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Magnesium in PDB 4nb4: Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus

Enzymatic activity of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus

All present enzymatic activity of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus:
2.7.1.33;

Protein crystallography data

The structure of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus, PDB code: 4nb4 was solved by S.J.Hughes, T.Antoshchenko, D.Smil, H.W.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.91 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.010, 70.740, 143.115, 90.00, 90.64, 90.00
R / Rfree (%) 23 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus (pdb code 4nb4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus, PDB code: 4nb4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4nb4

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Magnesium binding site 1 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:8.7
occ:1.00
 O2B A:ADP301 1.8 13.8 1.0
OAD A:SH3302 1.9 14.7 1.0
O A:HOH417 1.9 10.2 1.0
O A:HOH430 2.2 8.8 1.0
O A:HOH416 2.4 8.6 1.0
O A:HOH452 2.5 13.7 1.0
PB A:ADP301 3.1 13.6 1.0
PAB A:SH3302 3.4 13.9 1.0
O3A A:ADP301 3.5 13.4 1.0
O1B A:ADP301 3.6 13.6 1.0
OAA A:SH3302 3.8 14.3 1.0
O1A A:ADP301 4.0 13.2 1.0
NZ A:LYS13 4.1 14.8 1.0
O A:HOH419 4.1 14.8 1.0
O A:HOH431 4.2 11.8 1.0
OAE A:SH3302 4.2 14.1 1.0
PA A:ADP301 4.2 13.4 1.0
OAC A:SH3302 4.3 13.8 1.0
OD2 A:ASP6 4.3 16.2 1.0
OE1 A:GLU70 4.3 20.6 1.0
O3B A:ADP301 4.4 13.7 1.0
OD1 A:ASP6 4.6 17.0 1.0
CA A:GLY98 4.6 10.0 1.0
CA A:GLY8 4.7 15.1 1.0
ND2 A:ASN96 4.7 11.3 1.0
O A:HOH411 4.7 15.3 1.0
OD1 A:ASN96 4.8 11.8 1.0
CG A:ASP6 4.8 16.7 1.0
O2A A:ADP301 4.8 13.4 1.0
CE A:LYS13 4.9 15.0 1.0

Magnesium binding site 2 out of 8 in 4nb4

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Magnesium binding site 2 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:11.7
occ:1.00
 OAD A:SH3303 2.0 13.8 1.0
O A:HOH418 2.0 10.9 1.0
O1B B:ADP301 2.1 10.2 1.0
O B:HOH422 2.1 10.0 1.0
O B:HOH423 2.1 7.1 1.0
O B:HOH424 2.1 9.5 1.0
PAB A:SH3303 3.5 13.9 1.0
PB B:ADP301 3.5 10.5 1.0
OE1 B:GLU70 3.8 18.8 1.0
OAA A:SH3303 3.9 13.8 1.0
O3B B:ADP301 4.0 10.6 1.0
OD1 B:ASP6 4.0 16.3 1.0
O B:HOH405 4.1 7.1 1.0
O3A B:ADP301 4.1 10.1 1.0
NZ B:LYS13 4.1 11.1 1.0
OD2 B:ASP6 4.2 16.3 1.0
O1A B:ADP301 4.2 9.8 1.0
OAE A:SH3303 4.3 13.3 1.0
O B:HOH425 4.4 8.0 1.0
OAC A:SH3303 4.4 14.1 1.0
O B:HOH433 4.4 12.6 1.0
CG B:ASP6 4.4 16.0 1.0
O B:HOH466 4.5 21.8 1.0
ND2 B:ASN96 4.6 8.3 1.0
PA B:ADP301 4.6 9.8 1.0
O2B B:ADP301 4.6 10.2 1.0
CA B:GLY8 4.7 14.1 1.0
OD1 B:ASN96 4.8 8.6 1.0
CE B:LYS13 4.8 11.2 1.0
CD B:GLU70 4.9 18.2 1.0
O B:HOH407 4.9 6.4 1.0
O B:HOH454 5.0 16.3 1.0

Magnesium binding site 3 out of 8 in 4nb4

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Magnesium binding site 3 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:13.2
occ:1.00
 O2B C:ADP301 1.9 10.3 1.0
OAC C:SH3302 2.0 15.5 1.0
O C:HOH416 2.0 9.0 1.0
O C:HOH434 2.1 7.5 1.0
O C:HOH426 2.3 11.5 1.0
O C:HOH404 2.4 16.3 1.0
PB C:ADP301 3.2 10.3 1.0
PAB C:SH3302 3.5 15.4 1.0
O1B C:ADP301 3.7 10.2 1.0
O3A C:ADP301 3.7 10.2 1.0
O2A C:ADP301 4.0 10.2 1.0
OAD C:SH3302 4.1 15.1 1.0
NZ C:LYS13 4.1 14.4 1.0
OD2 C:ASP6 4.1 14.4 1.0
O C:HOH435 4.2 5.2 1.0
OAA C:SH3302 4.2 15.4 1.0
ND2 C:ASN96 4.3 13.4 1.0
OE1 C:GLU70 4.3 16.9 1.0
O3B C:ADP301 4.4 10.5 1.0
PA C:ADP301 4.4 10.3 1.0
O C:HOH412 4.4 14.3 1.0
O C:HOH405 4.4 12.3 1.0
OAE C:SH3302 4.5 14.7 1.0
OD1 C:ASN96 4.5 13.7 1.0
OD1 C:ASP6 4.6 14.2 1.0
O C:HOH409 4.7 15.4 1.0
CG C:ASN96 4.7 13.3 1.0
CG C:ASP6 4.8 13.9 1.0
CA C:GLY98 4.8 11.8 1.0
O C:HOH442 4.8 14.2 1.0
O C:HOH406 4.8 18.5 1.0
CE C:LYS13 4.9 14.5 1.0
CA C:GLY8 4.9 12.9 1.0
O1A C:ADP301 5.0 10.0 1.0

