Calcium in PDB 6k88: RGLG1 Midas Binds Calcium Ion
Enzymatic activity of RGLG1 Midas Binds Calcium Ion
All present enzymatic activity of RGLG1 Midas Binds Calcium Ion:
2.3.2.27;
Protein crystallography data
The structure of RGLG1 Midas Binds Calcium Ion, PDB code: 6k88
was solved by
Q.Wang,
Y.Wu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
37.00 /
1.79
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.876,
70.727,
146.403,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19.3 /
24
|
Calcium Binding Sites:
The binding sites of Calcium atom in the RGLG1 Midas Binds Calcium Ion
(pdb code 6k88). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
RGLG1 Midas Binds Calcium Ion, PDB code: 6k88:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 1 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:12.1
occ:1.00
|
O
|
A:LEU209
|
2.3
|
10.5
|
1.0
|
|
O
|
A:HOH643
|
2.4
|
17.4
|
1.0
|
|
OD1
|
A:ASP207
|
2.4
|
14.2
|
1.0
|
|
OD1
|
A:ASN156
|
2.4
|
19.9
|
1.0
|
|
O
|
A:HOH650
|
2.4
|
18.0
|
1.0
|
|
OD1
|
A:ASP205
|
2.5
|
12.6
|
1.0
|
|
OD2
|
A:ASP205
|
2.5
|
11.6
|
1.0
|
|
CG
|
A:ASP205
|
2.9
|
15.2
|
1.0
|
|
CG
|
A:ASN156
|
3.4
|
24.1
|
1.0
|
|
C
|
A:LEU209
|
3.5
|
12.8
|
1.0
|
|
CG
|
A:ASP207
|
3.5
|
20.0
|
1.0
|
|
N
|
A:LEU209
|
3.9
|
11.1
|
1.0
|
|
CB
|
A:ASN156
|
3.9
|
16.2
|
1.0
|
|
OD2
|
A:ASP207
|
3.9
|
20.8
|
1.0
|
|
CA
|
A:LEU209
|
4.1
|
13.5
|
1.0
|
|
CA
|
A:ASN156
|
4.3
|
13.6
|
1.0
|
|
N
|
A:ASP207
|
4.4
|
14.0
|
1.0
|
|
CB
|
A:ASP205
|
4.4
|
13.1
|
1.0
|
|
CB
|
A:LEU209
|
4.4
|
15.4
|
1.0
|
|
N
|
A:ASN208
|
4.5
|
12.2
|
1.0
|
|
N
|
A:LEU157
|
4.5
|
13.0
|
1.0
|
|
N
|
A:ILE210
|
4.6
|
13.0
|
1.0
|
|
ND2
|
A:ASN156
|
4.6
|
26.1
|
1.0
|
|
CD1
|
A:ILE210
|
4.7
|
15.5
|
1.0
|
|
CB
|
A:ASP207
|
4.7
|
18.2
|
1.0
|
|
CD
|
A:PRO211
|
4.8
|
12.6
|
1.0
|
|
N
|
A:GLU206
|
4.8
|
13.8
|
1.0
|
|
CA
|
A:ILE210
|
4.8
|
10.8
|
1.0
|
|
C
|
A:ASN208
|
4.9
|
16.4
|
1.0
|
|
CA
|
A:ASP207
|
4.9
|
15.8
|
1.0
|
|
C
|
A:ASP207
|
4.9
|
19.2
|
1.0
|
|
O
|
A:LEU157
|
4.9
|
13.9
|
1.0
|
|
C
|
A:ASN156
|
4.9
|
14.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 2 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:11.4
