Magnesium in PDB 3b1r: Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Enzymatic activity of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
All present enzymatic activity of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp:
2.7.1.143;
Protein crystallography data
The structure of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp, PDB code: 3b1r
was solved by
Y.Yasutake,
H.Ota,
E.Hino,
S.Sakasegawa,
T.Tamura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.35 /
2.00
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.222,
125.222,
115.002,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.7 /
20.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
(pdb code 3b1r). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp, PDB code: 3b1r:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 3b1r
Go back to
Magnesium Binding Sites List in 3b1r
Magnesium binding site 1 out
of 7 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:21.2
occ:1.00
|
O
|
A:HOH314
|
1.8
|
25.3
|
1.0
|
O
|
A:HOH313
|
2.0
|
23.3
|
1.0
|
O1P
|
A:AMP501
|
2.1
|
21.2
|
1.0
|
O
|
A:HOH315
|
2.1
|
27.4
|
1.0
|
O
|
A:HOH317
|
2.1
|
14.9
|
1.0
|
O
|
A:HOH316
|
2.2
|
13.4
|
1.0
|
P
|
A:AMP501
|
3.6
|
20.9
|
1.0
|
O
|
A:HOH763
|
3.9
|
15.7
|
1.0
|
OE2
|
A:GLU195
|
4.1
|
19.9
|
1.0
|
OE1
|
A:GLU195
|
4.1
|
18.2
|
1.0
|
OD2
|
A:ASP166
|
4.3
|
17.6
|
1.0
|
O5'
|
A:AMP501
|
4.3
|
18.6
|
1.0
|
OE1
|
A:GLN169
|
4.3
|
16.7
|
1.0
|
O3P
|
A:AMP501
|
4.4
|
19.8
|
1.0
|
O
|
A:HOH324
|
4.4
|
18.8
|
1.0
|
CA
|
A:GLY252
|
4.4
|
16.6
|
1.0
|
O
|
D:HOH319
|
4.5
|
11.7
|
1.0
|
O
|
A:HOH325
|
4.5
|
19.0
|
1.0
|
O2P
|
A:AMP501
|
4.5
|
19.1
|
1.0
|
CD
|
A:GLU195
|
4.6
|
18.6
|
1.0
|
NH2
|
A:ARG256
|
4.6
|
19.9
|
1.0
|
OD1
|
A:ASP166
|
4.6
|
17.1
|
1.0
|
O
|
A:HOH322
|
4.6
|
16.0
|
1.0
|
NE2
|
A:GLN169
|
4.7
|
17.2
|
1.0
|
CZ
|
A:ARG256
|
4.7
|
17.2
|
1.0
|
CD
|
A:GLN169
|
4.8
|
15.3
|
1.0
|
ND2
|
A:ASN192
|
4.8
|
18.0
|
1.0
|
CG
|
A:ASP166
|
4.9
|
14.8
|
1.0
|
NH1
|
A:ARG256
|
4.9
|
18.9
|
1.0
|
OD1
|
A:ASP253
|
5.0
|
20.1
|
1.0
|
CA
|
A:GLY168
|
5.0
|
15.6
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 3b1r
Go back to
Magnesium Binding Sites List in 3b1r
Magnesium binding site 2 out
of 7 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg503
b:13.4
occ:1.00
|
O
|
B:HOH314
|
2.0
|
27.7
|
1.0
|
O1P
|
B:AMP501
|
2.0
|
18.5
|
1.0
|
O
|
B:HOH316
|
2.1
|
11.2
|
1.0
|
O
|
B:HOH315
|
2.1
|
5.5
|
1.0
|
O
|
B:HOH313
|
2.1
|
12.0
|
1.0
|
O
|
B:HOH317
|
2.3
|
7.3
|
1.0
|
P
|
B:AMP501
|
3.5
|
19.5
|
1.0
|
O
|
B:HOH594
|
3.9
|
18.9
|
1.0
|
OD1
|
B:ASP253
|
4.0
|
19.3
|
1.0
|
OD2
|
B:ASP166
|
4.0
|
17.6
|
1.0
|
OE2
|
B:GLU195
|
4.1
|
22.8
|
1.0
|
NH2
|
B:ARG256
|
4.2
|
18.3
|
1.0
|
O5'
|
B:AMP501
|
4.2
|
17.4
|
1.0
|
OE1
|
B:GLN169
|
4.3
|
17.1
|
1.0
|
OD1
|
B:ASP166
|
4.3
|
14.7
|
1.0
|
O3P
|
B:AMP501
|
4.4
|
19.1
|
1.0
|
O
|
B:HOH318
|
4.4
|
22.0
|
1.0
|
OE1
|
B:GLU195
|
4.4
|
18.2
|
1.0
|
O2P
|
B:AMP501
|
4.4
|
18.3
|
1.0
|
O
|
B:HOH321
|
4.6
|
5.3
|
1.0
|
CG
|
B:ASP166
|
4.6
|
15.0
|
1.0
|
CD
|
B:GLU195
|
4.7
|
22.3
|
1.0
|
CA
|
B:GLY252
|
4.7
|
17.1
|
1.0
|
O
|
B:HOH323
|
4.8
|
19.4
|
1.0
|
NE2
|
B:GLN169
|
4.8
|
17.7
|
1.0
|
CZ
|
B:ARG256
|
4.8
|
17.1
|
1.0
|
CG
|
B:ASP253
|
4.8
|
18.8
|
1.0
|
CD
|
B:GLN169
|
4.8
|
18.4
|
1.0
|
O
|
B:HOH319
|
4.9
|
16.0
|
1.0
|
CA
|
B:GLY168
|
4.9
|
15.0
|
1.0
|
C
|
B:GLY252
|
5.0
|
17.2
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 3b1r
Go back to
Magnesium Binding Sites List in 3b1r
Magnesium binding site 3 out
of 7 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg503
b:22.1
occ:1.00
|
O
|
C:HOH316
|
1.9
|
23.2
|
1.0
|
O
|
C:HOH315
|
1.9
|
25.6
|
1.0
|
O
|
C:HOH314
|
2.0
|
16.2
|
1.0
|
O3P
|
C:AMP501
|
2.1
|
23.4
|
1.0
|
O
|
C:HOH313
|
2.1
|
16.7
|
1.0
|
O
|
C:HOH317
|
2.6
|
17.0
|
1.0
|
P
|
C:AMP501
|
3.5
|
21.9
|
1.0
|
OE1
|
C:GLN169
|
3.7
|
20.6
|
1.0
|
O
|
C:HOH784
|
3.8
|
25.6
|
1.0
|
O5'
|
C:AMP501
|
4.0
|
18.5
|
1.0
|
OE2
|
C:GLU195
|
4.1
|
24.1
|
1.0
|
OD2
|
C:ASP166
|
4.1
|
18.0
|
1.0
|
O1P
|
C:AMP501
|
4.1
|
23.6
|
1.0
|
OE1
|
C:GLU195
|
4.3
|
23.7
|
1.0
|
CD
|
C:GLN169
|
4.4
|
18.7
|
1.0
|
OD1
|
C:ASP166
|
4.4
|
21.4
|
1.0
|
NE2
|
C:GLN169
|
4.4
|
18.2
|
1.0
|
O
|
F:HOH320
|
4.5
|
8.2
|
1.0
|
CA
|
C:GLY168
|
4.6
|
17.6
|
1.0
|
O
|
C:HOH318
|
4.6
|
16.6
|
1.0
|
CD
|
C:GLU195
|
4.6
|
24.6
|
1.0
|
O2P
|
C:AMP501
|
4.6
|
21.9
|
1.0
|
OD1
|
C:ASP253
|
4.7
|
20.5
|
1.0
|
CG
|
C:ASP166
|
4.7
|
19.2
|
1.0
|
NH2
|
C:ARG256
|
5.0
|
22.4
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 3b1r
Go back to
Magnesium Binding Sites List in 3b1r
Magnesium binding site 4 out
of 7 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg503
b:19.3
occ:1.00
|
O
|
D:HOH317
|
1.9
|
18.7
|
1.0
|
O
|
D:HOH316
|
2.0
|
19.5
|
1.0
|
O
|
D:HOH318
|
2.0
|
28.3
|
1.0
|
O2P
|
D:AMP501
|
2.1
|
22.8
|
1.0
|
O
|
D:HOH314
|
2.1
|
14.7
|
1.0
|
O
|
D:HOH951
|
2.2
|
13.7
|
1.0
|
P
|
D:AMP501
|
3.6
|
24.3
|
1.0
|
OD2
|
D:ASP166
|
4.1
|
15.9
|
1.0
|
OE2
|
D:GLU195
|
4.1
|
19.1
|
1.0
|
O
|
D:HOH321
|
4.1
|
19.6
|
1.0
|
OE1
|
D:GLN169
|
4.2
|
11.9
|
1.0
|
NH2
|
D:ARG256
|
4.2
|
19.7
|
1.0
|
OE1
|
D:GLU195
|
4.2
|
18.0
|
1.0
|
O
|
D:HOH664
|
4.2
|
22.1
|
1.0
|
O1P
|
D:AMP501
|
4.3
|
23.6
|
1.0
|
O5'
|
D:AMP501
|
4.3
|
22.4
|
1.0
|
OD1
|
D:ASP166
|
4.4
|
13.9
|
1.0
|
OD1
|
D:ASP253
|
4.5
|
17.1
|
1.0
|
CA
|
D:GLY252
|
4.5
|
16.6
|
1.0
|
O3P
|
D:AMP501
|
4.6
|
24.2
|
1.0
|
CD
|
D:GLU195
|
4.6
|
18.9
|
1.0
|
O
|
D:HOH605
|
4.7
|
21.8
|
1.0
|
CG
|
D:ASP166
|
4.7
|
16.8
|
1.0
|
CD
|
D:GLN169
|
4.7
|
14.4
|
1.0
|
CZ
|
D:ARG256
|
4.7
|
19.1
|
1.0
|
NE2
|
D:GLN169
|
4.7
|
14.7
|
1.0
|
C
|
D:GLY252
|
4.9
|
16.7
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 3b1r
Go back to
Magnesium Binding Sites List in 3b1r
Magnesium binding site 5 out
of 7 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg313
b:35.9
occ:1.00
|
O
|
D:HOH1082
|
2.0
|
31.0
|
1.0
|
O
|
D:HOH1083
|
2.2
|
28.9
|
1.0
|
O
|
D:HOH1086
|
2.3
|
35.7
|
1.0
|
O
|
D:GLU184
|
2.3
|
19.8
|
1.0
|
O
|
D:HOH1085
|
2.6
|
30.8
|
1.0
|
C
|
D:GLU184
|
3.3
|
19.9
|
1.0
|
O
|
D:ARG213
|
3.3
|
24.3
|
1.0
|
CA
|
D:GLU184
|
3.8
|
20.0
|
1.0
|
O
|
D:ALA186
|
4.2
|
18.9
|
1.0
|
O
|
D:HOH602
|
4.3
|
23.9
|
1.0
|
O
|
D:ILE183
|
4.4
|
18.9
|
1.0
|
C
|
D:ARG213
|
4.5
|
24.3
|
1.0
|
N
|
D:LEU185
|
4.5
|
19.8
|
1.0
|
CB
|
D:GLU184
|
4.6
|
20.3
|
1.0
|
N
|
D:GLU184
|
4.9
|
19.9
|
1.0
|
CB
|
D:ARG213
|
5.0
|
24.7
|
1.0
|
CA
|
D:LEU185
|
5.0
|
19.6
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 3b1r
Go back to
Magnesium Binding Sites List in 3b1r
Magnesium binding site 6 out
of 7 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg503
b:17.7
occ:1.00
|
O
|
E:HOH314
|
1.9
|
12.4
|
1.0
|
O3P
|
E:AMP501
|
2.2
|
20.2
|
1.0
|
O
|
E:HOH320
|
2.2
|
15.3
|
1.0
|
O
|
E:HOH319
|
2.2
|
13.4
|
1.0
|
O
|
E:HOH318
|
2.4
|
15.2
|
1.0
|
O
|
E:HOH315
|
2.4
|
16.0
|
1.0
|
P
|
E:AMP501
|
3.7
|
20.5
|
1.0
|
OE1
|
E:GLN169
|
3.7
|
17.2
|
1.0
|
O
|
E:HOH584
|
3.8
|
22.5
|
1.0
|
NE2
|
E:GLN169
|
4.0
|
16.6
|
1.0
|
OE2
