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Magnesium in PDB 6avp: Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Adp and Pantothenate Analog Phosphate-Meo-N5PAN

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

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

Protein crystallography data

The structure of Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Adp and Pantothenate Analog Phosphate-Meo-N5PAN, PDB code: 6avp 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) 131.35 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.571, 56.705, 133.075, 90.00, 99.24, 90.00
R / Rfree (%) 24.5 / 29.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Adp and Pantothenate Analog Phosphate-Meo-N5PAN (pdb code 6avp). 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 Adp and Pantothenate Analog Phosphate-Meo-N5PAN, PDB code: 6avp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6avp

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Magnesium binding site 1 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Adp and Pantothenate Analog Phosphate-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 Adp and Pantothenate Analog Phosphate-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:34.2
occ:1.00
 O2B A:ADP301 1.9 19.9 1.0
O A:HOH424 2.0 29.1 1.0
O A:HOH416 2.0 24.7 1.0
O03 A:N7E302 2.2 20.1 1.0
O A:HOH427 2.2 22.4 1.0
O A:HOH412 2.4 19.0 1.0
PB A:ADP301 3.3 20.6 1.0
P02 A:N7E302 3.5 23.0 1.0
O3A A:ADP301 3.8 21.0 1.0
OD2 A:ASP6 3.9 30.5 1.0
O1B A:ADP301 3.9 19.7 1.0
NZ A:LYS13 4.0 20.5 1.0
OD1 A:ASP6 4.0 32.0 1.0
O04 A:N7E302 4.0 21.4 1.0
O A:HOH430 4.2 18.1 1.0
OE1 A:GLU70 4.2 29.3 1.0
O05 A:N7E302 4.3 20.7 1.0
CG A:ASP6 4.4 29.3 1.0
O3B A:ADP301 4.5 20.6 1.0
O1A A:ADP301 4.5 22.2 1.0
PA A:ADP301 4.5 21.8 1.0
OD1 A:ASN96 4.6 15.9 1.0
O01 A:N7E302 4.6 20.9 1.0
ND2 A:ASN96 4.7 15.7 1.0
CA A:GLY8 4.7 24.8 1.0
O A:HOH402 4.7 30.0 1.0
O2A A:ADP301 4.7 22.7 1.0
O A:HOH443 4.9 31.9 1.0
CD A:GLU70 5.0 29.5 1.0
CG A:ASN96 5.0 15.2 1.0

Magnesium binding site 2 out of 4 in 6avp

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Magnesium binding site 2 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Adp and Pantothenate Analog Phosphate-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 Adp and Pantothenate Analog Phosphate-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:40.4
occ:1.00
 O B:HOH410 1.9 21.9 1.0
O B:HOH409 2.0 28.4 1.0
O B:HOH408 2.0 30.0 1.0
O2B B:ADP301 2.2 28.4 1.0
O B:HOH413 2.3 31.9 1.0
O03 B:N7E302 2.3 21.3 1.0
PB B:ADP301 3.5 28.9 1.0
O B:HOH412 3.7 29.9 1.0
P02 B:N7E302 3.7 23.0 1.0
O3A B:ADP301 3.9 28.1 1.0
NZ B:LYS13 3.9 28.7 1.0
OD2 B:ASP6 4.0 31.2 1.0
O1A B:ADP301 4.1 28.4 1.0
O B:HOH427 4.1 23.3 1.0
OD1 B:ASN96 4.2 22.5 1.0
ND2 B:ASN96 4.2 20.5 1.0
O3B B:ADP301 4.3 30.3 1.0
OE1 B:GLU70 4.3 34.1 1.0
OD1 B:ASP6 4.3 32.7 1.0
O04 B:N7E302 4.3 22.6 1.0
PA B:ADP301 4.4 28.6 1.0
CG B:ASP6 4.5 31.6 1.0
CG B:ASN96 4.5 20.2 1.0
O05 B:N7E302 4.6 22.6 1.0
CE B:LYS13 4.6 28.5 1.0
O1B B:ADP301 4.7 27.5 1.0
O01 B:N7E302 4.7 22.1 1.0
O2A B:ADP301 4.9 27.4 1.0
O B:HOH424 5.0 27.9 1.0
O B:HOH414 5.0 40.3 1.0

