Calcium in PDB 9mg0: Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
Enzymatic activity of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
All present enzymatic activity of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah:
2.1.1.56;
Protein crystallography data
The structure of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah, PDB code: 9mg0
was solved by
D.J.Nilson,
E.Fedorov,
A.Ghosh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
24.96 /
1.30
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.616,
64.821,
73.524,
90,
94.48,
90
|
|
R / Rfree (%)
|
16.5 /
18.7
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Calcium atom in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
(pdb code 9mg0). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the
Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah, PDB code: 9mg0:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 1 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca507
b:31.9
occ:0.64
|
OE2
|
A:GLU257
|
2.5
|
40.1
|
1.0
|
|
O
|
A:GLU257
|
2.8
|
12.3
|
1.0
|
|
HB2
|
A:ARG261
|
3.1
|
15.9
|
1.0
|
|
HA
|
A:GLU257
|
3.1
|
16.4
|
1.0
|
|
HB2
|
A:ARG260
|
3.1
|
12.9
|
1.0
|
|
HG3
|
A:GLU257
|
3.1
|
30.3
|
1.0
|
|
CD
|
A:GLU257
|
3.3
|
24.4
|
1.0
|
|
H
|
A:ARG261
|
3.3
|
13.9
|
1.0
|
|
N
|
A:ARG261
|
3.5
|
11.6
|
1.0
|
|
C
|
A:GLU257
|
3.7
|
12.7
|
1.0
|
|
CG
|
A:GLU257
|
3.7
|
25.2
|
1.0
|
|
O
|
A:HOH813
|
3.7
|
36.1
|
1.0
|
|
HB3
|
A:ARG260
|
3.7
|
12.9
|
1.0
|
|
CA
|
A:GLU257
|
3.8
|
13.7
|
1.0
|
|
CB
|
A:ARG260
|
3.8
|
10.7
|
1.0
|
|
HA
|
A:ARG261
|
3.9
|
13.4
|
1.0
|
|
HD11
|
A:LEU264
|
3.9
|
22.6
|
0.5
|
|
CB
|
A:ARG261
|
3.9
|
13.2
|
1.0
|
|
HD2
|
A:ARG261
|
4.0
|
23.1
|
1.0
|
|
CA
|
A:ARG261
|
4.0
|
11.2
|
1.0
|
|
C
|
A:ARG260
|
4.1
|
11.9
|
1.0
|
|
CB
|
A:GLU257
|
4.3
|
17.8
|
1.0
|
|
OE1
|
A:GLU257
|
4.3
|
32.6
|
1.0
|
|
HB3
|
A:ARG261
|
4.4
|
15.9
|
1.0
|
|
HD13
|
A:LEU264
|
4.4
|
22.6
|
0.5
|
|
CA
|
A:ARG260
|
4.5
|
10.2
|
1.0
|
|
HG2
|
A:GLU257
|
4.5
|
30.3
|
1.0
|
|
CD1
|
A:LEU264
|
4.6
|
18.8
|
0.5
|
|
H
|
A:ARG260
|
4.6
|
12.7
|
1.0
|
|
O
|
A:HOH809
|
4.6
|
30.2
|
1.0
|
|
HD2
|
A:ARG260
|
4.7
|
15.1
|
1.0
|
|
O
|
A:ARG260
|
4.8
|
12.4
|
1.0
|
|
HB2
|
A:GLU257
|
4.8
|