occ:1.00
|
OG1
|
A:THR258
|
2.3
|
11.1
|
1.0
|
|
O
|
A:HOH518
|
2.4
|
11.6
|
1.0
|
|
O
|
A:HOH568
|
2.4
|
13.8
|
1.0
|
|
OG
|
A:SER166
|
2.5
|
13.7
|
1.0
|
|
OG1
|
A:THR164
|
2.5
|
10.2
|
1.0
|
|
O
|
A:GLN288
|
2.6
|
13.0
|
1.0
|
|
CB
|
A:SER166
|
3.3
|
14.2
|
1.0
|
|
CB
|
A:THR258
|
3.4
|
13.0
|
1.0
|
|
CB
|
A:THR164
|
3.5
|
9.1
|
1.0
|
|
CG2
|
A:THR258
|
3.7
|
10.8
|
1.0
|
|
C
|
A:GLN288
|
3.8
|
13.2
|
1.0
|
|
CB
|
A:GLN288
|
3.9
|
13.8
|
1.0
|
|
OD1
|
A:ASP286
|
4.1
|
13.6
|
1.0
|
|
CG2
|
A:THR164
|
4.2
|
11.2
|
1.0
|
|
N
|
A:SER166
|
4.2
|
9.6
|
1.0
|
|
CA
|
A:GLN288
|
4.3
|
12.3
|
1.0
|
|
CA
|
A:SER166
|
4.4
|
12.4
|
1.0
|
|
OD2
|
A:ASP286
|
4.6
|
12.6
|
1.0
|
|
OD2
|
A:ASP162
|
4.6
|
17.3
|
1.0
|
|
OD1
|
A:ASP162
|
4.7
|
11.6
|
1.0
|
|
CA
|
A:THR258
|
4.7
|
10.3
|
1.0
|
|
CA
|
A:THR164
|
4.7
|
10.2
|
1.0
|
|
CG
|
A:ASP286
|
4.8
|
13.1
|
1.0
|
|
C
|
A:THR164
|
4.9
|
11.5
|
1.0
|
|
N
|
A:VAL289
|
4.9
|
10.9
|
1.0
|
|
N
|
A:GLN288
|
4.9
|
12.9
|
1.0
|
|
O
|
A:HOH630
|
4.9
|
19.8
|
1.0
|
|
Calcium binding site 3 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 3 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:16.3
occ:1.00
|
OE1
|
A:GLN350
|
2.3
|
14.5
|
1.0
|
|
O
|
A:HOH611
|
2.3
|
23.4
|
1.0
|
|
OE2
|
A:GLU378
|
2.4
|
20.6
|
1.0
|
|
O
|
A:HOH549
|
2.4
|
21.9
|
1.0
|
|
O
|
A:HOH652
|
2.4
|
28.6
|
1.0
|
|
OD2
|
A:ASP338
|
2.5
|
14.6
|
1.0
|
|
OD1
|
A:ASP338
|
2.6
|
16.0
|
1.0
|
|
CG
|
A:ASP338
|
2.9
|
15.4
|
1.0
|
|
CD
|
A:GLN350
|
3.4
|
14.0
|
1.0
|
|
CD
|
A:GLU378
|
3.4
|
17.6
|
1.0
|
|
O
|
A:HOH570
|
3.7
|
16.5
|
1.0
|
|
NE2
|
A:GLN350
|
3.9
|
15.1
|
1.0
|
|
CA
|
A:CA404
|
3.9
|
15.2
|
1.0
|
|
OD1
|
A:ASP339
|
4.0
|
25.9
|
1.0
|
|
OE1
|
A:GLU378
|
4.2
|
22.1
|
1.0
|
|
CG
|
A:GLU378
|
4.3
|
18.1
|
1.0
|
|
CB
|
A:ASP338
|
4.4
|
14.1
|
1.0
|
|
N
|
A:PHE351
|
4.4
|
10.8
|
1.0
|
|
CA
|
A:GLN350
|
4.6
|
12.3
|
1.0
|
|
CG
|
A:GLN350
|
4.7
|
10.5
|
1.0
|
|
O
|
A:PHE351
|
4.7
|
14.1
|
1.0
|
|
CB
|
A:GLN350
|
4.9
|
12.9
|
1.0
|
|
Calcium binding site 4 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 4 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:15.2