Magnesium binding site 4 out of 8 in 4nb4

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Magnesium binding site 4 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:19.6
occ:1.00
 OAC C:SH3303 1.8 21.0 1.0
O D:HOH419 2.0 12.9 1.0
O D:HOH418 2.1 16.5 1.0
O D:HOH410 2.2 15.9 1.0
O1B D:ADP301 2.2 15.6 1.0
PAB C:SH3303 3.5 21.7 1.0
PB D:ADP301 3.6 15.5 1.0
OE1 D:GLU70 3.8 26.3 1.0
NZ D:LYS13 3.9 20.0 1.0
O3A D:ADP301 4.0 15.4 1.0
O3B D:ADP301 4.1 15.6 1.0
O1A D:ADP301 4.1 15.7 1.0
OAD C:SH3303 4.1 21.1 1.0
O D:HOH434 4.2 20.1 1.0
OAE C:SH3303 4.2 20.6 1.0
OD2 D:ASP6 4.2 23.5 1.0
O D:HOH414 4.3 21.2 1.0
ND2 D:ASN96 4.3 18.4 1.0
OD1 D:ASP6 4.3 22.9 1.0
OAA C:SH3303 4.3 21.7 1.0
OD1 D:ASN96 4.5 18.5 1.0
PA D:ADP301 4.6 15.5 1.0
CG D:ASP6 4.7 23.3 1.0
CG D:ASN96 4.7 18.6 1.0
O2B D:ADP301 4.8 15.7 1.0
CD D:GLU70 4.8 26.9 1.0
CA D:GLY8 4.8 21.7 1.0

Magnesium binding site 5 out of 8 in 4nb4

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Magnesium binding site 5 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:25.7
occ:1.00
 OAD F:SH3302 1.8 14.8 1.0
O1B E:ADP301 2.0 17.5 1.0
O E:HOH423 2.2 14.9 1.0
O E:HOH404 2.5 10.2 1.0
PAB F:SH3302 3.2 15.5 1.0
PB E:ADP301 3.3 17.8 1.0
O1A E:ADP301 3.7 18.0 1.0
OAA F:SH3302 3.7 14.9 1.0
O3A E:ADP301 3.7 17.8 1.0
O3B E:ADP301 3.8 17.9 1.0
O F:HOH426 3.8 14.8 1.0
OAC F:SH3302 4.1 15.2 1.0
OE2 E:GLU70 4.1 28.8 1.0
O E:HOH403 4.1 12.4 1.0
PA E:ADP301 4.2 17.9 1.0
OAE F:SH3302 4.3 15.3 1.0
NZ E:LYS13 4.3 16.5 1.0
ND2 E:ASN96 4.4 15.9 1.0
CA E:GLY98 4.4 15.6 1.0
OD1 E:ASN96 4.5 16.4 1.0
O2B E:ADP301 4.5 17.5 1.0
OD2 E:ASP6 4.5 17.1 1.0
O F:HOH423 4.6 11.1 1.0
OD1 E:ASP6 4.7 16.6 1.0
CG E:ASN96 4.7 16.4 1.0
O2A E:ADP301 4.9 18.4 1.0
CA E:GLY8 5.0 16.9 1.0
CG E:ASP6 5.0 17.3 1.0

Magnesium binding site 6 out of 8 in 4nb4

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Magnesium binding site 6 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg304

b:22.9
occ:1.00
 O2B F:ADP301 2.3 23.4 1.0
OAD F:SH3303 2.4 20.9 1.0
O F:HOH413 2.5 25.7 1.0
OE2 F:GLU70 2.9 36.6 1.0
OAA F:SH3303 3.3 20.7 1.0
O F:HOH406 3.3 22.9 1.0
PAB F:SH3303 3.4 20.7 1.0
PB F:ADP301 3.7 23.8 1.0
OD1 F:ASP6 3.7 25.4 1.0
OD2 F:ASP6 3.7 25.4 1.0
CD F:GLU70 3.9 37.5 1.0
CA F:GLY8 3.9 24.7 1.0
O1B F:ADP301 4.1 22.9 1.0
CG F:ASP6 4.1 25.7 1.0
NZ F:LYS13 4.2 26.1 1.0
OAE F:SH3303 4.2 21.0 1.0
O3A F:ADP301 4.5 23.4 1.0
CG F:GLU70 4.5 37.5 1.0
OAC F:SH3303 4.7 20.6 1.0
N F:GLY8 4.7 25.0 1.0
O3B F:ADP301 4.8 23.7 1.0
OE1 F:GLU70 4.8 38.0 1.0
O F:HOH427 4.8 11.9 1.0
O F:HOH425 4.9 18.7 1.0