21.4
|
1.0
|
|
CD
|
A:ARG261
|
4.8
|
19.3
|
1.0
|
|
O
|
A:HOH675
|
4.9
|
37.8
|
1.0
|
|
HD12
|
A:LEU264
|
4.9
|
22.6
|
0.5
|
|
O
|
A:GLU256
|
4.9
|
12.8
|
1.0
|
|
N
|
A:LYS258
|
4.9
|
11.7
|
1.0
|
|
N
|
A:ARG260
|
4.9
|
10.6
|
1.0
|
|
CG
|
A:ARG261
|
4.9
|
14.8
|
1.0
|
|
O
|
A:HOH651
|
5.0
|
18.2
|
1.0
|
|
Calcium binding site 2 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 2 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca508
b:37.0
occ:1.00
|
H
|
A:PHE323
|
2.1
|
20.0
|
1.0
|
|
HG3
|
A:GLU322
|
2.6
|
35.0
|
1.0
|
|
HA
|
A:GLU322
|
2.8
|
23.2
|
1.0
|
|
HD2
|
A:PHE323
|
2.9
|
21.4
|
1.0
|
|
N
|
A:PHE323
|
2.9
|
16.6
|
1.0
|
|
HD3
|
A:ARG287
|
3.2
|
27.1
|
0.7
|
|
HB2
|
A:PHE323
|
3.3
|
20.5
|
1.0
|
|
HH12
|
A:ARG287
|
3.3
|
22.6
|
0.3
|
|
O
|
A:HOH699
|
3.3
|
31.7
|
1.0
|
|
HE2
|
A:TYR316
|
3.4
|
16.4
|
1.0
|
|
HE
|
A:ARG287
|
3.4
|
30.3
|
0.3
|
|
HD3
|
A:ARG287
|
3.4
|
27.9
|
0.3
|
|
CA
|
A:GLU322
|
3.5
|
19.3
|
1.0
|
|
CG
|
A:GLU322
|
3.6
|
29.2
|
1.0
|
|
NE
|
A:ARG287
|
3.6
|
25.2
|
0.3
|
|
CD2
|
A:PHE323
|
3.6
|
17.8
|
1.0
|
|
C
|
A:GLU322
|
3.7
|
17.2
|
1.0
|
|
O
|
A:HOH854
|
3.7
|
26.6
|
1.0
|
|
HH11
|
A:ARG287
|
3.7
|
32.9
|
0.7
|
|
CB
|
A:PHE323
|
3.9
|
17.1
|
1.0
|
|
NH1
|
A:ARG287
|
3.9
|
18.8
|
0.3
|
|
CA
|
A:PHE323
|
4.0
|
17.7
|
1.0
|
|
CD
|
A:ARG287
|
4.0
|
23.2
|
0.3
|
|
HG2
|
A:GLU322
|
4.0
|
35.0
|
1.0
|
|
CB
|
A:GLU322
|
4.0
|
22.6
|
1.0
|
|
CZ
|
A:ARG287
|
4.1
|
21.7
|
0.3
|
|
CE2
|
A:TYR316
|
4.1
|
13.6
|
1.0
|
|
CD
|
A:ARG287
|
4.2
|
22.6
|
0.7
|
|
CG
|
A:PHE323
|
4.2
|
15.5
|
1.0
|
|
HB2
|
A:GLU322
|
4.3
|
27.1
|
1.0
|
|
HD2
|
A:ARG287
|
4.3
|
27.9
|
0.3
|
|
HD2
|
A:TYR316
|
4.3
|
17.0
|
1.0
|
|
HD2
|
A:ARG287
|
4.4
|
27.1
|
0.7
|
|
O
|
A:PHE323
|
4.5
|
21.8
|
1.0
|
|
OE2
|
A:GLU322
|
4.5
|
47.6
|
1.0
|
|
CD
|
A:GLU322
|
4.5
|
41.3
|
1.0
|
|
NH1
|
A:ARG287
|
4.6
|
27.4
|
0.7
|
|
CE2
|
A:PHE323
|
4.6
|
14.7
|
1.0
|
|
HH11
|
A:ARG287
|
4.6
|
22.6
|
0.3
|
|
CD2
|
A:TYR316
|
4.6
|
14.2
|
1.0
|
|
HE2
|
A:PHE323
|
4.7
|
17.7
|
1.0
|
|
HA
|
A:PHE323
|
4.7
|
21.2
|
1.0
|
|
C
|
A:PHE323
|
4.7
|
19.9
|
1.0
|
|
HG2
|
A:ARG287
|
4.8
|
16.9
|
0.7
|
|
N
|
A:GLU322
|
4.8
|
18.4
|
1.0
|
|
HB3
|
A:PHE323
|
4.8
|
20.5
|
1.0
|
|
NE
|
A:ARG287
|
4.9
|
24.8
|
