Manganese in PDB 6wb7: Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
Enzymatic activity of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
All present enzymatic activity of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp:
2.7.1.187;
Protein crystallography data
The structure of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp, PDB code: 6wb7
was solved by
P.D.Jeffrey,
J.N.Balaich,
M.A.Estrella,
M.S.Donia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.53 /
2.44
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.545,
50.268,
127.794,
89.06,
80.18,
71.81
|
R / Rfree (%)
|
18.7 /
25
|
Other elements in 6wb7:
The structure of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
(pdb code 6wb7). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the
Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp, PDB code: 6wb7:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
Manganese binding site 1 out
of 5 in 6wb7
Go back to
Manganese Binding Sites List in 6wb7
Manganese binding site 1 out
of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn303
b:29.7
occ:1.00
|
O2G
|
A:ANP302
|
2.1
|
28.4
|
1.0
|
O
|
A:HOH455
|
2.2
|
23.2
|
1.0
|
O
|
A:HOH444
|
2.2
|
31.1
|
1.0
|
O
|
A:HOH440
|
2.2
|
29.4
|
1.0
|
O2B
|
A:ANP302
|
2.3
|
30.4
|
1.0
|
ND1
|
A:HIS164
|
2.3
|
28.3
|
1.0
|
CE1
|
A:HIS164
|
3.1
|
22.4
|
1.0
|
PG
|
A:ANP302
|
3.3
|
49.8
|
1.0
|
CG
|
A:HIS164
|
3.4
|
27.7
|
1.0
|
PB
|
A:ANP302
|
3.6
|
52.8
|
1.0
|
O3G
|
A:ANP302
|
3.6
|
33.5
|
1.0
|
CB
|
A:HIS164
|
3.8
|
23.0
|
1.0
|
CA
|
A:HIS164
|
3.8
|
28.5
|
1.0
|
N3B
|
A:ANP302
|
4.0
|
38.0
|
1.0
|
OD1
|
A:ASP162
|
4.0
|
31.2
|
1.0
|
OD2
|
A:ASP162
|
4.2
|
23.0
|
1.0
|
O1B
|
A:ANP302
|
4.2
|
45.1
|
1.0
|
O
|
B:HOH458
|
4.3
|
30.6
|
1.0
|
NE2
|
A:HIS164
|
4.3
|
24.4
|
1.0
|
CG
|
A:ASP162
|
4.4
|
26.0
|
1.0
|
CD2
|
A:HIS164
|
4.5
|
24.7
|
1.0
|
O1G
|
A:ANP302
|
4.5
|
34.4
|
1.0
|
O6B
|
E:AC13
|
4.5
|
33.2
|
1.0
|
CA
|
A:GLY247
|
4.7
|
25.3
|
1.0
|
N
|
A:HIS164
|
4.7
|
25.6
|
1.0
|
OD1
|
A:ASP248
|
4.7
|
23.7
|
1.0
|
O3A
|
A:ANP302
|
4.8
|
44.4
|
1.0
|
C
|
A:HIS164
|
4.8
|
27.7
|
1.0
|
|
Manganese binding site 2 out
of 5 in 6wb7
Go back to
Manganese Binding Sites List in 6wb7