Magnesium binding site 7 out of 8 in 4nb4

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Magnesium binding site 7 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg303

b:2.6
occ:1.00
 O G:HOH426 2.0 9.0 1.0
O G:HOH425 2.0 6.5 1.0
O3B G:ADP301 2.0 8.1 1.0
OAD G:SH3302 2.1 10.6 1.0
O G:HOH427 2.1 6.9 1.0
O G:HOH436 2.4 11.2 1.0
PB G:ADP301 3.5 8.1 1.0
PAB G:SH3302 3.5 10.4 1.0
OAA G:SH3302 3.7 10.6 1.0
O3A G:ADP301 3.8 8.3 1.0
O G:HOH406 4.1 8.4 1.0
O1B G:ADP301 4.1 8.1 1.0
NZ G:LYS13 4.1 12.4 1.0
O2A G:ADP301 4.1 8.6 1.0
OD2 G:ASP6 4.1 13.4 1.0
O G:HOH447 4.2 13.9 1.0
OE1 G:GLU70 4.2 17.7 1.0
OD1 G:ASP6 4.2 13.3 1.0
O G:HOH403 4.4 13.3 1.0
OAE G:SH3302 4.4 10.1 1.0
OAC G:SH3302 4.5 10.6 1.0
PA G:ADP301 4.5 8.3 1.0
CA G:GLY8 4.5 12.2 1.0
O G:HOH411 4.5 9.6 1.0
CG G:ASP6 4.6 13.8 1.0
ND2 G:ASN96 4.6 9.5 1.0
O2B G:ADP301 4.6 7.9 1.0
OD1 G:ASN96 4.6 9.6 1.0
O G:HOH453 4.7 12.3 1.0
CG G:ASN96 4.9 9.4 1.0
CE G:LYS13 4.9 12.4 1.0
O1A G:ADP301 4.9 8.3 1.0
CA G:GLY98 5.0 7.5 1.0

Magnesium binding site 8 out of 8 in 4nb4

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Magnesium binding site 8 out of 8 in the Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pantothenamide-Bound Pantothenate Kinase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg303

b:9.3
occ:1.00
 O H:HOH423 1.8 7.0 1.0
O H:HOH421 2.0 7.2 1.0
O H:HOH434 2.1 16.4 1.0
O3B H:ADP301 2.1 12.3 1.0
OAD H:SH3302 2.2 12.5 1.0
O H:HOH422 2.2 8.6 1.0
PB H:ADP301 3.6 12.9 1.0
PAB H:SH3302 3.6 12.4 1.0
OE2 H:GLU70 3.8 20.1 1.0
O H:HOH417 3.8 9.5 1.0
OD2 H:ASP6 3.8 16.6 1.0
O H:HOH432 4.0 12.8 1.0
OAA H:SH3302 4.0 12.9 1.0
O1A H:ADP301 4.1 12.5 1.0
O3A H:ADP301 4.1 12.6 1.0
O2B H:ADP301 4.2 12.6 1.0
NZ H:LYS13 4.2 17.6 1.0
O H:HOH402 4.3 7.9 1.0
OAC H:SH3302 4.4 12.5 1.0
O H:HOH438 4.5 16.5 1.0
O H:HOH408 4.5 19.3 1.0
OD1 H:ASP6 4.5 16.8 1.0
CG H:ASP6 4.5 16.6 1.0
PA H:ADP301 4.6 12.6 1.0
CD H:GLU70 4.6 19.7 1.0
OD1 H:ASN96 4.6 10.7 1.0
ND2 H:ASN96 4.6 10.4 1.0
OAE H:SH3302 4.7 12.8 1.0
O1B H:ADP301 4.7 13.3 1.0
O H:HOH403 4.8 9.0 1.0
CA H:GLY8 4.8 14.6 1.0
CE H:LYS13 4.9 17.5 1.0
CG H:ASN96 5.0 10.4 1.0
O H:HOH431 5.0 8.4 1.0

Reference:

S.J.Hughes, T.Antoshchenko, K.P.Kim, D.Smil, H.W.Park. Structural Characterization of A New N-Substituted Pantothenamide Bound to Pantothenate Kinases From Klebsiella Pneumoniae and Staphylococcus Aureus. Proteins V. 82 1542 2014.
ISSN: ISSN 0887-3585
PubMed: 24470271
DOI: 10.1002/PROT.24524
Page generated: Mon Dec 14 19:13:53 2020

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