0.7
|
|
O
|
A:ASN321
|
4.9
|
19.2
|
1.0
|
|
HB3
|
A:GLU322
|
4.9
|
27.1
|
1.0
|
|
O
|
A:GLU322
|
4.9
|
17.9
|
1.0
|
|
Calcium binding site 3 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 3 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca509
b:28.5
occ:0.57
|
O
|
A:HOH822
|
2.4
|
31.3
|
1.0
|
|
O
|
A:LEU363
|
2.8
|
13.5
|
1.0
|
|
HB3
|
A:LEU363
|
3.3
|
16.0
|
1.0
|
|
H
|
A:LEU363
|
3.3
|
14.7
|
1.0
|
|
HB3
|
A:GLU362
|
3.4
|
19.4
|
1.0
|
|
N
|
A:LEU363
|
3.7
|
12.3
|
1.0
|
|
C
|
A:LEU363
|
3.7
|
12.2
|
1.0
|
|
HH21
|
A:ARG353
|
3.8
|
36.3
|
1.0
|
|
CA
|
A:LEU363
|
4.0
|
12.2
|
1.0
|
|
CB
|
A:LEU363
|
4.1
|
13.3
|
1.0
|
|
CB
|
A:GLU362
|
4.3
|
16.2
|
1.0
|
|
NH2
|
A:ARG353
|
4.3
|
30.2
|
1.0
|
|
O
|
A:HOH759
|
4.4
|
18.6
|
1.0
|
|
C
|
A:GLU362
|
4.4
|
13.5
|
1.0
|
|
HH22
|
A:ARG353
|
4.4
|
36.3
|
1.0
|
|
HB2
|
A:GLU362
|
4.5
|
19.4
|
1.0
|
|
HB2
|
A:LEU363
|
4.6
|
16.0
|
1.0
|
|
HD23
|
A:LEU363
|
4.9
|
18.2
|
1.0
|
|
CA
|
A:GLU362
|
4.9
|
12.7
|
1.0
|
|
HA
|
A:GLU364
|
5.0
|
14.5
|
1.0
|
|
N
|
A:GLU364
|
5.0
|
11.4
|
1.0
|
|
HG
|
A:LEU363
|
5.0
|
16.2
|
1.0
|
|
HA
|
A:LEU363
|
5.0
|
14.6
|
1.0
|
|
O
|
A:GLU362
|
5.0
|
12.0
|
1.0
|
|
Calcium binding site 4 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 4 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca510
b:18.0
occ:0.94
|
H
|
A:GLN366
|
2.4
|
12.7
|
1.0
|
|
HE21
|
A:GLN366
|
2.5
|
23.7
|
1.0
|
|
HG3
|
A:GLN366
|
2.9
|
21.7
|
1.0
|
|
HA
|
A:LEU365
|
2.9
|
14.9
|
1.0
|
|
HG3
|
A:LYS367
|
3.0
|
21.8
|
1.0
|
|
HD12
|
A:LEU365
|
3.0
|
21.6
|
1.0
|
|
N
|
A:GLN366
|
3.2
|
10.6
|
1.0
|
|
O
|
A:HOH860
|
3.3
|
29.8
|
1.0
|
|
NE2
|
A:GLN366
|
3.3
|
19.8
|
1.0
|
|
HZ3
|
A:LYS367
|
3.6
|
44.7
|
1.0
|
|
HE2
|
A:LYS367
|
3.7
|
39.7
|
1.0
|
|
CG
|
A:GLN366
|
3.8
|
18.1
|
1.0
|
|
HG2
|
A:LYS367
|
3.8
|
21.8
|
1.0
|
|
H
|
A:LYS367
|
3.8
|
15.7
|
1.0
|
|
CG
|
A:LYS367
|
3.8
|
18.1
|
1.0
|
|
CA
|
A:LEU365
|
3.8
|
12.4
|
1.0
|
|
HE22
|
A:GLN366
|
3.9
|
23.7
|
1.0
|
|
C
|
A:LEU365
|
4.0
|
11.2
|
1.0
|
|
CD1
|
A:LEU365
|
4.0
|
18.0
|
1.0
|
|
N
|
A:LYS367
|
4.0
|
13.0
|
1.0
|
|
CD
|
A:GLN366
|
4.1
|
20.0
|
1.0
|
|
CA
|
A:GLN366
|
4.2
|
11.6
|
1.0
|
|
C
|
A:GLN366
|
4.3
|
10.5
|
1.0
|
|
NZ
|
A:LYS367
|
4.3
|
37.3
|
1.0
|
