:POP208
|
2.3
|
8.3
|
0.6
|
|
O1
|
B:EDO207
|
2.3
|
16.6
|
0.6
|
|
O
|
B:HOH327
|
2.5
|
17.0
|
1.0
|
|
O1
|
B:EDO207
|
2.6
|
14.0
|
0.3
|
|
C1
|
B:EDO207
|
2.9
|
18.7
|
0.6
|
|
P1
|
B:POP208
|
3.3
|
12.5
|
0.4
|
|
CG
|
B:ASP71
|
3.5
|
11.2
|
1.0
|
|
O1
|
B:EDO207
|
3.6
|
9.4
|
0.1
|
|
OD1
|
B:ASP68
|
3.6
|
24.0
|
0.3
|
|
P1
|
B:POP208
|
3.7
|
7.7
|
0.6
|
|
O1
|
B:POP208
|
3.7
|
13.8
|
0.4
|
|
C1
|
B:EDO207
|
3.8
|
12.5
|
0.3
|
|
C2
|
B:EDO207
|
3.8
|
15.2
|
0.3
|
|
O2
|
B:POP208
|
3.9
|
11.1
|
0.4
|
|
CA
|
B:CA202
|
3.9
|
9.5
|
1.0
|
|
O2
|
B:POP208
|
4.0
|
8.6
|
0.6
|
|
OD1
|
B:ASP71
|
4.1
|
11.2
|
1.0
|
|
CG
|
B:ASP68
|
4.2
|
22.2
|
0.3
|
|
CG2
|
B:ILE58
|
4.3
|
13.4
|
1.0
|
|
C2
|
B:EDO207
|
4.3
|
23.0
|
0.6
|
|
OE1
|
B:GLU22
|
4.3
|
11.0
|
1.0
|
|
O
|
B:PRO69
|
4.4
|
11.5
|
1.0
|
|
C1
|
B:EDO207
|
4.4
|
9.3
|
0.1
|
|
NZ
|
B:LYS30
|
4.5
|
9.3
|
1.0
|
|
O
|
B:HOH356
|
4.5
|
13.2
|
1.0
|
|
O1
|
B:POP208
|
4.5
|
8.6
|
0.6
|
|
CE2
|
B:TYR56
|
4.6
|
11.4
|
1.0
|
|
O
|
B:POP208
|
4.6
|
7.3
|
0.4
|
|
CB
|
B:ASP71
|
4.6
|
8.3
|
1.0
|
|
OH
|
B:TYR56
|
4.7
|
16.7
|
1.0
|
|
O
|
B:POP208
|
4.7
|
6.5
|
0.6
|
|
OD2
|
B:ASP68
|
4.7
|
25.8
|
0.3
|
|
O1
|
B:EDO206
|
4.7
|
16.7
|
0.2
|
|
O
|
B:HOH344
|
4.7
|
11.0
|
1.0
|
|
OD2
|
B:ASP68
|
4.7
|
34.6
|
0.7
|
|
CB
|
B:ASP68
|
4.8
|
16.9
|
0.3
|
|
CB
|
B:ASP68
|
4.8
|
20.1
|
0.7
|
|
O
|
B:GLY57
|
4.9
|
7.0
|
1.0
|
|
CA
|
B:ASP71
|
4.9
|
8.3
|
1.0
|
|
OE2
|
B:GLU22
|
5.0
|
11.2
|
1.0
|
|
Calcium binding site 5 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 5 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:9.5
occ:1.00
|
O2
|
B:POP208
|
2.3
|
11.1
|
0.4
|
|
O
|
B:HOH327
|
2.3
|
17.0
|
1.0
|
|
OD1
|
B:ASP71
|
2.4
|
11.2
|
1.0
|
|
OD2
|
B:ASP66
|
2.4
|
12.3
|
1.0
|
|
O
|
B:HOH356
|
2.4
|
13.2
|
1.0
|
|
OD1
|
B:ASP103
|
2.4
|
11.3
|
1.0
|
|
O2
|
B:POP208
|
2.4
|
8.6
|
0.6
|
|
OD2
|
B:ASP103
|
2.6
|
11.7
|
1.0
|
|
CG
|
B:ASP103
|
2.9
|
9.5
|
1.0
|
|
CG
|
B:ASP71
|
3.1
|
11.2
|
1.0
|
|
OD2
|
B:ASP71
|
3.1
|
12.2
|
1.0
|
|
CG
|
B:ASP66
|
3.4
|
14.0
|
1.0
|
|
P1
|
B:POP208
|
3.5
|
12.5
|
0.4
|
|
O3
|
B:POP208
|
3.6
|
14.3
|
0.4
|
|
P1
|
B:POP208
|
3.6
|
7.7
|
0.6
|
|
OD1
|
B:ASP66
|
3.8
|
15.0
|
1.0
|
|
CA
|
B:CA203
|
3.8
|
9.9
|
1.0
|
|
O
|
B:HOH368
|
3.9
|
19.9
|
1.0
|
|
O3
|
B:POP208
|
3.9
|
8.3
|
0.6
|
|
CA
|
B:CA201
|
3.9
|
12.0
|
1.0
|
|
O1
|
B:EDO206
|
4.0
|
71.2
|
0.8
|
|
O
|
B:HOH352
|
4.0
|
10.6
|
1.0
|
|
NZ
|
B:LYS105
|
4.2
|
9.8
|
1.0
|
|
O1
|
B:POP208
|
4.2
|
13.8
|
0.4
|
|
CB
|
B:ASP68
|
4.3
|
16.9
|
0.3
|
|
O1
|
B:POP208
|
4.3
|
8.6
|
0.6
|
|
CB
|
B:ASP103
|
4.4
|
9.1
|
1.0
|
|
C1
|
B:EDO206
|
4.4
|
20.6
|
0.2
|
|
O
|
B:HOH304
|
4.5
|
19.3
|
1.0
|
|
CB
|
B:ASP71
|
4.5
|
8.3
|
1.0
|
|
CB
|
B:ASP68
|
4.6
|
20.1
|
0.7
|
|
O1
|
B:EDO206
|
4.6
|
16.7
|
0.2
|
|
O
|
B:PRO69
|
4.7
|
11.5
|
1.0
|
|
CB
|
B:ASP66
|
4.7
|
16.0
|
1.0
|
|
O
|
B:HOH329
|
4.7
|
11.0
|
1.0
|
|
CG
|
B:ASP68
|
4.7
|
22.2
|
0.3
|
|
O
|
B:POP208
|
4.7
|
7.3
|
0.4
|
|
OH
|
B:TYR56
|
4.8
|
16.7
|
1.0
|
|
O
|
B:POP208
|
4.9
|
6.5
|
0.6
|
|
OD2
|
B:ASP68
|
4.9
|
34.6
|
0.7
|
|
C1
|
B:EDO206
|
4.9
|
70.7
|
0.8
|
|
Calcium binding site 6 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 6 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:9.9
occ:1.00
|
OD2
|
B:ASP98
|
2.2
|
11.9
|
1.0
|
|
O
|
B:HOH368
|
2.3
|
19.9
|
1.0
|
|
O4
|
B:POP208
|
2.3
|
6.5
|
0.6
|
|
OD2
|
B:ASP103
|
2.3
|
11.7
|
1.0
|
|
O2
|
B:POP208
|
2.4
|
8.6
|
0.6
|
|
O4
|
B:POP208
|
2.4
|
9.4
|
0.4
|
|
O2
|
B:POP208
|
2.5
|
11.1
|
0.4
|
|
O
|
B:HOH329
|
2.5
|
11.0
|
1.0
|
|
CG
|
B:ASP98
|
3.3
|
9.1
|
1.0
|
|
P1
|
B:POP208
|
3.4
|
7.7
|
0.6
|
|
P2
|
B:POP208
|
3.5
|
10.7
|
0.4
|
|
CG
|
B:ASP103
|
3.5
|
9.5
|
1.0
|
|
P2
|
B:POP208
|
3.5
|
6.3
|
0.6
|
|
P1
|
B:POP208
|
3.5
|
12.5
|
0.4
|
|
O
|
B:POP208
|
3.6
|
7.3
|
0.4
|
|
O
|
B:POP208
|
3.7
|
6.5
|
0.6
|
|
O1
|
B:POP208
|
3.7
|
8.6
|
0.6
|
|
O1
|
B:EDO206
|
3.8
|
71.2
|
0.8
|
|
CA
|
B:CA202
|
3.8
|
9.5
|
1.0
