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Magnesium in PDB 2y27: Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia

Enzymatic activity of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia

All present enzymatic activity of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia:
6.2.1.30;

Protein crystallography data

The structure of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia, PDB code: 2y27 was solved by A.Law, M.J.Boulanger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.710, 62.470, 78.490, 90.97, 109.81, 106.51
R / Rfree (%) 16.4 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia (pdb code 2y27). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia, PDB code: 2y27:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2y27

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Magnesium binding site 1 out of 6 in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg509

b:15.9
occ:1.00
 O A:HOH720 2.0 15.4 1.0
O A:HOH702 2.0 14.4 1.0
O1B A:ATP508 2.0 15.7 1.0
O3G A:ATP508 2.0 15.8 1.0
O A:HOH638 2.1 14.2 1.0
O A:HOH735 2.2 12.9 1.0
PG A:ATP508 3.2 16.7 1.0
PB A:ATP508 3.2 15.3 1.0
O2G A:ATP508 3.6 17.2 1.0
O3B A:ATP508 3.6 14.1 1.0
O3A A:ATP508 3.8 13.6 1.0
NZ A:LYS68 3.9 19.5 1.0
OE2 A:GLU241 4.0 17.2 1.0
NH1 A:ARG326 4.0 14.9 1.0
OE1 A:GLU241 4.2 17.2 1.0
O A:HOH926 4.2 25.6 1.0
O2A A:ATP508 4.3 13.4 1.0
CE A:LYS68 4.3 17.7 1.0
O3' A:ATP508 4.5 12.4 1.0
O1G A:ATP508 4.5 15.4 1.0
O A:HOH828 4.5 17.6 1.0
O A:HOH633 4.5 15.3 1.0
O2B A:ATP508 4.6 16.8 1.0
CD A:GLU241 4.6 15.0 1.0
C4' A:ATP508 4.6 15.9 1.0
PA A:ATP508 4.6 14.9 1.0
C5' A:ATP508 4.7 15.0 1.0
O5' A:ATP508 4.7 15.5 1.0
CB A:SER93 4.9 14.3 1.0
O A:HOH789 4.9 31.2 1.0

Magnesium binding site 2 out of 6 in 2y27

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Magnesium binding site 2 out of 6 in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg510

b:23.3
occ:1.00
 O A:HOH618 2.2 60.4 1.0
O A:HOH848 2.3 17.0 1.0
O A:LEU353 2.4 15.3 1.0
O A:HOH713 2.4 24.9 1.0
O A:GLN350 2.4 16.0 1.0
O A:HOH635 2.7 37.7 1.0
C A:GLN350 3.4 15.8 1.0
C A:LEU353 3.5 15.0 1.0
CA A:ARG351 3.8 16.3 1.0
C A:ARG351 4.0 17.8 1.0
O A:ARG351 4.0 17.8 1.0
N A:ARG351 4.0 15.2 1.0
N A:LEU353 4.1 15.0 1.0
CA A:LEU353 4.3 14.8 1.0
C A:ALA354 4.3 16.1 1.0
O A:ALA354 4.4 17.8 1.0
O A:LEU348 4.5 20.9 1.0
O A:LEU347 4.5 15.4 1.0
N A:ALA354 4.5 16.8 1.0
N A:SCN501 4.6 43.9 1.0
CA A:GLN350 4.6 12.6 1.0
CA A:ALA354 4.6 15.9 1.0
N A:PRO355 4.7 17.1 1.0
CB A:LEU353 4.7 14.4 1.0
N A:ALA352 4.7 19.2 1.0
CD1 A:LEU348 4.7 30.2 1.0
N A:GLN350 4.8 16.2 1.0
CA A:LEU348 4.8 19.8 1.0
C A:LEU348 4.9 17.9 1.0
SG A:CYS377 4.9 29.6 1.0

Magnesium binding site 3 out of 6 in 2y27

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Magnesium binding site 3 out of 6 in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg511

b:17.9
occ:1.00
 O A:LEU207 2.7 19.8 1.0
O A:MSE229 2.7 20.4 1.0
O A:SER205 2.8 21.9 1.0
O A:VAL203 2.9 25.7 1.0
O A:GLY230 2.9 21.6 1.0
O A:HOH960 3.0 41.5 1.0
OG A:SER205 3.1 31.2 1.0
C A:GLY230 3.6 22.2 1.0
C A:SER205 3.7 21.8 1.0
C A:VAL203 3.7 23.9 1.0
C A:LEU207 3.8 19.2 1.0
C A:MSE229 3.9 22.4 1.0
CA A:GLY230 3.9 21.6 1.0
N A:SER205 3.9 25.9 1.0
O A:PRO202 4.0 25.8 1.0
CA A:SER205 4.1 24.7 1.0
O A:HOH700 4.2 46.4 1.0
CB A:SER205 4.2 25.5 1.0
CG2 A:ILE231 4.2 17.7 1.0
N A:LEU207 4.3 18.6 1.0
O A:HOH921 4.3 45.8 1.0
N A:GLY230 4.4 20.9 1.0
CA A:VAL203 4.4 24.2 1.0
CA A:LEU207 4.5 17.7 1.0
C A:GLN204 4.5 26.2 1.0
N A:GLN204 4.6 24.6 1.0
C A:SER206 4.6 19.1 1.0
N A:ILE231 4.7 19.8 1.0
CB A:LEU207 4.7 18.4 1.0
N A:SER206 4.8 19.5 1.0
CA A:GLN204 4.8 26.6 1.0
N A:ARG208 4.9 15.9 1.0
O A:SER206 5.0 18.5 1.0

