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Potassium in PDB 6u1k: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+

Enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+

All present enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+:
6.3.2.4;

Protein crystallography data

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+, PDB code: 6u1k 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) 43.58 / 1.67
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.909, 68.174, 90.641, 70.79, 79.22, 66.21
R / Rfree (%) 21.8 / 25.4

Other elements in 6u1k:

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ (pdb code 6u1k). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+, PDB code: 6u1k:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6u1k

Go back to Potassium Binding Sites List in 6u1k
Potassium binding site 1 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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 Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:14.5
occ:1.00
 O A:HOH622 2.7 23.8 1.0
O A:LEU283 2.7 17.1 1.0
O A:CYS113 2.8 16.6 1.0
O A:HOH608 2.9 12.1 1.0
OE1 A:GLU282 2.9 14.0 1.0
O A:HOH616 3.1 12.3 1.0
OD1 A:ASN284 3.1 17.7 1.0
MG A:MG403 3.6 11.5 0.9
C A:LEU283 3.8 14.2 1.0
SD A:MET114 3.8 20.1 1.0
C A:CYS113 3.8 18.9 1.0
CG A:ASN284 3.9 18.9 1.0
CD A:GLU282 4.0 14.7 1.0
CA A:ASN284 4.0 16.4 1.0
CA A:MET114 4.1 11.6 1.0
O A:HOH575 4.2 17.1 1.0
N A:ASN284 4.3 12.9 1.0
N A:MET114 4.4 12.9 1.0
CB A:ASN284 4.5 17.2 1.0
NZ A:LYS116 4.6 18.7 1.0
CB A:GLU282 4.7 13.7 1.0
ND2 A:ASN284 4.8 14.8 1.0
OE2 A:GLU282 4.8 12.3 1.0
OE2 A:GLU87 4.8 14.6 1.0
O3B A:ADP406 4.8 11.9 1.0
O A:THR157 4.8 15.0 1.0
CG A:MET114 4.8 18.4 1.0
C A:MET114 4.8 18.3 1.0
CG A:GLU282 4.9 14.1 1.0
N A:LEU283 4.9 16.0 1.0
O A:HOH602 4.9 15.2 1.0
CA A:CYS113 4.9 19.4 1.0
O A:HOH564 4.9 13.7 1.0
CB A:CYS113 4.9 14.9 1.0
CE A:MET114 4.9 15.1 1.0
CA A:LEU283 5.0 13.2 1.0
O A:MET114 5.0 29.7 1.0

Potassium binding site 2 out of 4 in 6u1k

Go back to Potassium Binding Sites List in 6u1k
Potassium binding site 2 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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 Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:16.6
occ:1.00
 O B:HOH619 2.7 16.4 1.0
O B:LEU283 2.7 20.6 1.0
OE1 B:GLU282 2.8 15.1 1.0
O B:CYS113 2.9 15.6 1.0
O B:HOH567 3.0 16.6 1.0
O B:HOH512 3.0 18.7 1.0
OD1 B:ASN284 3.0 13.8 1.0
MG B:MG404 3.7 15.4 1.0
CG B:ASN284 3.8 18.3 1.0
C B:CYS113 3.8 18.8 1.0
C B:LEU283 3.8 16.7 1.0
SD B:MET114 3.9 24.9 1.0
CD B:GLU282 3.9 20.0 1.0
CA B:MET114 4.0 13.3 1.0
CA B:ASN284 4.1 16.6 1.0
O B:HOH589 4.2 18.4 1.0
N B:MET114 4.3 13.0 1.0
N B:ASN284 4.4 15.1 1.0
CB B:ASN284 4.4 19.2 1.0
NZ B:LYS116 4.5 19.2 1.0
O B:MET114 4.5 17.0 1.0
C B:MET114 4.6 17.7 1.0
CB B:GLU282 4.6 17.5 1.0
OE2 B:GLU282 4.7 16.5 1.0
ND2 B:ASN284 4.7 19.7 1.0
O B:THR157 4.7 17.1 1.0
CE B:MET114 4.7 19.3 1.0
O1B B:ADP406 4.8 16.9 1.0
CG B:GLU282 4.8 17.2 1.0
CG B:MET114 4.9 22.6 1.0
O B:HOH591 4.9 18.0 1.0
O B:HOH556 4.9 12.6 1.0
CB B:CYS113 5.0 18.0 1.0
CA B:CYS113 5.0 19.1 1.0
N B:LEU283 5.0 15.4 1.0
OE2 B:GLU87 5.0 19.6 1.0