|
CE
|
A:LYS367
|
4.3
|
33.1
|
1.0
|
|
HG3
|
B:PRO294
|
4.4
|
36.3
|
1.0
|
|
HD13
|
A:LEU365
|
4.4
|
21.6
|
1.0
|
|
HG2
|
A:GLN366
|
4.4
|
21.7
|
1.0
|
|
HD3
|
B:PRO294
|
4.4
|
23.6
|
1.0
|
|
HD11
|
A:LEU365
|
4.4
|
21.6
|
1.0
|
|
HZ1
|
A:LYS367
|
4.5
|
44.7
|
1.0
|
|
CB
|
A:GLN366
|
4.5
|
13.2
|
1.0
|
|
O
|
A:GLU364
|
4.6
|
14.8
|
1.0
|
|
CD
|
A:LYS367
|
4.7
|
20.9
|
1.0
|
|
HG
|
A:LEU365
|
4.7
|
15.1
|
1.0
|
|
HA
|
A:LYS367
|
4.7
|
15.2
|
1.0
|
|
N
|
A:LEU365
|
4.7
|
10.9
|
1.0
|
|
CG
|
A:LEU365
|
4.8
|
12.6
|
1.0
|
|
CB
|
A:LEU365
|
4.8
|
11.5
|
1.0
|
|
CA
|
A:LYS367
|
4.8
|
12.7
|
1.0
|
|
CB
|
A:LYS367
|
4.8
|
14.1
|
1.0
|
|
Calcium binding site 5 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 5 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca511
b:22.4
occ:0.62
|
H
|
A:GLY368
|
2.2
|
14.1
|
1.0
|
|
OE1
|
A:GLU371
|
2.6
|
31.8
|
1.0
|
|
O
|
A:HOH858
|
2.7
|
23.7
|
1.0
|
|
HB3
|
A:GLU371
|
2.9
|
19.7
|
1.0
|
|
N
|
A:GLY368
|
2.9
|
11.8
|
1.0
|
|
O
|
A:HOH749
|
2.9
|
16.5
|
1.0
|
|
HB3
|
B:LYS292
|
3.0
|
17.9
|
1.0
|
|
HB2
|
A:GLU371
|
3.1
|
19.7
|
1.0
|
|
HE2
|
B:LYS292
|
3.1
|
17.8
|
1.0
|
|
HA
|
A:LYS367
|
3.2
|
15.2
|
1.0
|
|
HA3
|
A:GLY368
|
3.3
|
14.0
|
1.0
|
|
CB
|
A:GLU371
|
3.4
|
16.4
|
1.0
|
|
HE3
|
B:LYS292
|
3.5
|
17.8
|
1.0
|
|
HG3
|
B:LYS292
|
3.6
|
18.1
|
1.0
|
|
CA
|
A:GLY368
|
3.7
|
11.7
|
1.0
|
|
CD
|
A:GLU371
|
3.7
|
37.4
|
1.0
|
|
CE
|
B:LYS292
|
3.8
|
14.9
|
1.0
|
|
CB
|
B:LYS292
|
3.8
|
14.9
|
1.0
|
|
HB2
|
B:LYS292
|
3.8
|
17.9
|
1.0
|
|
C
|
A:LYS367
|
3.9
|
12.5
|
1.0
|
|
CA
|
A:LYS367
|
3.9
|
12.7
|
1.0
|
|
HB3
|
A:LYS367
|
3.9
|
17.0
|
1.0
|
|
H
|
A:GLU371
|
4.1
|
16.5
|
1.0
|
|
CG
|
B:LYS292
|
4.1
|
15.1
|
1.0
|
|
CG
|
A:GLU371
|
4.2
|
26.8
|
1.0
|
|
O
|
A:GLY368
|
4.3
|
12.2
|
1.0
|
|
HG2
|
A:LYS367
|
4.3
|
21.8
|
1.0
|
|
CB
|
A:LYS367
|
4.4
|
14.1
|
1.0
|
|
C
|
A:GLY368
|
4.4
|
10.9
|
1.0
|
|
HA2
|
A:GLY368
|
4.5
|
14.0
|
1.0
|
|
O
|
B:HOH692
|
4.5
|
34.1
|
1.0
|
|
CD
|
B:LYS292
|
4.6
|
13.7
|
1.0
|
|
O
|
B:HOH660
|
4.6
|
17.2
|
1.0
|
|
HG3
|
A:GLU371
|
4.6
|
32.2
|
1.0
|
|
O
|
B:HOH743
|
4.7
|
17.9
|
1.0
|
|
CA
|
A:GLU371
|
4.7
|
16.1
|
1.0
|
|
O
|
B:LYS292
|
4.7
|
17.8
|
1.0
|
|
N
|
A:GLU371
|
4.8
|
13.7
|
1.0
|
|
O
|
A:HOH816