Magnesium binding site 4 out of 6 in 2y27

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Magnesium binding site 4 out of 6 in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg513

b:22.3
occ:1.00
 O B:HOH642 2.1 41.9 1.0
O B:HOH654 2.4 27.2 1.0
O B:LEU353 2.4 15.6 1.0
O B:HOH871 2.4 14.5 1.0
O B:GLN350 2.5 15.3 1.0
O B:HOH869 2.6 35.9 1.0
C B:GLN350 3.5 15.1 1.0
C B:LEU353 3.5 16.2 1.0
CA B:ARG351 3.8 14.8 1.0
C B:ARG351 4.0 16.5 1.0
O B:ARG351 4.1 20.5 1.0
N B:ARG351 4.1 16.1 1.0
N B:LEU353 4.1 15.2 1.0
O B:ALA354 4.3 15.0 1.0
C B:ALA354 4.3 15.2 1.0
CA B:LEU353 4.3 15.6 1.0
O B:LEU348 4.4 16.4 1.0
N B:ALA354 4.5 14.7 1.0
CA B:ALA354 4.6 17.6 1.0
O B:LEU347 4.6 15.9 1.0
CA B:GLN350 4.6 15.7 1.0
N B:SCN502 4.7 35.5 1.0
CB B:LEU353 4.7 14.9 1.0
N B:PRO355 4.8 15.4 1.0
N B:ALA352 4.8 15.8 1.0
O1 B:BME511 4.8 69.1 1.0
N B:GLN350 4.8 16.1 1.0
CA B:LEU348 4.8 17.1 1.0
C B:LEU348 4.8 17.1 1.0
SG B:CYS377 4.9 33.8 1.0
CD B:PRO355 5.0 17.1 1.0

Magnesium binding site 5 out of 6 in 2y27

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Magnesium binding site 5 out of 6 in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg514

b:14.9
occ:1.00
 O1B B:ATP512 2.0 9.9 1.0
O B:HOH752 2.0 13.0 1.0
O B:HOH666 2.0 10.8 1.0
O B:HOH777 2.0 12.9 1.0
O3G B:ATP512 2.1 15.2 1.0
O B:HOH620 2.2 14.2 1.0
PB B:ATP512 3.2 13.1 1.0
PG B:ATP512 3.2 13.9 1.0
O3B B:ATP512 3.6 16.9 1.0
O2G B:ATP512 3.7 17.9 1.0
O3A B:ATP512 3.7 11.9 1.0
NH1 B:ARG326 3.8 14.8 1.0
NZ B:LYS68 4.1 16.0 1.0
OE2 B:GLU241 4.1 15.6 1.0
OE1 B:GLU241 4.2 14.8 1.0
O2A B:ATP512 4.3 13.5 1.0
O3' B:ATP512 4.4 12.5 1.0
O B:HOH952 4.4 23.7 1.0
CE B:LYS68 4.4 19.1 1.0
C4' B:ATP512 4.5 16.9 1.0
O B:HOH645 4.5 13.4 1.0
O2B B:ATP512 4.5 15.4 1.0
C5' B:ATP512 4.5 10.8 1.0
PA B:ATP512 4.5 12.8 1.0
O B:HOH699 4.6 13.1 1.0
O1G B:ATP512 4.6 14.0 1.0
CD B:GLU241 4.6 14.7 1.0
O5' B:ATP512 4.7 12.8 1.0
O B:HOH882 4.9 29.2 1.0
CZ B:ARG326 5.0 17.2 1.0
CB B:SER93 5.0 10.6 1.0

Magnesium binding site 6 out of 6 in 2y27

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Magnesium binding site 6 out of 6 in the Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of PAAK1 in Complex with Atp From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg515

b:17.5
occ:1.00
 O B:LEU207 2.6 16.1 1.0
O B:MSE229 2.7 21.8 1.0
O B:VAL203 2.8 25.3 1.0
O B:SER205 2.8 21.4 1.0
O B:GLY230 3.0 18.9 1.0
OG B:SER205 3.1 23.1 1.0
C B:SER205 3.7 20.1 1.0
C B:GLY230 3.7 20.2 1.0
C B:VAL203 3.7 22.9 1.0
C B:LEU207 3.8 16.1 1.0
C B:MSE229 3.9 20.0 1.0
N B:SER205 4.0 22.1 1.0
O B:PRO202 4.0 26.9 1.0
CA B:GLY230 4.0 18.8 1.0
CA B:SER205 4.1 21.6 1.0
CB B:SER205 4.2 19.3 1.0
CG2 B:ILE231 4.2 14.7 1.0
N B:LEU207 4.4 15.3 1.0
CA B:VAL203 4.4 24.6 1.0
N B:GLY230 4.5 19.0 1.0
C B:GLN204 4.5 25.0 1.0
CA B:LEU207 4.5 15.6 1.0
C B:SER206 4.6 16.1 1.0
N B:GLN204 4.6 22.0 1.0
N B:ILE231 4.7 18.4 1.0
CB B:LEU207 4.8 14.9 1.0
N B:SER206 4.8 19.0 1.0
O B:HOH789 4.8 49.3 1.0
CA B:GLN204 4.8 26.2 1.0
N B:ARG208 4.9 16.5 1.0

Reference:

A.Law, M.J.Boulanger. Defining A Structural and Kinetic Rationale For Paralogous Copies of Phenylacetate-Coa Ligases From the Cystic Fibrosis Pathogen Burkholderia Cenocepacia J2315. J.Biol.Chem. V. 286 15577 2011.
ISSN: ISSN 0021-9258
PubMed: 21388965
DOI: 10.1074/JBC.M111.219683
Page generated: Mon Dec 14 07:47:52 2020

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