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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

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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

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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

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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

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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

Go back to 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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