|
|
CB
|
B:ASP98
|
3.9
|
8.9
|
1.0
|
|
C1
|
B:EDO206
|
4.0
|
20.6
|
0.2
|
|
NZ
|
B:LYS141
|
4.0
|
12.0
|
1.0
|
|
OD2
|
B:ASP66
|
4.1
|
12.3
|
1.0
|
|
O1
|
B:POP208
|
4.2
|
13.8
|
0.4
|
|
O6
|
B:POP208
|
4.3
|
11.3
|
0.4
|
|
NZ
|
B:LYS105
|
4.3
|
9.8
|
1.0
|
|
OD1
|
B:ASP98
|
4.3
|
10.8
|
1.0
|
|
CB
|
B:ASP103
|
4.3
|
9.1
|
1.0
|
|
O6
|
B:POP208
|
4.4
|
6.0
|
0.6
|
|
OH
|
B:TYR140
|
4.4
|
8.2
|
1.0
|
|
OD1
|
B:ASP103
|
4.4
|
11.3
|
1.0
|
|
O
|
B:HOH378
|
4.4
|
22.9
|
1.0
|
|
O1
|
B:EDO206
|
4.5
|
16.7
|
0.2
|
|
O5
|
B:POP208
|
4.6
|
9.2
|
0.6
|
|
O5
|
B:POP208
|
4.7
|
9.0
|
0.4
|
|
O3
|
B:POP208
|
4.8
|
8.3
|
0.6
|
|
C1
|
B:EDO206
|
4.8
|
70.7
|
0.8
|
|
O3
|
B:POP208
|
4.8
|
14.3
|
0.4
|
|
OD1
|
B:ASP71
|
4.8
|
11.2
|
1.0
|
|
O
|
B:HOH327
|
4.8
|
17.0
|
1.0
|
|
CE
|
B:LYS141
|
4.8
|
19.1
|
1.0
|
|
Calcium binding site 7 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 7 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:8.7
occ:1.00
|
OD2
|
C:ASP98
|
2.2
|
10.8
|
1.0
|
|
O3
|
C:POP206
|
2.2
|
7.9
|
0.8
|
|
OD2
|
C:ASP103
|
2.3
|
10.0
|
1.0
|
|
O
|
C:HOH348
|
2.3
|
12.7
|
1.0
|
|
O5
|
C:POP206
|
2.3
|
16.2
|
0.2
|
|
O6
|
C:POP206
|
2.4
|
7.3
|
0.8
|
|
O
|
C:HOH326
|
2.4
|
9.6
|
1.0
|
|
O2
|
C:POP206
|
2.4
|
12.4
|
0.2
|
|
CG
|
C:ASP98
|
3.3
|
8.7
|
1.0
|
|
P2
|
C:POP206
|
3.3
|
8.6
|
0.8
|
|
P1
|
C:POP206
|
3.5
|
7.3
|
0.8
|
|
CG
|
C:ASP103
|
3.5
|
9.1
|
1.0
|
|
P2
|
C:POP206
|
3.5
|
16.1
|
0.2
|
|
P1
|
C:POP206
|
3.6
|
11.7
|
0.2
|
|
O
|
C:POP206
|
3.7
|
13.2
|
0.2
|
|
O5
|
C:POP206
|
3.7
|
9.0
|
0.8
|
|
O
|
C:POP206
|
3.7
|
6.2
|
0.8
|
|
CA
|
C:CA202
|
3.8
|
8.7
|
1.0
|
|
CB
|
C:ASP98
|
3.9
|
9.0
|
1.0
|
|
OD2
|
C:ASP66
|
4.0
|
11.6
|
1.0
|
|
NZ
|
C:LYS141
|
4.1
|
9.0
|
0.5
|
|
NZ
|
C:LYS141
|
4.1
|
8.5
|
0.5
|
|
OH
|
C:TYR140
|
4.2
|
8.6
|
1.0
|
|
NZ
|
C:LYS105
|
4.2
|
9.3
|
1.0
|
|
O2
|
C:POP206
|
4.3
|
6.5
|
0.8
|
|
O6
|
C:POP206
|
4.3
|
15.4
|
0.2
|
|
OD1
|
C:ASP98
|
4.3
|
10.5
|
1.0
|
|
OD1
|
C:ASP103
|
4.4
|