|
E:GLU195
|
4.1
|
13.9
|
1.0
|
O5'
|
E:AMP501
|
4.1
|
19.9
|
1.0
|
OD1
|
E:ASP253
|
4.2
|
14.8
|
1.0
|
CD
|
E:GLN169
|
4.2
|
17.4
|
1.0
|
OD2
|
E:ASP166
|
4.2
|
20.6
|
1.0
|
OD1
|
E:ASP166
|
4.3
|
20.8
|
1.0
|
NH2
|
E:ARG256
|
4.3
|
16.8
|
1.0
|
OE1
|
E:GLU195
|
4.5
|
15.0
|
1.0
|
O2P
|
E:AMP501
|
4.5
|
19.5
|
1.0
|
O
|
E:HOH324
|
4.5
|
11.2
|
1.0
|
CA
|
E:GLY168
|
4.6
|
15.9
|
1.0
|
O1P
|
E:AMP501
|
4.6
|
21.1
|
1.0
|
CG
|
E:ASP166
|
4.7
|
18.4
|
1.0
|
CD
|
E:GLU195
|
4.7
|
17.3
|
1.0
|
CG
|
E:ASP253
|
4.9
|
15.4
|
1.0
|
CA
|
E:GLY252
|
4.9
|
14.6
|
1.0
|
O
|
E:HOH326
|
4.9
|
17.4
|
1.0
|
SG
|
E:CYS49
|
5.0
|
10.4
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 3b1r
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Magnesium Binding Sites List in 3b1r
Magnesium binding site 7 out
of 7 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Amp-Mg-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg503
b:22.4
occ:1.00
|
O
|
F:HOH317
|
1.8
|
15.7
|
1.0
|
O
|
F:HOH318
|
1.9
|
25.3
|
1.0
|
O3P
|
F:AMP501
|
1.9
|
17.0
|
1.0
|
O
|
F:HOH313
|
2.0
|
20.1
|
1.0
|
O
|
F:HOH315
|
2.1
|
18.5
|
1.0
|
O
|
F:HOH316
|
2.4
|
12.6
|
1.0
|
P
|
F:AMP501
|
3.4
|
19.2
|
1.0
|
O
|
F:HOH322
|
3.9
|
22.5
|
1.0
|
O5'
|
F:AMP501
|
4.1
|
19.0
|
1.0
|
O1P
|
F:AMP501
|
4.1
|
20.5
|
1.0
|
OE2
|
F:GLU195
|
4.2
|
20.7
|
1.0
|
O
|
F:HOH323
|
4.2
|
20.4
|
1.0
|
OD2
|
F:ASP166
|
4.2
|
23.0
|
1.0
|
O2P
|
F:AMP501
|
4.3
|
18.0
|
1.0
|
O
|
F:HOH328
|
4.4
|
19.3
|
1.0
|
OD1
|
F:ASP253
|
4.4
|
23.7
|
1.0
|
CA
|
F:GLY252
|
4.4
|
18.9
|
1.0
|
OE1
|
F:GLN169
|
4.4
|
19.4
|
1.0
|
O
|
F:HOH876
|
4.5
|
22.9
|
1.0
|
OE1
|
F:GLU195
|
4.6
|
20.9
|
1.0
|
OD1
|
F:ASP166
|
4.6
|
25.1
|
1.0
|
NE2
|
F:GLN169
|
4.7
|
15.8
|
1.0
|
NH2
|
F:ARG256
|
4.7
|
25.7
|
1.0
|
CZ
|
F:ARG256
|
4.8
|
24.4
|
1.0
|
C
|
F:GLY252
|
4.9
|
19.4
|
1.0
|
CD
|
F:GLU195
|
4.9
|
22.1
|
1.0
|
CG
|
F:ASP166
|
4.9
|
23.7
|
1.0
|
CD
|
F:GLN169
|
4.9
|
20.1
|
1.0
|
|
Reference:
Y.Yasutake,
H.Ota,
E.Hino,
S.Sakasegawa,
T.Tamura.
Structures of Burkholderia Thailandensis Nucleoside Kinase: Implications For the Catalytic Mechanism and Nucleoside Selectivity Acta Crystallogr.,Sect.D V. 67 945 2011.
ISSN: ISSN 0907-4449
PubMed: 22101821
DOI: 10.1107/S0907444911038777
Page generated: Wed Aug 14 08:50:01 2024
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