occ:1.00
|
OD1
|
A:ASP338
|
2.3
|
16.0
|
1.0
|
|
OE1
|
A:GLU378
|
2.3
|
22.1
|
1.0
|
|
O
|
A:ASP338
|
2.4
|
16.9
|
1.0
|
|
OD1
|
A:ASP347
|
2.4
|
18.7
|
1.0
|
|
O
|
A:PHE349
|
2.4
|
16.7
|
1.0
|
|
O
|
A:HOH570
|
2.4
|
16.5
|
1.0
|
|
OD2
|
A:ASP347
|
2.5
|
24.1
|
1.0
|
|
OE2
|
A:GLU378
|
2.7
|
20.6
|
1.0
|
|
CG
|
A:ASP347
|
2.8
|
23.2
|
1.0
|
|
CD
|
A:GLU378
|
2.8
|
17.6
|
1.0
|
|
C
|
A:ASP338
|
3.3
|
19.4
|
1.0
|
|
CG
|
A:ASP338
|
3.5
|
15.4
|
1.0
|
|
C
|
A:PHE349
|
3.6
|
14.7
|
1.0
|
|
CA
|
A:ASP338
|
3.8
|
14.7
|
1.0
|
|
CA
|
A:CA403
|
3.9
|
16.3
|
1.0
|
|
CB
|
A:ASP338
|
4.2
|
14.1
|
1.0
|
|
O
|
A:HOH538
|
4.2
|
24.9
|
1.0
|
|
CB
|
A:ASP347
|
4.3
|
22.6
|
1.0
|
|
CG
|
A:GLU378
|
4.3
|
18.1
|
1.0
|
|
CA
|
A:GLN350
|
4.3
|
12.3
|
1.0
|
|
OD1
|
A:ASP339
|
4.4
|
25.9
|
1.0
|
|
N
|
A:GLN350
|
4.4
|
10.2
|
1.0
|
|
OD2
|
A:ASP338
|
4.4
|
14.6
|
1.0
|
|
N
|
A:ASP339
|
4.4
|
16.9
|
1.0
|
|
O
|
A:HOH509
|
4.5
|
31.0
|
1.0
|
|
OE1
|
A:GLN350
|
4.5
|
14.5
|
1.0
|
|
NH2
|
A:ARG344
|
4.5
|
20.4
|
1.0
|
|
N
|
A:PHE349
|
4.6
|
15.8
|
1.0
|
|
CA
|
A:PHE349
|
4.6
|
14.3
|
1.0
|
|
CA
|
A:ASP339
|
4.8
|
19.3
|
1.0
|
|
CB
|
A:GLU378
|
5.0
|
17.7
|
1.0
|
|
Calcium binding site 5 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 5 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:18.1
occ:1.00
|
OD1
|
B:ASP338
|
2.3
|
21.2
|
1.0
|
|
O
|
B:ASP338
|
2.4
|
17.0
|
1.0
|
|
OE1
|
B:GLU378
|
2.4
|
22.9
|
1.0
|
|
O
|
B:PHE349
|
2.4
|
13.0
|
1.0
|
|
OD1
|
B:ASP347
|
2.5
|
20.0
|
1.0
|
|
OD2
|
B:ASP347
|
2.5
|
21.3
|
1.0
|
|
O
|
B:HOH548
|
2.6
|
23.0
|
1.0
|
|
OE2
|
B:GLU378
|
2.6
|
25.6
|
1.0
|
|
CG
|
B:ASP347
|
2.8
|
23.9
|
1.0
|
|
CD
|
B:GLU378
|
2.8
|
22.2
|
1.0
|
|
C
|
B:ASP338
|
3.3
|
18.2
|
1.0
|
|
CG
|
B:ASP338
|
3.5
|
19.4
|
1.0
|
|
C
|
B:PHE349
|
3.6
|
14.1
|
1.0
|
|
CA
|
B:ASP338
|
3.8
|
15.8
|
1.0
|
|
CA
|
B:CA402
|
4.0
|
21.3
|
1.0
|
|
CB
|
B:ASP338
|
4.2
|
15.9
|
1.0
|
|
CB
|
B:ASP347
|
4.3
|
20.9
|
1.0
|
|
CG
|
B:GLU378
|
4.3
|
22.0
|
1.0
|
|
CA
|
B:GLN350
|
4.4
|
13.2
|
1.0
|
|
OD1
|
B:ASP339
|
4.4
|
25.7
|
1.0
|
|
N
|
B:GLN350
|
4.4
|
14.5
|
1.0
|
|
N
|
B:ASP339
|
4.4
|
19.0
|
1.0
|
|
O
|
B:HOH555
|
4.4
|
23.5
|
1.0
|
|
NH2
|
B:ARG344
|
4.4
|
19.2
|
1.0
|
|
OD2
|
B:ASP338
|
4.5
|
14.8
|
1.0
|
|
N
|
B:PHE349
|
4.5
|
16.6
|
1.0
|
|
CA
|
B:PHE349
|
4.6
|
16.2
|
1.0
|
|
OE1
|
B:GLN350
|
4.6
|
16.0
|
1.0
|
|
O
|
A:HOH676
|
4.7
|
34.2
|
1.0
|
|
CA
|
B:ASP339
|
4.8
|
21.2
|
1.0
|
|
O
|
B:HOH632
|
4.9
|
31.4
|
1.0
|
|
Calcium binding site 6 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 6 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:21.3
occ:1.00
|
OE1
|
B:GLN350
|
2.3
|
16.0
|
1.0
|
|
O
|
B:HOH606
|
2.3
|
30.5
|
1.0
|
|
O
|
B:HOH639
|
2.4
|
28.3
|
1.0
|
|
OE2
|
B:GLU378
|
2.4
|
25.6
|
1.0
|
|
O
|
B:HOH534
|
2.4
|
22.6
|
1.0
|
|
OD2
|
B:ASP338
|
2.5
|
14.8
|
1.0
|
|
OD1
|
B:ASP338
|
2.6
|
21.2
|
1.0
|
|
CG
|
B:ASP338
|
2.9
|
19.4
|
1.0
|
|
CD
|
B:GLN350
|
3.4
|
16.0
|
1.0
|
|
O
|
A:HOH616
|
3.5
|
34.7
|
1.0
|
|
CD
|
B:GLU378
|
3.5
|
22.2
|
1.0
|
|
O
|
B:HOH548
|
3.7
|
23.0
|
1.0
|
|
NE2
|
B:GLN350
|
3.9
|
18.2
|
1.0
|
|
O
|
B:HOH632
|
3.9
|
31.4
|
1.0
|
|
CA
|
B:CA401
|
4.0
|
18.1
|
1.0
|
|
OD1
|
B:ASP339
|
4.1
|
25.7
|
1.0
|
|
CG
|
B:GLU378
|
4.3
|
22.0
|
1.0
|
|
OE1
|
B:GLU378
|
4.4
|
22.9
|
1.0
|
|
CB
|
B:ASP338
|
4.4
|
15.9
|
1.0
|
|
N
|
B:PHE351
|
4.5
|
12.2
|
1.0
|
|
O
|
A:HOH676
|
4.6
|
34.2
|
1.0
|
|
CA
|
B:GLN350
|
4.7
|
13.2
|
1.0
|
|
CG
|
B:GLN350
|
4.7
|
14.7
|
1.0
|
|
O
|
B:PHE351
|
4.7
|
14.7
|
1.0
|
|
O
|
B:HOH650
|
4.8
|
34.2
|
1.0
|
|
O
|
A:HOH660
|
4.9
|
34.6
|
1.0
|
|
CB
|
B:GLN350
|
4.9
|
13.0
|
1.0
|
|
Calcium binding site 7 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 7 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:17.7
occ:1.00
|
O
|
B:LEU209
|
2.3
|
18.6
|
1.0
|
|
OD1
|
B:ASP207
|
2.3
|
15.3
|
1.0
|
|
O
|
B:HOH583
|
2.4
|
15.4
|
1.0
|
|
O
|
B:HOH611
|
2.4
|
19.4
|
1.0
|
|
OD2
|
B:ASP205
|
2.4
|
23.2
|
1.0
|
|
OD1
|
B:ASP205
|
2.5
|
23.3
|
1.0
|
|
OD1
|
B:ASN156
|
2.6
|
23.4
|
1.0
|
|
CG
|
B:ASP205
|
2.8
|
26.3
|
1.0
|
|
CG
|
B:ASP207
|
3.4
|
25.3
|
1.0
|
|
C
|
B:LEU209
|
3.5
|
19.2
|
1.0
|
|
CG
|
B:ASN156
|
3.6
|
26.9
|
1.0
|
|
OD2
|
B:ASP207
|
3.9
|
23.6
|
1.0
|
|
N
|
B:LEU209
|
3.9
|
22.6
|
1.0
|
|
CB
|
B:ASN156