Magnesium binding site 3 out of 4 in 6avp

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Magnesium binding site 3 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Adp and Pantothenate Analog Phosphate-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 Adp and Pantothenate Analog Phosphate-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.0
occ:1.00
 O03 C:N7E302 1.9 35.1 1.0
O C:HOH418 2.0 36.8 1.0
O C:HOH413 2.0 37.9 1.0
O C:HOH426 2.2 26.6 1.0
O C:HOH411 2.2 32.7 1.0
O1B C:ADP301 2.3 24.8 1.0
P02 C:N7E302 3.4 35.3 1.0
OE1 C:GLU70 3.7 47.2 1.0
PB C:ADP301 3.7 27.5 1.0
OD1 C:ASP6 4.0 48.0 1.0
OD2 C:ASP6 4.0 46.7 1.0
O05 C:N7E302 4.1 28.3 1.0
O04 C:N7E302 4.1 32.8 1.0
O1A C:ADP301 4.2 26.8 1.0
O C:HOH407 4.3 22.5 1.0
NZ C:LYS13 4.3 34.4 1.0
O3A C:ADP301 4.3 28.8 1.0
O2B C:ADP301 4.4 26.9 1.0
O01 C:N7E302 4.4 36.2 1.0
OD1 C:ASN96 4.4 31.7 1.0
ND2 C:ASN96 4.4 30.1 1.0
CG C:ASP6 4.4 46.5 1.0
CD C:GLU70 4.6 46.8 1.0
CG C:ASN96 4.7 29.5 1.0
PA C:ADP301 4.8 28.2 1.0
OE2 C:GLU70 4.8 47.7 1.0
O3B C:ADP301 4.9 27.0 1.0
CA C:GLY8 4.9 38.4 1.0
CE C:LYS13 5.0 35.7 1.0

Magnesium binding site 4 out of 4 in 6avp

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Magnesium binding site 4 out of 4 in the Staphylococcus Aureus Type II Pantothenate Kinase in Complex with Adp and Pantothenate Analog Phosphate-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 Adp and Pantothenate Analog Phosphate-Meo-N5PAN within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:39.6
occ:1.00
 O2B D:ADP301 2.0 30.8 1.0
O D:HOH406 2.1 40.5 1.0
O D:HOH403 2.1 34.4 1.0
O D:HOH402 2.1 33.5 1.0
O03 D:N7E302 2.2 53.1 1.0
O D:HOH401 2.3 39.5 1.0
PB D:ADP301 3.3 33.2 1.0
P02 D:N7E302 3.4 51.0 1.0
O3A D:ADP301 3.5 33.6 1.0
NZ D:LYS13 3.9 44.0 1.0
O04 D:N7E302 4.0 49.5 1.0
O1B D:ADP301 4.0 33.6 1.0
OE1 D:GLU70 4.0 55.0 1.0
OD2 D:ASP6 4.1 56.0 1.0
OD1 D:ASP6 4.1 59.4 1.0
O2A D:ADP301 4.2 30.5 1.0
PA D:ADP301 4.3 31.3 1.0
O05 D:N7E302 4.3 45.0 1.0
CG D:ASP6 4.4 56.8 1.0
O D:HOH409 4.4 38.0 1.0
O01 D:N7E302 4.4 50.7 1.0
O3B D:ADP301 4.5 32.4 1.0
OD1 D:ASN96 4.6 32.7 1.0
ND2 D:ASN96 4.7 32.3 1.0
CA D:GLY8 4.7 48.1 1.0
O1A D:ADP301 4.9 30.2 1.0
CD D:GLU70 5.0 54.2 1.0
CG D:ASN96 5.0 31.8 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: Wed Aug 13 02:21:39 2025

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