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Caesium in PDB 6u1g: 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: 6u1g 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) 47.85 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.692, 95.692, 192.402, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.3

Other elements in 6u1g:

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 6u1g). 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: 6u1g:
Jump to Caesium binding site number: 1; 2; 3; 4;

Caesium binding site 1 out of 4 in 6u1g

Go back to Caesium Binding Sites List in 6u1g
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:Cs403

b:45.0
occ:0.66
O A:CYS113 3.1 50.8 1.0
OE1 A:GLU282 3.1 47.4 1.0
O A:HOH512 3.1 39.5 1.0
O A:LEU283 3.2 46.5 1.0
O A:HOH514 3.4 50.7 1.0
OD1 A:ASN284 3.4 47.6 1.0
MG A:MG406 3.5 44.4 0.8
O A:HOH533 3.6 48.5 1.0
O A:HOH513 3.9 51.5 1.0
C A:CYS113 3.9 43.8 1.0
C A:LEU283 4.0 37.6 1.0
CA A:MET114 4.0 39.8 1.0
SD A:MET114 4.1 60.3 1.0
CD A:GLU282 4.1 49.4 1.0
CG A:ASN284 4.1 42.9 1.0
CA A:ASN284 4.2 37.2 1.0
N A:MET114 4.4 42.9 1.0
N A:ASN284 4.4 39.4 1.0
O A:MET114 4.5 60.8 1.0
C A:MET114 4.6 48.2 1.0
CB A:GLU282 4.6 34.6 1.0
N A:LEU283 4.6 45.7 1.0
CB A:ASN284 4.7 39.5 1.0
OE2 A:GLU87 4.7 48.3 1.0
NZ A:LYS116 4.8 47.0 1.0
CG A:GLU282 4.9 46.6 1.0
OE2 A:GLU282 4.9 48.8 1.0
CG A:MET114 4.9 58.3 1.0
O A:HOH544 4.9 43.8 1.0
O A:THR157 4.9 52.3 1.0
ND2 A:ASN284 4.9 42.4 1.0

Caesium binding site 2 out of 4 in 6u1g

Go back to Caesium Binding Sites List in 6u1g
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:Cs404

b:0.9
occ:0.72
O A:HOH578 3.1 59.1 1.0
O A:TRP133 3.2 45.6 1.0
O A:HOH571 3.9 64.8 1.0
CZ3 A:TRP133 4.0 49.7 1.0
CH2 A:TRP133 4.0 52.0 1.0
O A:HOH581 4.1 64.5 1.0
CE3 A:TRP133 4.1 50.0 1.0
CZ2 A:TRP133 4.1 47.5 1.0
CE2 A:TRP133 4.1 53.7 1.0
CD2 A:TRP133 4.1 50.6 1.0
C A:TRP133 4.3 49.5 1.0
NE2 B:GLN125 4.4 49.2 1.0
O B:HOH543 4.5 45.4 1.0
O A:HOH552 4.7 65.1 1.0
NE1 A:TRP133 4.8 53.3 1.0
CG A:TRP133 4.8 56.8 1.0
N A:TRP133 4.8 52.9 1.0

Caesium binding site 3 out of 4 in 6u1g

Go back to Caesium Binding Sites List in 6u1g
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:Cs403

b:44.3
occ:0.81
O B:CYS113 3.0 45.2 1.0
OE1 B:GLU282 3.0 36.2 1.0
O B:LEU283 3.1 45.9 1.0
O B:HOH516 3.2 38.2 1.0
O B:HOH519 3.2 44.2 1.0
OD1 B:ASN284 3.3 43.6 1.0
O B:HOH558 3.4 42.2 1.0
MG B:MG405 3.4 37.2 1.0
C B:CYS113 3.8 36.1 1.0
C B:LEU283 3.9 35.3 1.0
CA B:MET114 4.0 45.1 1.0
CG B:ASN284 4.0 41.1 1.0
CA B:ASN284 4.2 37.5 1.0
CD B:GLU282 4.2 44.0 1.0
SD B:MET114 4.2 57.1 1.0
N B:MET114 4.3 36.4 1.0
N B:ASN284 4.4 41.6 1.0
CB B:GLU282 4.5 34.4 1.0
CB B:ASN284 4.6 39.3 1.0
C B:MET114 4.6 45.5 1.0
NZ B:LYS116 4.7 36.9 1.0
CG B:MET114 4.7 50.3 1.0
N B:LEU283 4.8 39.7 1.0
O B:MET114 4.8 58.2 1.0
ND2 B:ASN284 4.8 45.9 1.0
O B:HOH526 4.9 37.6 1.0
CG B:GLU282 4.9 38.2 1.0
CB B:CYS113 4.9 38.6 1.0
CA B:CYS113 5.0 32.6 1.0
CB B:MET114 5.0 44.7 1.0

Caesium binding site 4 out of 4 in 6u1g

Go back to Caesium Binding Sites List in 6u1g
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:Cs404

b:72.4
occ:0.66
O B:TRP133 3.0 37.2 1.0
O B:HOH589 3.2 46.0 1.0
O A:HOH563 3.5 70.9 1.0
CZ2 B:TRP133 3.6 31.1 1.0
CE2 B:TRP133 3.6 29.1 1.0
CH2 B:TRP133 3.6 36.6 1.0
CD2 B:TRP133 3.7 36.8 1.0
CZ3 B:TRP133 3.7 35.1 1.0
CE3 B:TRP133 3.8 32.2 1.0
C B:TRP133 4.1 40.3 1.0
NE1 B:TRP133 4.2 43.6 1.0
NE2 A:GLN125 4.3 51.0 1.0
CG B:TRP133 4.4 32.8 1.0
CD1 B:TRP133 4.7 35.2 1.0
CA B:VAL134 4.8 37.1 1.0
N B:VAL134 4.8 35.5 1.0
N B:TRP133 4.9 34.5 1.0
O B:HOH561 5.0 43.2 1.0
CA B:TRP133 5.0 35.2 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 Dec 13 10:57:14 2020

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