Magnesium in PDB 6awh: Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN

Enzymatic activity of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN

All present enzymatic activity of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN:
2.7.1.33;

Protein crystallography data

The structure of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN, PDB code: 6awh was solved by Y.Chen, T.Antoshchenko, E.Strauss, L.Barnard, Y.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.27 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.776, 136.671, 141.393, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN (pdb code 6awh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN, PDB code: 6awh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6awh

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Magnesium binding site 1 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:19.6
occ:1.00
 O2B A:ATP301 2.0 16.1 1.0
O1G A:ATP301 2.0 19.3 1.0
O A:HOH448 2.1 17.5 1.0
O A:HOH437 2.2 19.4 1.0
O A:HOH419 2.2 20.0 1.0
O A:HOH421 2.2 21.5 1.0
PB A:ATP301 3.2 17.1 1.0
PG A:ATP301 3.3 23.0 1.0
O3B A:ATP301 3.5 18.6 1.0
O3A A:ATP301 3.7 17.5 1.0
O A:HOH468 3.8 23.4 1.0
O2G A:ATP301 3.9 20.9 1.0
NZ A:LYS13 4.1 19.8 1.0
O A:HOH424 4.1 23.5 1.0
OE1 A:GLU70 4.1 22.3 1.0
O2A A:ATP301 4.3 17.3 1.0
OD2 A:ASP6 4.3 21.8 1.0
O A:HOH445 4.3 23.3 1.0
O A:HOH463 4.3 16.2 1.0
OD1 A:ASP6 4.4 24.1 1.0
O3G A:ATP301 4.4 22.1 1.0
ND2 A:ASN96 4.5 22.7 1.0
PA A:ATP301 4.5 18.0 1.0
O1B A:ATP301 4.5 16.9 1.0
CA A:GLY8 4.6 19.2 1.0
OD1 A:ASN96 4.7 22.9 1.0
CG A:ASP6 4.7 22.1 1.0
CA A:GLY98 4.9 15.7 1.0
CE A:LYS13 4.9 20.4 1.0
CG A:ASN96 4.9 19.0 1.0
O1A A:ATP301 5.0 17.6 1.0
O A:HOH464 5.0 25.3 1.0
O A:HOH467 5.0 24.9 1.0

Magnesium binding site 2 out of 4 in 6awh

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Magnesium binding site 2 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:23.5
occ:1.00
 O B:HOH492 2.0 29.6 1.0
O3G B:ATP301 2.0 29.1 1.0
O B:HOH414 2.0 17.2 1.0
O B:HOH432 2.1 17.9 1.0
O2B B:ATP301 2.2 19.9 1.0
O B:HOH429 2.3 21.1 1.0
PG B:ATP301 3.3 27.1 0.8
PB B:ATP301 3.4 21.5 1.0
O3B B:ATP301 3.7 24.1 1.0
OE1 B:GLU70 4.0 29.4 1.0
O B:HOH451 4.0 23.7 1.0
O3A B:ATP301 4.0 19.0 1.0
O1G B:ATP301 4.0 26.6 1.0
O B:HOH530 4.1 23.4 1.0
OD2 B:ASP6 4.1 30.6 1.0
NZ B:LYS13 4.1 21.3 1.0
O B:HOH453 4.1 33.4 1.0
OD1 B:ASP6 4.1 30.6 1.0
O B:HOH438 4.2 25.6 1.0
O2A B:ATP301 4.3 18.8 1.0
O2G B:ATP301 4.4 27.9 1.0
CG B:ASP6 4.5 28.3 1.0
ND2 B:ASN96 4.5 21.1 1.0
CA B:GLY8 4.6 23.6 1.0
PA B:ATP301 4.6 19.0 1.0
O1B B:ATP301 4.7 21.8 1.0
OD1 B:ASN96 4.8 22.1 1.0
CD B:GLU70 4.9 29.6 1.0
O B:HOH482 4.9 26.9 1.0
CE B:LYS13 4.9 20.6 1.0
O B:HOH540 5.0 22.9 1.0