|
4.8
|
32.1
|
1.0
|
|
HZ1
|
B:LYS292
|
4.8
|
19.4
|
1.0
|
|
OE2
|
A:GLU371
|
4.8
|
36.1
|
1.0
|
|
O
|
A:GLN366
|
4.8
|
12.4
|
1.0
|
|
HE22
|
A:GLN366
|
4.9
|
23.7
|
1.0
|
|
O
|
A:HOH625
|
4.9
|
17.5
|
1.0
|
|
HG2
|
A:GLU371
|
4.9
|
32.2
|
1.0
|
|
NZ
|
B:LYS292
|
4.9
|
16.2
|
1.0
|
|
CG
|
A:LYS367
|
4.9
|
18.1
|
1.0
|
|
HG2
|
B:LYS292
|
5.0
|
18.1
|
1.0
|
|
Calcium binding site 6 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 6 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca508
b:33.1
occ:1.00
|
O
|
B:HOH689
|
2.8
|
19.1
|
1.0
|
|
O
|
B:HOH847
|
2.9
|
22.4
|
1.0
|
|
HA2
|
B:GLY273
|
3.0
|
16.7
|
1.0
|
|
HG12
|
B:VAL421
|
3.1
|
19.2
|
1.0
|
|
HA
|
B:VAL421
|
3.1
|
15.8
|
1.0
|
|
HD3
|
B:ARG419
|
3.4
|
13.7
|
1.0
|
|
CZ
|
B:ARG419
|
3.6
|
13.5
|
1.0
|
|
NE
|
B:ARG419
|
3.7
|
13.0
|
1.0
|
|
NH1
|
B:ARG419
|
3.7
|
13.6
|
1.0
|
|
HG2
|
B:ARG419
|
3.8
|
14.4
|
1.0
|
|
HH11
|
B:ARG419
|
3.8
|
16.4
|
1.0
|
|
CA
|
B:GLY273
|
3.8
|
13.9
|
1.0
|
|
O
|
B:LYS420
|
3.9
|
12.7
|
1.0
|
|
CD
|
B:ARG419
|
3.9
|
11.4
|
1.0
|
|
NH2
|
B:ARG419
|
4.0
|
14.5
|
1.0
|
|
HB
|
B:VAL421
|
4.0
|
17.6
|
1.0
|
|
HH12
|
B:ARG419
|
4.0
|
16.4
|
1.0
|
|
HE
|
B:ARG419
|
4.0
|
15.6
|
1.0
|
|
CG1
|
B:VAL421
|
4.0
|
16.0
|
1.0
|
|
H
|
B:GLY273
|
4.0
|
16.6
|
1.0
|
|
CA
|
B:VAL421
|
4.1
|
13.2
|
1.0
|
|
HA3
|
B:GLY273
|
4.1
|
16.7
|
1.0
|
|
N
|
B:GLY273
|
4.2
|
13.8
|
1.0
|
|
HH21
|
B:ARG419
|
4.2
|
17.4
|
1.0
|
|
CB
|
B:VAL421
|
4.3
|
14.6
|
1.0
|
|
HH22
|
B:ARG419
|
4.3
|
17.4
|
1.0
|
|
HG22
|
B:ILE272
|
4.4
|
20.9
|
1.0
|
|
CG
|
B:ARG419
|
4.4
|
12.0
|
1.0
|
|
HG23
|
B:ILE272
|
4.5
|
20.9
|
1.0
|
|
HG11
|
B:VAL421
|
4.5
|
19.2
|
1.0
|
|
HG13
|
B:VAL421
|
4.6
|
19.2
|
1.0
|
|
C
|
B:LYS420
|
4.7
|
11.2
|
1.0
|
|
O
|
B:VAL421
|
4.7
|
15.5
|
1.0
|
|
HD2
|
B:ARG419
|
4.8
|
13.7
|
1.0
|
|
N
|
B:VAL421
|
4.9
|
11.7
|
1.0
|
|
CG2
|
B:ILE272
|
4.9
|
17.4
|
1.0
|
|
C
|
B:VAL421
|
4.9
|
14.3
|
1.0
|
|
C
|
B:GLY273
|
5.0
|
12.8
|
1.0
|
|
Calcium binding site 7 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 7 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca509
b:42.0
occ:1.00
|
O
|
B:HOH784
|
2.6
|
19.4
|
1.0
|
|
O
|
B:HOH801
|
2.7
|
28.4
|
1.0
|
|
O
|
B:VAL214
|
2.9
|
17.9
|
1.0
|
|
HD21
|
B:LEU201
|
3.0
|
23.2
|
1.0
|
|
HA
|
B:ILE215
|
3.1
|
16.7
|
1.0
|
|
HD23
|
B:LEU201
|
3.2
|
23.2
|
1.0
|
|
H
|
B:LEU216
|
3.2
|
15.2
|
1.0
|
|
HE2
|
B:TYR204
|
3.3
|
36.4
|
1.0
|
|
CD2
|
B:LEU201
|
3.4
|
19.3
|
1.0
|
|
HD22
|
B:LEU201
|
3.5
|
23.2
|
1.0
|
|
HG12
|
B:VAL214
|
3.5
|
20.9
|
1.0
|
|
HD2
|
B:TYR204
|
3.6
|
32.0
|
1.0
|
|
HB2
|
B:LEU216
|
3.7
|
17.1
|
1.0
|
|
CE2
|
B:TYR204
|
3.7
|
30.3
|
1.0
|
|
C
|
B:VAL214
|
3.7
|
14.8
|
1.0
|
|
HD12
|
B:LEU216
|
3.8
|
19.8
|
1.0
|
|
N
|
B:LEU216
|
3.8
|
12.7
|
1.0
|
|
O
|
B:HOH663
|
3.9
|
33.0
|
1.0
|
|
O
|
B:HOH887
|
3.9
|
29.5
|
1.0
|
|
CA
|
B:ILE215
|
3.9
|
13.9
|
1.0
|
|
CD2
|
B:TYR204
|
3.9
|
26.7
|
1.0
|
|
N
|
B:ILE215
|
4.2
|
13.6
|
1.0
|
|
C
|
B:ILE215
|
4.3
|
13.7
|
1.0
|
|
HG
|
B:LEU216
|
4.3
|
16.9
|
1.0
|
|
HB
|
B:VAL214
|
4.4
|
21.7
|
1.0
|
|
CB
|
B:LEU216
|
4.4
|
14.2
|
1.0
|
|
CG1
|
B:VAL214
|
4.5
|
17.4
|
1.0
|
|
CD1
|
B:LEU216
|
4.7
|
16.4
|
1.0
|
|
CG
|
B:LEU216
|
4.7
|
14.1
|
1.0
|
|
NE2
|
B:HIS205
|
4.7
|
26.4
|
1.0
|
|
CZ
|
B:TYR204
|
4.7
|
27.8
|
1.0
|
|
CA
|
B:LEU216
|
4.7
|
13.9
|
1.0
|
|
O
|
B:HOH853
|
4.8
|
27.2
|
1.0
|
|
HH
|
B:TYR204
|
4.8
|
41.9
|
1.0
|
|
CB
|
B:VAL214
|
4.8
|
18.1
|
1.0
|
|
CG
|
B:LEU201
|
4.9
|
17.9
|
1.0
|
|
CA
|
B:VAL214
|
4.9
|
16.3
|
1.0
|
|
HG11
|
B:VAL214
|
5.0
|
20.9
|
1.0
|
|
H
|
B:ILE215
|
5.0
|
16.3
|
1.0
|
|
HG13
|
B:VAL214
|
5.0
|
20.9
|
1.0
|
|
Calcium binding site 8 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 8 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca510
b:48.5
occ:1.00
|
OG
|
B:SER351
|
2.5
|
15.0
|
0.7
|
|
O
|
B:HOH830
|
2.8
|
21.4
|
1.0
|
|
HB2
|
B:PRO348
|
3.0
|
13.1
|
1.0
|
|
HB2
|
B:SER351
|
3.0
|
15.7
|
0.3
|
|
H
|
B:SER351
|
3.2
|
15.5
|
1.0
|
|
HB3
|
B:PRO348
|
3.2
|
13.1
|
1.0
|
|
HH22
|
B:ARG287
|
3.3
|
34.2
|
1.0
|
|
HB2
|
B:GLU350
|
3.3
|
21.6
|
1.0
|
|
HB3
|
B:SER351
|
3.5
|
15.7
|
0.3
|
|
CB
|
B:PRO348
|
3.5
|
10.9
|
1.0
|
|
HG3
|
B:PRO326
|
3.6
|
21.1
|
1.0
|
|
CB
|
B:SER351
|
3.7
|
13.1
|
0.3
|
|
CB
|
B:SER351
|
3.7
|
13.0
|
0.7
|
|
HB3
|
B:PRO326
|
3.7
|
14.6
|
1.0
|
|
N
|
B:SER351
|
3.7
|
12.9
|
1.0
|
|
HB2
|
B:SER351
|
3.8
|
15.7
|
0.7
|
|
NH2
|
B:ARG287
|
3.9
|
28.4
|
1.0
|
|
HH21
|
B:ARG287
|
4.0
|
34.2
|
1.0
|
|
HG2
|
