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Caesium in PDB 6u1f: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+

Enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+

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

Protein crystallography data

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+, PDB code: 6u1f 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) 47.72 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.431, 95.431, 192.075, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.6

Other elements in 6u1f:

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

Magnesium (Mg) 4 atoms

Caesium Binding Sites:

The binding sites of Caesium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+ (pdb code 6u1f). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 4 binding sites of Caesium where determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+, PDB code: 6u1f:
Jump to Caesium binding site number: 1; 2; 3; 4;

Caesium binding site 1 out of 4 in 6u1f

Go back to Caesium Binding Sites List in 6u1f
Caesium binding site 1 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs405

b:47.4
occ:0.73
 O A:CYS113 3.0 44.4 1.0
O A:LEU283 3.1 44.6 1.0
OE1 A:GLU282 3.1 44.9 1.0
O A:HOH504 3.2 45.4 1.0
O A:HOH503 3.2 43.5 1.0
O A:HOH526 3.4 48.3 1.0
OD1 A:ASN284 3.5 46.9 1.0
MG A:MG404 3.5 43.6 1.0
O A:HOH507 3.8 47.8 1.0
C A:CYS113 3.9 45.6 1.0
CA A:MET114 3.9 41.6 1.0
C A:LEU283 4.0 43.3 1.0
CD A:GLU282 4.0 47.0 1.0
SD A:MET114 4.2 61.8 1.0
CG A:ASN284 4.2 43.4 1.0
CA A:ASN284 4.3 43.9 1.0
N A:MET114 4.3 40.4 1.0
O A:MET114 4.4 54.0 1.0
C A:MET114 4.5 47.8 1.0
N A:ASN284 4.5 41.0 1.0
CB A:GLU282 4.6 40.2 1.0
NZ A:LYS116 4.7 45.7 1.0
N A:LEU283 4.7 46.8 1.0
OE2 A:GLU282 4.7 46.8 1.0
CB A:ASN284 4.8 39.6 1.0
OE2 A:GLU87 4.8 43.7 1.0
CG A:GLU282 4.9 46.6 1.0
CG A:MET114 4.9 55.7 1.0
O A:HOH547 4.9 40.4 1.0
O A:THR157 4.9 50.4 1.0
CB A:MET114 5.0 46.7 1.0

Caesium binding site 2 out of 4 in 6u1f

Go back to Caesium Binding Sites List in 6u1f
Caesium binding site 2 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs406

b:0.5
occ:0.71
 O A:TRP133 3.1 48.5 1.0
O A:HOH583 3.1 57.7 1.0
CH2 A:TRP133 3.8 53.2 1.0
CZ3 A:TRP133 3.8 51.8 1.0
O A:HOH570 3.8 63.9 1.0
O A:HOH595 3.8 67.7 1.0
CZ2 A:TRP133 3.8 48.2 1.0
CE3 A:TRP133 3.8 49.0 1.0
CE2 A:TRP133 3.8 48.1 1.0
CD2 A:TRP133 3.9 49.4 1.0
C A:TRP133 4.1 50.4 1.0
NE2 B:GLN125 4.3 51.6 1.0
NE1 A:TRP133 4.5 50.4 1.0
CG A:TRP133 4.6 53.1 1.0
N A:TRP133 4.7 46.6 1.0
CA A:VAL134 4.9 52.2 1.0
O A:HOH593 4.9 54.7 1.0
N A:VAL134 4.9 52.5 1.0
CD1 A:TRP133 4.9 48.6 1.0
CA A:TRP133 5.0 48.6 1.0

Caesium binding site 3 out of 4 in 6u1f

Go back to Caesium Binding Sites List in 6u1f
Caesium binding site 3 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs405

b:45.0
occ:0.86
 O B:LEU283 2.9 39.5 1.0
O B:CYS113 3.0 38.9 1.0
OE1 B:GLU282 3.0 34.9 1.0
O B:HOH542 3.1 34.2 1.0
O B:HOH547 3.1 36.6 1.0
O B:HOH532 3.2 43.0 1.0
OD1 B:ASN284 3.5 36.0 1.0
MG B:MG403 3.5 38.9 1.0
O B:HOH516 3.9 43.0 1.0
C B:CYS113 3.9 38.2 1.0
CA B:MET114 3.9 39.7 1.0
C B:LEU283 4.0 37.3 1.0
CG B:ASN284 4.2 39.8 1.0
SD B:MET114 4.2 52.0 1.0
CD B:GLU282 4.2 40.2 1.0
CA B:ASN284 4.3 38.0 1.0
N B:MET114 4.3 37.7 1.0
O B:MET114 4.4 47.9 1.0
C B:MET114 4.5 44.4 1.0
N B:ASN284 4.5 37.8 1.0
CB B:GLU282 4.6 36.6 1.0
NZ B:LYS116 4.7 37.8 1.0
CB B:ASN284 4.7 36.4 1.0
O B:THR157 4.9 39.9 1.0
CG B:MET114 4.9 47.0 1.0
N B:LEU283 4.9 39.6 1.0
ND2 B:ASN284 4.9 42.2 1.0
CG B:GLU282 5.0 38.1 1.0
OE2 B:GLU87 5.0 41.0 1.0
CB B:MET114 5.0 38.4 1.0

Caesium binding site 4 out of 4 in 6u1f

Go back to Caesium Binding Sites List in 6u1f
Caesium binding site 4 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs406

b:58.7
occ:0.63
 O B:TRP133 3.0 34.1 1.0
O B:HOH609 3.2 41.2 1.0
CZ2 B:TRP133 3.5 34.5 1.0
CE2 B:TRP133 3.5 41.7 1.0
CH2 B:TRP133 3.6 41.4 1.0
O B:HOH616 3.6 66.6 1.0
O B:HOH592 3.6 59.3 1.0
CD2 B:TRP133 3.7 37.6 1.0
O A:HOH584 3.7 70.9 1.0
CZ3 B:TRP133 3.7 40.2 1.0
CE3 B:TRP133 3.7 39.2 1.0
O B:HOH626 4.1 61.3 1.0
C B:TRP133 4.1 40.0 1.0
NE1 B:TRP133 4.2 41.4 1.0
NE2 A:GLN125 4.4 56.0 1.0
CG B:TRP133 4.4 36.2 1.0
CD1 B:TRP133 4.6 37.7 1.0
CA B:VAL134 4.8 36.9 1.0
N B:TRP133 4.8 37.0 1.0
O B:HOH568 4.9 37.6 1.0
N B:VAL134 4.9 32.0 1.0
CG1 B:VAL134 5.0 43.6 1.0
CA B:TRP133 5.0 39.1 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: Sun Jul 13 23:01:15 2025

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