Manganese binding site 2 out
of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn303
b:26.3
occ:1.00
|
O2G
|
B:ANP302
|
2.0
|
28.2
|
1.0
|
O
|
B:HOH442
|
2.2
|
21.6
|
1.0
|
O
|
B:HOH437
|
2.2
|
27.0
|
1.0
|
O
|
B:HOH461
|
2.2
|
24.4
|
1.0
|
ND1
|
B:HIS164
|
2.2
|
24.1
|
1.0
|
O2B
|
B:ANP302
|
2.3
|
30.0
|
1.0
|
CE1
|
B:HIS164
|
3.0
|
20.3
|
1.0
|
PG
|
B:ANP302
|
3.3
|
51.9
|
1.0
|
CG
|
B:HIS164
|
3.4
|
26.7
|
1.0
|
PB
|
B:ANP302
|
3.7
|
49.2
|
1.0
|
O3G
|
B:ANP302
|
3.7
|
28.9
|
1.0
|
CB
|
B:HIS164
|
3.8
|
22.4
|
1.0
|
CA
|
B:HIS164
|
3.9
|
27.3
|
1.0
|
N3B
|
B:ANP302
|
4.0
|
34.1
|
1.0
|
O
|
B:HOH466
|
4.1
|
21.5
|
1.0
|
OD2
|
B:ASP162
|
4.1
|
20.5
|
1.0
|
OD1
|
B:ASP162
|
4.2
|
23.4
|
1.0
|
NE2
|
B:HIS164
|
4.2
|
22.1
|
1.0
|
CD2
|
B:HIS164
|
4.4
|
20.9
|
1.0
|
O
|
A:HOH424
|
4.4
|
26.2
|
1.0
|
O1G
|
B:ANP302
|
4.5
|
38.4
|
1.0
|
O1B
|
B:ANP302
|
4.5
|
51.8
|
1.0
|
CG
|
B:ASP162
|
4.5
|
24.3
|
1.0
|
N
|
B:HIS164
|
4.7
|
23.9
|
1.0
|
O3A
|
B:ANP302
|
4.7
|
42.6
|
1.0
|
OD1
|
B:ASP248
|
4.7
|
27.9
|
1.0
|
CA
|
B:GLY247
|
4.8
|
22.5
|
1.0
|
CB
|
B:SER186
|
4.9
|
29.0
|
1.0
|
C
|
B:HIS164
|
4.9
|
28.3
|
1.0
|
|
Manganese binding site 3 out
of 5 in 6wb7
Go back to
Manganese Binding Sites List in 6wb7
Manganese binding site 3 out
of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn303
b:35.1
occ:1.00
|
O2B
|
C:ANP302
|
2.1
|
32.2
|
1.0
|
O2G
|
C:ANP302
|
2.1
|
37.5
|
0.7
|
O
|
C:HOH452
|
2.2
|
24.5
|
1.0
|
O
|
C:HOH439
|
2.2
|
30.0
|
1.0
|
ND1
|
C:HIS164
|
2.3
|
29.7
|
1.0
|
CE1
|
C:HIS164
|
3.1
|
26.9
|
1.0
|
CG
|
C:HIS164
|
3.4
|
27.5
|
1.0
|
PG
|
C:ANP302
|
3.4
|
51.6
|
0.7
|
PB
|
C:ANP302
|
3.5
|
38.7
|
0.7
|
CB
|
C:HIS164
|
3.8
|
25.5
|
1.0
|
O3G
|
C:ANP302
|
3.9
|
23.8
|
0.7
|
CA
|
C:HIS164
|
4.0
|
31.9
|
1.0
|
N3B
|
C:ANP302
|
4.0
|
35.6
|
1.0
|
O
|
C:HOH474
|
4.0
|
28.5
|
1.0
|
O1B
|
C:ANP302
|
4.0
|
38.0
|
1.0
|
OD2
|
C:ASP162
|
4.2
|
30.2
|
1.0
|
NE2
|
C:HIS164
|
4.3
|
29.0
|
1.0
|
OD1
|
C:ASP162
|
4.3
|
30.0
|
1.0
|
CD2
|
C:HIS164
|
4.4
|
25.4
|
1.0
|
O6B
|
G:AC13
|
4.4
|
34.9
|
1.0
|
CG
|
C:ASP162
|
4.6
|
31.4
|
1.0
|
O1G
|
C:ANP302
|
4.6
|
36.4
|
0.7
|
O3A
|
C:ANP302
|
4.6
|
41.9
|
1.0
|
CA
|
C:GLY247
|
4.7
|
25.8
|
1.0
|
N
|
C:HIS164
|
4.9
|
31.8
|
1.0
|
OD1
|
C:ASP248
|
4.9
|
23.9
|
1.0
|
|
Manganese binding site 4 out
of 5 in 6wb7
Go back to
Manganese Binding Sites List in 6wb7
Manganese binding site 4 out
of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn305
b:42.6
occ:1.00
|
O
|
C:ASP202
|
2.6
|
39.3
|
1.0
|
O
|
C:GLY204
|
2.9
|
29.9
|
1.0
|
C
|
C:ASP202
|
3.5
|
37.9
|
1.0
|
O
|
C:ILE201
|
3.6
|
37.2
|
1.0
|
C
|
C:GLY204
|
4.1
|
30.9
|
1.0
|
CA
|
C:ASP202
|
4.2
|
31.6
|
1.0
|
NH2
|
C:ARG223
|
4.2
|
29.2
|
1.0
|
C
|
C:ARG203
|
4.3
|
35.3
|
1.0
|
N
|
C:GLY204
|
4.3
|
36.3
|
1.0
|
N
|
C:ARG203
|
4.4
|
37.3
|
1.0
|
C
|
C:ILE201
|
4.6
|
35.8
|
1.0
|
O
|
C:ARG203
|
4.6
|
32.6
|
1.0
|
CA
|
C:ARG203
|
4.6
|
33.2
|
1.0
|
NH1
|
C:ARG223
|
4.6
|
28.5
|
1.0
|
CA
|
C:GLY204
|
4.8
|
31.4
|
1.0
|
N
|
C:ASP202
|
4.9
|
33.4
|
1.0
|
CZ
|
C:ARG223
|
4.9
|
31.3
|
1.0
|
|
Manganese binding site 5 out
of 5 in 6wb7
Go back to
Manganese Binding Sites List in 6wb7
Manganese binding site 5 out
of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn303
b:38.7
occ:1.00
|
O2G
|
D:ANP302
|
1.8
|
51.1
|
0.4
|
O2B
|
D:ANP302
|
2.1
|
49.9
|
1.0
|
O
|
D:HOH402
|
2.2
|
37.0
|
1.0
|
O
|
D:HOH442
|
2.2
|
27.4
|
1.0
|
ND1
|
D:HIS164
|
2.2
|
29.1
|
1.0
|
PG
|
D:ANP302
|
3.1
|
82.2
|
0.4
|
CE1
|
D:HIS164
|
3.2
|
26.5
|
1.0
|
CG
|
D:HIS164
|
3.3
|
34.6
|
1.0
|
PB
|
D:ANP302
|
3.3
|
60.5
|
1.0
|
CB
|
D:HIS164
|
3.6
|
30.6
|
1.0
|
O3G
|
D:ANP302
|
3.6
|
46.2
|
0.4
|
CA
|
D:HIS164
|
3.7
|
30.1
|
1.0
|
O1B
|
D:ANP302
|
3.8
|
62.3
|
1.0
|
N3B
|
D:ANP302
|
3.8
|
48.6
|
1.0
|
OD1
|
D:ASP162
|
4.1
|
34.2
|
1.0
|
O1G
|
D:ANP302
|
4.3
|
59.0
|
0.4
|
NE2
|
D:HIS164
|
4.3
|
33.9
|
1.0
|
OD2
|
D:ASP162
|
4.3
|
27.6
|
1.0
|
CD2
|
D:HIS164
|
4.4
|
36.0
|
1.0
|
CG
|
D:ASP162
|
4.6
|
29.8
|
1.0
|
O6B
|
H:AC13
|
4.6
|
35.9
|
0.8
|
O3A
|
D:ANP302
|
4.6
|
38.5
|
1.0
|
N
|
D:HIS164
|
4.6
|
29.0
|
1.0
|
CA
|
D:GLY247
|
4.7
|
29.3
|
1.0
|
C
|
D:HIS164
|
4.8
|
38.4
|
1.0
|
OD1
|
D:ASP248
|
4.9
|
33.9
|
1.0
|
|
Reference:
J.N.Balaich,
M.A.Estrella,
P.D.Jeffrey,
A.Biswas,
A.Korennykh,
M.S.Donia.
Acarbose Sugar Kinases Encoded By the Human Microbiome Mediates Microbial Competition For Complex Carbohydrates To Be Published.
Page generated: Sun Oct 6 07:41:46 2024
|