B:PRO348
|
4.1
|
15.2
|
1.0
|
|
OE1
|
B:GLU350
|
4.2
|
31.6
|
1.0
|
|
CA
|
B:SER351
|
4.2
|
12.3
|
0.3
|
|
CA
|
B:SER351
|
4.2
|
12.3
|
0.7
|
|
CB
|
B:GLU350
|
4.2
|
18.0
|
1.0
|
|
O
|
B:HOH678
|
4.3
|
32.5
|
1.0
|
|
CG
|
B:PRO326
|
4.4
|
17.6
|
1.0
|
|
HA
|
B:SER351
|
4.4
|
14.8
|
1.0
|
|
HB3
|
B:SER351
|
4.4
|
15.7
|
0.7
|
|
CG
|
B:PRO348
|
4.4
|
12.7
|
1.0
|
|
CB
|
B:PRO326
|
4.5
|
12.2
|
1.0
|
|
HB3
|
B:GLU350
|
4.6
|
21.6
|
1.0
|
|
H
|
B:GLU350
|
4.6
|
14.4
|
1.0
|
|
C
|
B:GLU350
|
4.6
|
14.3
|
1.0
|
|
HA
|
B:PRO326
|
4.7
|
16.7
|
1.0
|
|
O
|
B:HOH638
|
4.7
|
31.7
|
1.0
|
|
HG2
|
B:PRO326
|
4.8
|
21.1
|
1.0
|
|
CA
|
B:GLU350
|
4.8
|
13.3
|
1.0
|
|
CA
|
B:PRO348
|
4.8
|
10.3
|
1.0
|
|
O
|
B:PRO348
|
4.9
|
11.3
|
1.0
|
|
OG
|
B:SER351
|
4.9
|
13.2
|
0.3
|
|
HH12
|
B:ARG287
|
4.9
|
43.5
|
1.0
|
|
HG
|
B:SER351
|
4.9
|
15.9
|
0.3
|
|
N
|
B:GLU350
|
4.9
|
12.0
|
1.0
|
|
C
|
B:PRO348
|
4.9
|
10.9
|
1.0
|
|
HG3
|
B:PRO348
|
5.0
|
15.2
|
1.0
|
|
CZ
|
B:ARG287
|
5.0
|
34.4
|
1.0
|
|
Calcium binding site 9 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 9 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca511
b:30.4
occ:0.63
|
H
|
B:GLU371
|
2.1
|
13.9
|
1.0
|
|
HB3
|
B:ASN370
|
2.7
|
18.2
|
1.0
|
|
O
|
B:HOH629
|
2.8
|
15.1
|
1.0
|
|
HB2
|
B:GLU371
|
2.8
|
17.4
|
1.0
|
|
O
|
A:HOH637
|
2.8
|
17.8
|
1.0
|
|
O
|
B:HOH623
|
2.8
|
17.1
|
1.0
|
|
HA3
|
B:GLY368
|
2.9
|
12.6
|
1.0
|
|
N
|
B:GLU371
|
2.9
|
11.6
|
1.0
|
|
HB3
|
B:GLU371
|
3.2
|
17.4
|
1.0
|
|
O
|
A:HOH635
|
3.2
|
28.0
|
1.0
|
|
O
|
B:HOH859
|
3.3
|
25.9
|
1.0
|
|
CB
|
B:GLU371
|
3.3
|
14.5
|
1.0
|
|
H
|
B:ASN370
|
3.5
|
13.0
|
1.0
|
|
CA
|
B:GLY368
|
3.5
|
10.5
|
1.0
|
|
CB
|
B:ASN370
|
3.6
|
15.2
|
1.0
|
|
H
|
B:GLY368
|
3.6
|
12.7
|
1.0
|
|
C
|
B:GLY368
|
3.7
|
9.9
|
1.0
|
|
O
|
B:GLY368
|
3.7
|
10.3
|
1.0
|
|
CA
|
B:GLU371
|
3.7
|
11.8
|
1.0
|
|
N
|
B:ASN370
|
3.8
|
10.8
|
1.0
|
|
HH
|
A:TYR288
|
3.8
|
15.7
|
1.0
|
|
C
|
B:ASN370
|
3.9
|
11.0
|
1.0
|
|
N
|
B:GLY368
|
3.9
|
10.6
|
1.0
|
|
CA
|
B:ASN370
|
3.9
|
11.5
|
1.0
|
|
HB2
|
B:ASN370
|
3.9
|
18.2
|
1.0
|
|
HD22
|
B:ASN370
|
4.0
|
31.3
|
1.0
|
|
HA
|
B:GLU371
|
4.2
|
14.2
|
1.0
|
|
HA2
|
B:GLY368
|
4.4
|
12.6
|
1.0
|
|
OE1
|
B:GLU371
|
4.4
|
35.8
|
1.0
|