Magnesium binding site 3 out of 4 in 6awh

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Magnesium binding site 3 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:19.7
occ:1.00
 O3G C:ATP301 1.9 22.0 1.0
O C:HOH478 2.1 22.7 1.0
O1B C:ATP301 2.1 17.6 1.0
O C:HOH437 2.1 23.7 1.0
O C:HOH463 2.1 16.9 1.0
O C:HOH445 2.2 22.3 1.0
PG C:ATP301 3.2 20.5 1.0
PB C:ATP301 3.3 17.7 1.0
O3B C:ATP301 3.5 19.0 1.0
O C:HOH523 3.9 22.4 1.0
O3A C:ATP301 3.9 18.3 1.0
O1G C:ATP301 4.0 17.5 1.0
OE1 C:GLU70 4.0 23.0 1.0
NZ C:LYS13 4.2 22.6 1.0
O C:HOH443 4.2 25.1 1.0
O C:HOH448 4.2 19.5 1.0
O1A C:ATP301 4.3 16.9 1.0
O C:HOH477 4.3 16.0 1.0
O2G C:ATP301 4.3 19.3 1.0
OD2 C:ASP6 4.3 24.4 1.0
OD1 C:ASP6 4.4 26.7 1.0
ND2 C:ASN96 4.5 22.3 1.0
PA C:ATP301 4.6 19.8 1.0
O2B C:ATP301 4.6 16.9 1.0
CA C:GLY8 4.6 19.5 1.0
OD1 C:ASN96 4.7 21.1 1.0
CG C:ASP6 4.7 25.0 1.0
CG C:ASN96 5.0 20.1 1.0
CA C:GLY98 5.0 15.3 1.0
CD C:GLU70 5.0 23.2 1.0
O C:HOH484 5.0 27.6 1.0

Magnesium binding site 4 out of 4 in 6awh

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Magnesium binding site 4 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Atp and Pantothenate Analog Deoxy-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:33.0
occ:1.00
 O D:HOH411 2.0 29.6 1.0
O1G D:ATP301 2.1 32.3 1.0
O1B D:ATP301 2.1 24.5 1.0
O D:HOH441 2.1 40.1 1.0
O D:HOH452 2.2 36.8 1.0
O D:HOH424 2.2 22.8 1.0
PB D:ATP301 3.3 25.5 1.0
PG D:ATP301 3.3 32.0 0.8
O3B D:ATP301 3.7 27.6 1.0
O3A D:ATP301 3.8 23.4 1.0
OE1 D:GLU70 4.0 34.3 1.0
O D:HOH503 4.0 28.0 1.0
O D:HOH466 4.0 45.8 1.0
OD2 D:ASP6 4.1 40.6 1.0
O2G D:ATP301 4.1 30.3 1.0
O D:HOH429 4.1 28.1 1.0
NZ D:LYS13 4.2 29.6 1.0
OD1 D:ASP6 4.3 42.5 1.0
O1A D:ATP301 4.3 23.4 1.0
ND2 D:ASN96 4.3 23.5 1.0
O D:HOH453 4.3 25.6 1.0
O3G D:ATP301 4.5 32.0 1.0
CG D:ASP6 4.5 39.8 1.0
PA D:ATP301 4.6 25.3 1.0
OD1 D:ASN96 4.6 27.0 1.0
O2B D:ATP301 4.7 23.2 1.0
CA D:GLY8 4.7 27.9 1.0
O D:HOH455 4.7 34.5 1.0
CG D:ASN96 4.8 25.1 1.0
CD D:GLU70 4.9 32.1 1.0
O D:HOH465 4.9 30.5 1.0
CE D:LYS13 5.0 28.1 1.0

Reference:

Y.Chen, T.Antoshchenko, E.Strauss, L.Barnard, Y.H.Huang. Structure-Based Identification of Uncompetitive Inhibitors For Staphylococcus Aureus Pantothenate Kinase. To Be Published.
Page generated: Mon Dec 14 22:21:43 2020

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