Atomistry » Magnesium » PDB 3ay9-3bc1 » 3b1r
Atomistry »
  Magnesium »
    PDB 3ay9-3bc1 »
      3b1r »

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

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

Last articles

Ca in 2RA3
Ca in 2R9F
Ca in 2R9C
Ca in 2R8P
Ca in 2R8O
Ca in 2R8K
Ca in 2R8J
Ca in 2R8I
Ca in 2R28
Ca in 2R8H
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy