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Rubidium in PDB 6u1e: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+

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

All present enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+:
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 Rb+, PDB code: 6u1e 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) 38.36 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.433, 95.433, 193.461, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.4

Other elements in 6u1e:

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

Magnesium (Mg) 4 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+ (pdb code 6u1e). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 4 binding sites of Rubidium where determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+, PDB code: 6u1e:
Jump to Rubidium binding site number: 1; 2; 3; 4;

Rubidium binding site 1 out of 4 in 6u1e

Go back to Rubidium Binding Sites List in 6u1e
Rubidium 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 Rb+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb405

b:37.9
occ:0.85
 O A:LEU283 2.8 35.4 1.0
O A:CYS113 2.9 34.6 1.0
OE1 A:GLU282 2.9 31.3 1.0
O A:HOH516 3.0 33.5 1.0
O A:HOH596 3.1 37.1 1.0
O A:HOH585 3.1 27.8 1.0
OD1 A:ASN284 3.2 31.3 1.0
MG A:MG404 3.6 32.1 1.0
C A:LEU283 3.8 33.0 1.0
C A:CYS113 3.9 33.6 1.0
CD A:GLU282 4.0 36.5 1.0
SD A:MET114 4.0 51.3 1.0
CG A:ASN284 4.0 36.3 1.0
CA A:MET114 4.0 32.4 1.0
O A:HOH564 4.1 35.5 1.0
CA A:ASN284 4.1 30.9 1.0
N A:MET114 4.4 34.3 1.0
N A:ASN284 4.4 31.2 1.0
CB A:ASN284 4.6 31.4 1.0
CB A:GLU282 4.6 31.7 1.0
OE2 A:GLU282 4.7 34.6 1.0
NZ A:LYS116 4.7 33.7 1.0
C A:MET114 4.7 38.9 1.0
N A:LEU283 4.8 35.2 1.0
CG A:GLU282 4.8 34.4 1.0
O A:MET114 4.8 50.6 1.0
OE2 A:GLU87 4.9 36.9 1.0
CG A:MET114 4.9 43.2 1.0
ND2 A:ASN284 4.9 40.7 1.0
O A:HOH540 4.9 36.8 1.0
O2B A:ATP407 5.0 35.8 1.0
CA A:CYS113 5.0 27.5 1.0
CA A:LEU283 5.0 34.0 1.0
CB A:CYS113 5.0 33.9 1.0

Rubidium binding site 2 out of 4 in 6u1e

Go back to Rubidium Binding Sites List in 6u1e
Rubidium 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 Rb+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb406

b:77.7
occ:0.61
 O B:HOH605 2.8 63.0 1.0
O A:TRP133 3.0 33.9 1.0
O A:HOH641 3.0 46.0 1.0
O A:HOH660 3.4 63.1 1.0
CZ2 A:TRP133 3.6 40.3 1.0
CE2 A:TRP133 3.6 35.8 1.0
CH2 A:TRP133 3.6 38.7 1.0
CZ3 A:TRP133 3.7 36.4 1.0
CD2 A:TRP133 3.7 36.8 1.0
CE3 A:TRP133 3.7 35.9 1.0
O A:HOH522 4.1 54.4 1.0
C A:TRP133 4.1 35.7 1.0
NE1 A:TRP133 4.3 35.5 1.0
CG A:TRP133 4.4 35.7 1.0
NE2 B:GLN125 4.5 50.5 1.0
CD1 A:TRP133 4.7 37.9 1.0
N A:TRP133 4.8 35.8 1.0
O B:HOH537 4.8 59.6 1.0
CA A:VAL134 4.9 36.5 1.0
O A:HOH627 4.9 43.3 1.0
N A:VAL134 4.9 34.1 1.0
CA A:TRP133 5.0 38.5 1.0

Rubidium binding site 3 out of 4 in 6u1e

Go back to Rubidium Binding Sites List in 6u1e
Rubidium 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 Rb+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb405

b:41.0
occ:0.82
 O B:LEU283 2.7 39.0 1.0
O B:HOH510 2.9 38.0 1.0
O B:CYS113 3.0 42.0 1.0
OE1 B:GLU282 3.0 36.2 1.0
O B:HOH574 3.1 32.6 1.0
O B:HOH569 3.2 46.2 1.0
OD1 B:ASN284 3.2 39.2 1.0
MG B:MG404 3.6 39.4 1.0
C B:LEU283 3.7 37.7 1.0
C B:CYS113 3.9 34.8 1.0
SD B:MET114 3.9 58.1 1.0
O B:HOH532 4.0 41.0 1.0
CG B:ASN284 4.0 40.1 1.0
CA B:MET114 4.0 39.1 1.0
CD B:GLU282 4.0 44.6 1.0
CA B:ASN284 4.1 38.2 1.0
N B:ASN284 4.3 35.6 1.0
N B:MET114 4.3 35.2 1.0
N B:LEU283 4.6 41.0 1.0
CB B:ASN284 4.6 38.5 1.0
C B:MET114 4.7 44.1 1.0
NZ B:LYS116 4.7 41.0 1.0
O B:MET114 4.7 46.6 1.0
CB B:GLU282 4.7 37.4 1.0
OE2 B:GLU87 4.8 40.6 1.0
OE2 B:GLU282 4.8 40.5 1.0
CA B:LEU283 4.8 33.6 1.0
ND2 B:ASN284 4.9 45.3 1.0
CG B:GLU282 4.9 40.9 1.0
CE B:MET114 4.9 42.8 1.0
CG B:MET114 4.9 52.8 1.0
O B:HOH556 4.9 37.0 1.0

Rubidium binding site 4 out of 4 in 6u1e

Go back to Rubidium Binding Sites List in 6u1e
Rubidium 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 Rb+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb406

b:83.7
occ:0.59
 O A:HOH642 2.9 71.5 1.0
O B:HOH607 2.9 51.5 1.0
O B:TRP133 2.9 45.7 1.0
CZ3 B:TRP133 3.6 47.1 1.0
CE3 B:TRP133 3.7 42.8 1.0
CH2 B:TRP133 3.8 48.4 1.0
CD2 B:TRP133 3.9 44.8 1.0
CZ2 B:TRP133 4.0 41.1 1.0
O B:HOH578 4.0 61.5 1.0
CE2 B:TRP133 4.0 46.1 1.0
C B:TRP133 4.1 46.2 1.0
NE2 A:GLN125 4.5 52.2 1.0
N B:TRP133 4.6 41.8 1.0
O A:HOH558 4.6 54.6 1.0
CG B:TRP133 4.7 48.0 1.0
NE1 B:TRP133 4.8 49.7 1.0
CA B:TRP133 4.9 42.7 1.0
N B:VAL134 4.9 45.7 1.0
CA B:VAL134 5.0 49.9 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: Thu Oct 10 12:15:43 2024

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