|
4.0
|
23.5
|
1.0
|
|
CA
|
B:LEU209
|
4.1
|
23.6
|
1.0
|
|
O
|
B:HOH649
|
4.2
|
29.7
|
1.0
|
|
CB
|
B:ASP205
|
4.2
|
21.4
|
1.0
|
|
CB
|
B:LEU209
|
4.3
|
21.7
|
1.0
|
|
N
|
B:ASP207
|
4.4
|
24.2
|
1.0
|
|
N
|
B:ASN208
|
4.5
|
24.2
|
1.0
|
|
N
|
B:LEU157
|
4.5
|
14.8
|
1.0
|
|
N
|
B:ILE210
|
4.5
|
20.2
|
1.0
|
|
CA
|
B:ASN156
|
4.6
|
16.5
|
1.0
|
|
O
|
B:LEU157
|
4.6
|
16.4
|
1.0
|
|
CD
|
B:PRO211
|
4.7
|
17.5
|
1.0
|
|
CB
|
B:ASP207
|
4.7
|
23.4
|
1.0
|
|
ND2
|
B:ASN156
|
4.7
|
23.0
|
1.0
|
|
CA
|
B:ILE210
|
4.8
|
18.0
|
1.0
|
|
C
|
B:ASN208
|
4.8
|
24.3
|
1.0
|
|
N
|
B:GLU206
|
4.9
|
28.4
|
1.0
|
|
C
|
B:ASP207
|
4.9
|
20.9
|
1.0
|
|
CA
|
B:ASP205
|
4.9
|
27.4
|
1.0
|
|
CA
|
B:ASP207
|
4.9
|
21.8
|
1.0
|
|
CD1
|
B:ILE210
|
4.9
|
18.2
|
1.0
|
|
C
|
B:ASP205
|
4.9
|
28.2
|
1.0
|
|
Calcium binding site 8 out
of 8 in 6k88
Go back to
Calcium Binding Sites List in 6k88
Calcium binding site 8 out
of 8 in the RGLG1 Midas Binds Calcium Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca404
b:10.9
occ:1.00
|
OG
|
B:SER166
|
2.4
|
8.9
|
1.0
|
|
O
|
B:HOH529
|
2.4
|
9.0
|
1.0
|
|
OG1
|
B:THR258
|
2.4
|
11.1
|
1.0
|
|
OG1
|
B:THR164
|
2.5
|
11.3
|
1.0
|
|
O
|
B:HOH586
|
2.6
|
15.0
|
1.0
|
|
O
|
B:GLN288
|
2.6
|
11.1
|
1.0
|
|
CB
|
B:SER166
|
3.3
|
11.2
|
1.0
|
|
CB
|
B:THR258
|
3.4
|
12.0
|
1.0
|
|
CB
|
B:THR164
|
3.5
|
11.4
|
1.0
|
|
CG2
|
B:THR258
|
3.7
|
11.6
|
1.0
|
|
C
|
B:GLN288
|
3.8
|
10.4
|
1.0
|
|
CB
|
B:GLN288
|
3.9
|
9.6
|
1.0
|
|
CG2
|
B:THR164
|
4.1
|
11.6
|
1.0
|
|
OD1
|
B:ASP286
|
4.1
|
10.7
|
1.0
|
|
N
|
B:SER166
|
4.3
|
8.8
|
1.0
|
|
CA
|
B:SER166
|
4.4
|
12.6
|
1.0
|
|
CA
|
B:GLN288
|
4.4
|
10.6
|
1.0
|
|
OD2
|
B:ASP162
|
4.6
|
17.8
|
1.0
|
|
OD2
|
B:ASP286
|
4.6
|
11.2
|
1.0
|
|
OD1
|
B:ASP162
|
4.6
|
13.2
|
1.0
|
|
CA
|
B:THR164
|
4.7
|
12.0
|
1.0
|
|
CA
|
B:THR258
|
4.8
|
10.4
|
1.0
|
|
CG
|
B:ASP286
|
4.8
|
13.5
|
1.0
|
|
C
|
B:THR164
|
4.8
|
12.0
|
1.0
|
|
N
|
B:VAL289
|
4.9
|
8.3
|
1.0
|
|
N
|
B:GLN288
|
4.9
|
8.9
|
1.0
|
|
O
|
B:HOH614
|
5.0
|
13.6
|
1.0
|
|
Reference:
Q.Wang,
Y.Wu.
RGLG1 Midas Binds Calcium Ion To Be Published.
Page generated: Tue Jul 16 10:16:22 2024
|