Potassium binding site 3 out of 4 in 6u1k

Go back to Potassium Binding Sites List in 6u1k
Potassium binding site 3 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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 Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K405

b:15.7
occ:1.00
 O C:LEU283 2.6 18.0 1.0
OE1 C:GLU282 2.8 14.3 1.0
O C:HOH604 2.8 12.2 1.0
O C:CYS113 2.9 16.5 1.0
O C:HOH537 3.0 21.5 1.0
OD1 C:ASN284 3.0 14.4 1.0
O C:HOH558 3.1 12.1 1.0
MG C:MG404 3.7 12.3 1.0
C C:LEU283 3.7 14.8 1.0
CG C:ASN284 3.8 20.6 1.0
C C:CYS113 3.9 18.9 1.0
CD C:GLU282 3.9 14.7 1.0
SD C:MET114 3.9 23.9 1.0
CA C:ASN284 4.0 14.1 1.0
CA C:MET114 4.1 15.2 1.0
O C:HOH621 4.2 15.9 1.0
N C:ASN284 4.3 13.2 1.0
N C:MET114 4.4 16.1 1.0
CB C:ASN284 4.4 13.3 1.0
CB C:GLU282 4.6 15.0 1.0
NZ C:LYS116 4.6 19.1 1.0
O C:MET114 4.6 24.8 1.0
C C:MET114 4.7 22.4 1.0
O C:THR157 4.7 12.9 1.0
OE2 C:GLU282 4.7 18.3 1.0
ND2 C:ASN284 4.7 19.3 1.0
N C:LEU283 4.8 14.5 1.0
CG C:GLU282 4.8 14.5 1.0
O1B C:ADP406 4.8 13.7 1.0
CA C:LEU283 4.9 15.4 1.0
OE2 C:GLU87 4.9 17.3 1.0
O C:HOH588 4.9 14.2 1.0
CG C:MET114 4.9 24.8 1.0
CA C:CYS113 5.0 18.0 1.0
CB C:CYS113 5.0 11.4 1.0

Potassium binding site 4 out of 4 in 6u1k

Go back to Potassium Binding Sites List in 6u1k
Potassium binding site 4 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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 Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K405

b:14.7
occ:0.84
 O D:HOH587 2.7 17.0 1.0
O D:LEU283 2.7 17.0 1.0
OE1 D:GLU282 2.8 16.6 1.0
O D:CYS113 2.9 17.6 1.0
O D:HOH523 3.0 19.6 1.0
O D:HOH567 3.0 16.5 1.0
OD1 D:ASN284 3.0 19.2 1.0
MG D:MG404 3.6 16.8 1.0
C D:CYS113 3.8 19.5 1.0
C D:LEU283 3.8 16.2 1.0
CG D:ASN284 3.9 20.1 1.0
CA D:MET114 3.9 15.3 1.0
CD D:GLU282 3.9 17.3 1.0
SD D:MET114 4.0 25.6 1.0
CA D:ASN284 4.1 19.2 1.0
O D:HOH575 4.2 17.2 1.0
N D:MET114 4.3 13.9 1.0
N D:ASN284 4.4 16.0 1.0
CB D:ASN284 4.5 17.1 1.0
O D:MET114 4.6 19.8 1.0
NZ D:LYS116 4.6 19.0 1.0
C D:MET114 4.6 17.0 1.0
CB D:GLU282 4.6 18.2 1.0
O D:THR157 4.6 22.2 1.0
OE2 D:GLU282 4.7 19.8 1.0
ND2 D:ASN284 4.7 19.6 1.0
CG D:MET114 4.7 21.3 1.0
O3B D:ADP406 4.8 17.9 1.0
CG D:GLU282 4.8 17.7 1.0
OE2 D:GLU87 4.8 21.4 1.0
O D:HOH539 4.9 16.0 1.0
CB D:MET114 4.9 14.2 1.0
O D:HOH613 4.9 20.2 1.0
N D:LEU283 4.9 16.8 1.0
CB D:CYS113 5.0 15.1 1.0
CA D:CYS113 5.0 19.1 1.0

Reference:

J.L.Pederick, A.P.Thompson, S.G.Bell, J.B.Bruning. D-Alanine-D-Alanine Ligase As A Model For the Activation of Atp-Grasp Enzymes By Monovalent Cations. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32335509
DOI: 10.1074/JBC.RA120.012936
Page generated: Mon Aug 12 17:43:45 2024

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