9.8
|
1.0
|
|
CB
|
C:ASP103
|
4.4
|
8.8
|
1.0
|
|
O
|
C:HOH364
|
4.5
|
14.4
|
1.0
|
|
O1
|
C:POP206
|
4.6
|
12.6
|
0.2
|
|
O3
|
C:POP206
|
4.6
|
9.0
|
0.2
|
|
O1
|
C:POP206
|
4.6
|
8.8
|
0.8
|
|
O4
|
C:POP206
|
4.7
|
16.2
|
0.2
|
|
OD1
|
C:ASP71
|
4.7
|
10.1
|
1.0
|
|
O4
|
C:POP206
|
4.7
|
9.5
|
0.8
|
|
CE
|
C:LYS141
|
4.8
|
10.2
|
0.5
|
|
O
|
C:HOH301
|
4.8
|
11.0
|
0.6
|
|
Calcium binding site 8 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 8 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca202
b:8.7
occ:1.00
|
OD2
|
C:ASP66
|
2.3
|
11.6
|
1.0
|
|
OD1
|
C:ASP71
|
2.4
|
10.1
|
1.0
|
|
O
|
C:HOH334
|
2.4
|
13.1
|
1.0
|
|
O6
|
C:POP206
|
2.4
|
7.3
|
0.8
|
|
OD1
|
C:ASP103
|
2.4
|
9.8
|
1.0
|
|
OD2
|
C:ASP68
|
2.5
|
8.9
|
0.4
|
|
O
|
C:HOH301
|
2.5
|
11.0
|
0.6
|
|
O5
|
C:POP206
|
2.6
|
16.2
|
0.2
|
|
OD2
|
C:ASP103
|
2.7
|
10.0
|
1.0
|
|
CG
|
C:ASP103
|
2.9
|
9.1
|
1.0
|
|
OD2
|
C:ASP71
|
3.0
|
10.4
|
1.0
|
|
CG
|
C:ASP71
|
3.0
|
8.9
|
1.0
|
|
CG
|
C:ASP66
|
3.3
|
11.9
|
1.0
|
|
P2
|
C:POP206
|
3.6
|
8.6
|
0.8
|
|
CG
|
C:ASP68
|
3.6
|
11.8
|
0.4
|
|
OD1
|
C:ASP66
|
3.7
|
14.3
|
1.0
|
|
P2
|
C:POP206
|
3.7
|
16.1
|
0.2
|
|
CA
|
C:CA201
|
3.8
|
8.7
|
1.0
|
|
O4
|
C:POP206
|
3.8
|
9.5
|
0.8
|
|
CA
|
C:CA203
|
3.9
|
10.2
|
1.0
|
|
O4
|
C:POP206
|
3.9
|
16.2
|
0.2
|
|
O
|
C:HOH356
|
3.9
|
10.0
|
1.0
|
|
O
|
C:HOH348
|
3.9
|
12.7
|
1.0
|
|
CB
|
C:ASP68
|
4.1
|
12.2
|
0.4
|
|
O6
|
C:POP206
|
4.1
|
15.4
|
0.2
|
|
NZ
|
C:LYS105
|
4.3
|
9.3
|
1.0
|
|
O5
|
C:POP206
|
4.3
|
9.0
|
0.8
|
|
CB
|
C:ASP103
|
4.4
|
8.8
|
1.0
|
|
CB
|
C:ASP71
|
4.4
|
8.3
|
1.0
|
|
O
|
C:PRO69
|
4.5
|
9.1
|
0.6
|
|
O
|
C:HOH345
|
4.5
|
21.5
|
0.4
|
|
O
|
C:PRO69
|
4.6
|
10.3
|
0.4
|
|
CB
|
C:ASP66
|
4.7
|
12.2
|
1.0
|
|
O
|
C:HOH302
|
4.7
|
12.3
|
0.6
|
|
OD1
|
C:ASP68
|
4.7
|
18.7
|
0.4
|
|
O
|
C:HOH326
|
4.7
|
9.6
|
1.0
|
|
O
|
C:HOH302
|
4.7
|
12.4
|
0.4
|
|
CB
|
C:ASP68
|
4.8
|
13.8
|
0.6
|
|
O
|
C:POP206
|
4.8
|
6.2
|
0.8
|
|
OH
|
C:TYR56
