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Potassium in PDB 7u9k: Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+

Enzymatic activity of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+

All present enzymatic activity of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+:
6.3.2.4;

Protein crystallography data

The structure of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+, PDB code: 7u9k was solved by J.L.Pederick, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.68 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.447, 70.058, 91.598, 90, 102.58, 90
R / Rfree (%) 24 / 27.7

Other elements in 7u9k:

The structure of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ (pdb code 7u9k). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+, PDB code: 7u9k:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7u9k

Go back to Potassium Binding Sites List in 7u9k
Potassium binding site 1 out of 4 in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:25.6
occ:0.85
 O A:HOH611 2.7 34.7 1.0
O A:THR307 2.7 23.0 1.0
O A:SER127 2.8 30.7 1.0
O A:HOH654 2.9 41.2 1.0
OE1 A:GLU306 3.0 27.1 1.0
O A:HOH507 3.1 35.4 1.0
O A:HOH555 3.1 25.9 1.0
O A:HOH538 3.6 33.7 1.0
C A:SER127 3.9 33.5 1.0
C A:THR307 3.9 22.6 1.0
CD A:GLU306 4.0 30.0 1.0
CB A:GLU306 4.4 21.4 1.0
CA A:MET128 4.4 31.3 1.0
CA A:ASN308 4.5 26.1 1.0
SD A:MET133 4.5 21.8 1.0
N A:MET128 4.6 27.7 1.0
CG A:GLU306 4.6 26.8 1.0
N A:ASN308 4.7 18.2 1.0
N A:THR307 4.7 20.7 1.0
OD1 A:ASN308 4.7 30.1 1.0
CB A:SER127 4.7 30.4 1.0
OG A:SER127 4.8 30.9 1.0
NZ A:LYS130 4.8 36.4 1.0
O A:MET128 4.8 41.5 1.0
O A:HOH542 4.8 37.2 1.0
OE2 A:GLU306 4.8 27.7 1.0
CA A:SER127 4.8 32.8 1.0
CA A:THR307 5.0 20.8 1.0

Potassium binding site 2 out of 4 in 7u9k

Go back to Potassium Binding Sites List in 7u9k
Potassium binding site 2 out of 4 in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K401

b:30.0
occ:0.87
 O2A B:ATP405 2.7 36.5 1.0
O3G B:ATP405 2.7 21.9 1.0
OD2 B:ASP293 2.7 27.8 1.0
O B:HOH519 2.8 29.1 1.0
OE2 B:GLU306 2.8 20.8 1.0
O3B B:ATP405 3.0 19.4 1.0
O B:HOH551 3.3 35.9 1.0
PG B:ATP405 3.5 22.9 1.0
CG B:ASP293 3.6 30.0 1.0
CD B:GLU306 3.7 17.3 1.0
ND2 B:ASN305 3.8 31.1 1.0
NH2 B:ARG291 3.8 24.3 1.0
CG B:GLU306 3.8 21.8 1.0
CB B:ASP293 4.0 25.8 1.0
PA B:ATP405 4.0 28.9 1.0
PB B:ATP405 4.3 20.8 1.0
O2G B:ATP405 4.4 30.5 1.0
O5' B:ATP405 4.5 29.8 1.0
ND2 B:ASN308 4.5 29.5 1.0
O3A B:ATP405 4.5 29.4 1.0
O2B B:ATP405 4.6 26.2 1.0
OD1 B:ASP293 4.6 26.4 1.0
C5' B:ATP405 4.6 25.2 1.0
MG B:MG404 4.6 19.6 1.0
O1G B:ATP405 4.6 32.2 1.0
OE2 B:GLU222 4.8 34.8 1.0
NZ B:LYS251 4.8 29.7 1.0
O3' B:ATP405 4.8 30.7 1.0
OE1 B:GLU306 4.9 20.3 1.0
CG B:ASN305 4.9 25.8 1.0

Potassium binding site 3 out of 4 in 7u9k

Go back to Potassium Binding Sites List in 7u9k
Potassium binding site 3 out of 4 in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:23.9
occ:0.93
 O B:THR307 2.7 19.3 1.0
O B:HOH507 2.8 25.8 1.0
O B:HOH579 2.9 22.4 1.0
O B:SER127 2.9 18.0 1.0
OE1 B:GLU306 3.0 20.3 1.0
O B:HOH535 3.2 16.1 1.0
OD1 B:ASN308 3.5 18.6 1.0
MG B:MG404 3.8 19.6 1.0
C B:THR307 3.9 21.6 1.0
C B:SER127 4.0 22.4 1.0
CD B:GLU306 4.1 17.3 1.0
CG B:ASN308 4.1 24.7 1.0
CA B:MET128 4.2 21.4 1.0
CA B:ASN308 4.2 23.1 1.0
O B:MET128 4.3 18.2 1.0
NZ B:LYS130 4.4 22.1 1.0
N B:MET128 4.5 20.5 1.0
N B:ASN308 4.5 17.6 1.0
C B:MET128 4.6 22.1 1.0
SD B:MET133 4.7 19.1 1.0
CB B:GLU306 4.7 19.7 1.0
CB B:ASN308 4.7 20.9 1.0
OE2 B:GLU306 4.7 20.8 1.0
SD B:MET128 4.8 32.2 1.0
N B:THR307 4.8 19.4 1.0
CE B:MET128 4.9 24.3 1.0
O B:LEU181 4.9 22.1 1.0
CG B:LYS130 4.9 23.6 1.0
CE B:LYS130 4.9 26.7 1.0
ND2 B:ASN308 4.9 29.5 1.0
CG B:GLU306 5.0 21.8 1.0

Potassium binding site 4 out of 4 in 7u9k

Go back to Potassium Binding Sites List in 7u9k
Potassium binding site 4 out of 4 in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:25.4
occ:0.81
 O B:TYR172 2.7 25.1 1.0
OD1 B:ASN171 3.1 38.7 1.0
O B:HOH549 3.4 27.0 1.0
C B:TYR172 3.8 20.9 1.0
CG B:ASN171 4.2 41.1 1.0
N B:TYR172 4.3 17.3 1.0
CA B:TYR172 4.5 23.2 1.0
CB B:TYR172 4.6 26.4 1.0
N B:PRO173 4.8 21.6 1.0
ND2 B:ASN171 4.9 46.0 1.0
O B:HOH583 5.0 44.1 1.0

Reference:

J.L.Pederick, J.B.Bruning. Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ To Be Published.
Page generated: Sat Aug 9 15:02:19 2025

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