|
OH
|
A:TYR288
|
4.4
|
13.1
|
1.0
|
|
N
|
B:PHE369
|
4.4
|
10.1
|
1.0
|
|
H
|
B:PHE372
|
4.4
|
13.1
|
1.0
|
|
HZ2
|
A:LYS289
|
4.5
|
24.0
|
1.0
|
|
HZ3
|
A:LYS289
|
4.6
|
24.0
|
1.0
|
|
HE2
|
A:LYS292
|
4.6
|
17.8
|
1.0
|
|
ND2
|
B:ASN370
|
4.6
|
26.1
|
1.0
|
|
O
|
A:HOH652
|
4.6
|
10.5
|
1.0
|
|
CG
|
B:ASN370
|
4.7
|
18.7
|
1.0
|
|
C
|
B:PHE369
|
4.7
|
10.3
|
1.0
|
|
CG
|
B:GLU371
|
4.7
|
20.8
|
1.0
|
|
H
|
B:PHE369
|
4.8
|
12.2
|
1.0
|
|
HG3
|
A:LYS292
|
4.8
|
18.7
|
1.0
|
|
HO2
|
A:EDO503
|
4.8
|
39.3
|
1.0
|
|
O
|
B:ALA410
|
4.8
|
15.2
|
1.0
|
|
HA
|
B:ASN370
|
4.9
|
13.8
|
1.0
|
|
C
|
B:GLU371
|
4.9
|
10.8
|
1.0
|
|
NZ
|
A:LYS289
|
5.0
|
20.0
|
1.0
|
|
N
|
B:PHE372
|
5.0
|
10.9
|
1.0
|
|
Calcium binding site 10 out
of 13 in 9mg0
Go back to
Calcium Binding Sites List in 9mg0
Calcium binding site 10 out
of 13 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sah within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca512
b:58.5
occ:1.00
|
O
|
B:HOH662
|
2.5
|
31.6
|
1.0
|
|
O
|
B:HOH783
|
2.9
|
40.1
|
1.0
|
|
O
|
B:GLY180
|
3.0
|
22.6
|
1.0
|
|
HB2
|
B:GLU211
|
3.0
|
51.9
|
1.0
|
|
HD1
|
B:TYR212
|
3.3
|
29.7
|
1.0
|
|
HA2
|
B:GLY180
|
3.5
|
23.5
|
1.0
|
|
HE1
|
B:TYR212
|
3.5
|
32.6
|
1.0
|
|
C
|
B:GLY180
|
3.7
|
21.9
|
1.0
|
|
HA3
|
B:GLY180
|
3.8
|
23.5
|
1.0
|
|
CA
|
B:GLY180
|
3.9
|
19.6
|
1.0
|
|
HA2
|
B:GLY183
|
3.9
|
20.4
|
1.0
|
|
CB
|
B:GLU211
|
3.9
|
43.3
|
1.0
|
|
CD1
|
B:TYR212
|
4.0
|
24.7
|
1.0
|
|
CE1
|
B:TYR212
|
4.1
|
27.2
|
1.0
|
|
HG3
|
B:GLU211
|
4.1
|
59.6
|
1.0
|
|
HG2
|
B:GLU211
|
4.2
|
59.6
|
1.0
|
|
H
|
B:GLU211
|
4.2
|
43.6
|
1.0
|
|
HB3
|
B:GLU211
|
4.3
|
51.9
|
1.0
|
|
CG
|
B:GLU211
|
4.3
|
49.7
|
1.0
|
|
H
|
B:GLY183
|
4.5
|
20.1
|
1.0
|
|
CA
|
B:GLY183
|
4.7
|
17.0
|
1.0
|
|
N
|
B:ALA181
|
4.8
|
21.2
|
1.0
|
|
N
|
B:GLU211
|
4.9
|
36.3
|
1.0
|
|
CA
|
B:GLU211
|
4.9
|
43.1
|
1.0
|
|
HA
|
B:ALA181
|
4.9
|
27.3
|
1.0
|
|
Reference:
D.J.Nilson,
B.Schwer,
S.Shuman,
S.C.Almo.
Structural Basis For Sensitivity and Acquired Resistance of Fungal Cap Guanine-N7 Methyltransferases to the Antifungal Antibiotic Sinefungin Nucleic Acids Res. 2025.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAF538
Page generated: Mon Aug 4 18:58:22 2025
|