|
4.9
|
11.4
|
1.0
|
|
Calcium binding site 9 out
of 9 in 5ucq
Go back to
Calcium Binding Sites List in 5ucq
Calcium binding site 9 out
of 9 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca203
b:10.2
occ:1.00
|
O
|
C:HOH302
|
2.1
|
12.3
|
0.6
|
|
O4
|
C:POP206
|
2.3
|
9.5
|
0.8
|
|
OD2
|
C:ASP71
|
2.3
|
10.4
|
1.0
|
|
O
|
C:HOH336
|
2.3
|
11.2
|
1.0
|
|
O
|
C:HOH301
|
2.4
|
11.0
|
0.6
|
|
O
|
C:HOH429
|
2.4
|
16.5
|
1.0
|
|
O
|
C:HOH302
|
2.5
|
12.4
|
0.4
|
|
OD2
|
C:ASP68
|
2.5
|
8.9
|
0.4
|
|
O4
|
C:POP206
|
2.6
|
16.2
|
0.2
|
|
OD1
|
C:ASP68
|
3.2
|
18.7
|
0.4
|
|
CG
|
C:ASP68
|
3.3
|
11.8
|
0.4
|
|
O6
|
C:POP206
|
3.4
|
15.4
|
0.2
|
|
CG
|
C:ASP71
|
3.5
|
8.9
|
1.0
|
|
P2
|
C:POP206
|
3.5
|
16.1
|
0.2
|
|
P2
|
C:POP206
|
3.6
|
8.6
|
0.8
|
|
CA
|
C:CA202
|
3.9
|
8.7
|
1.0
|
|
O6
|
C:POP206
|
4.0
|
7.3
|
0.8
|
|
O5
|
C:POP206
|
4.0
|
16.2
|
0.2
|
|
O
|
C:HOH345
|
4.1
|
21.5
|
0.4
|
|
OD1
|
C:ASP71
|
4.1
|
10.1
|
1.0
|
|
O
|
C:PRO69
|
4.2
|
10.3
|
0.4
|
|
O
|
C:HOH313
|
4.2
|
42.1
|
1.0
|
|
OE1
|
C:GLU22
|
4.3
|
11.5
|
1.0
|
|
O
|
C:HOH366
|
4.3
|
30.8
|
1.0
|
|
OD2
|
C:ASP68
|
4.3
|
25.2
|
0.6
|
|
O
|
C:PRO69
|
4.4
|
9.1
|
0.6
|
|
NZ
|
C:LYS30
|
4.4
|
10.7
|
1.0
|
|
O5
|
C:POP206
|
4.4
|
9.0
|
0.8
|
|
CG2
|
C:ILE58
|
4.4
|
12.8
|
1.0
|
|
CE2
|
C:TYR56
|
4.5
|
8.9
|
1.0
|
|
O
|
C:HOH334
|
4.5
|
13.1
|
1.0
|
|
CB
|
C:ASP71
|
4.6
|
8.3
|
1.0
|
|
O
|
C:POP206
|
4.6
|
6.2
|
0.8
|
|
O
|
C:HOH344
|
4.6
|
11.5
|
1.0
|
|
OH
|
C:TYR56
|
4.7
|
11.4
|
1.0
|
|
CB
|
C:ASP68
|
4.7
|
12.2
|
0.4
|
|
CB
|
C:ASP68
|
4.8
|
13.8
|
0.6
|
|
CA
|
C:ASP71
|
4.8
|
6.9
|
1.0
|
|
O
|
C:GLY57
|
4.9
|
7.3
|
1.0
|
|
O
|
C:POP206
|
4.9
|
13.2
|
0.2
|
|
CG
|
C:ASP68
|
5.0
|
21.1
|
0.6
|
|
OE2
|
C:GLU22
|
5.0
|
11.3
|
1.0
|
|
Reference:
N.Inoguchi,
R.C.Hughes,
E.J.Meehan,
J.D.Ng.
The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate To Be Published.
Page generated: Wed Jul 9 10:26:26 2025
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