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Rubidium in PDB 6u1d: 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: 6u1d 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) 42.68 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.435, 95.435, 193.318, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.6

Other elements in 6u1d:

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 6u1d). 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: 6u1d:
Jump to Rubidium binding site number: 1; 2; 3; 4;

Rubidium binding site 1 out of 4 in 6u1d

Go back to Rubidium Binding Sites List in 6u1d
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:28.8
occ:0.84
 O A:LEU283 2.8 31.1 1.0
OE1 A:GLU282 2.9 28.8 1.0
O A:CYS113 2.9 30.5 1.0
O A:HOH572 3.0 31.9 1.0
O A:HOH568 3.1 34.5 1.0
O A:HOH594 3.1 28.6 1.0
OD1 A:ASN284 3.3 28.8 1.0
MG A:MG404 3.7 29.0 1.0
C A:LEU283 3.8 33.0 1.0
C A:CYS113 3.9 28.1 1.0
SD A:MET114 3.9 42.1 1.0
CD A:GLU282 4.0 33.2 1.0
CA A:MET114 4.0 26.6 1.0
CG A:ASN284 4.1 35.5 1.0
CA A:ASN284 4.1 26.8 1.0
O A:HOH615 4.2 32.5 1.0
N A:MET114 4.3 28.2 1.0
N A:ASN284 4.4 27.3 1.0
O A:MET114 4.5 41.3 1.0
CB A:GLU282 4.6 29.9 1.0
C A:MET114 4.6 35.0 1.0
CB A:ASN284 4.6 27.0 1.0
OE2 A:GLU282 4.7 30.7 1.0
NZ A:LYS116 4.7 29.1 1.0
OE2 A:GLU87 4.8 30.6 1.0
CG A:MET114 4.8 39.8 1.0
CG A:GLU282 4.9 30.1 1.0
O A:THR157 4.9 29.8 1.0
N A:LEU283 4.9 29.0 1.0
ND2 A:ASN284 4.9 33.5 1.0
O2B A:ATP407 4.9 29.4 1.0
CB A:CYS113 4.9 29.3 1.0
O A:HOH583 4.9 30.8 1.0
CA A:CYS113 5.0 25.8 1.0

Rubidium binding site 2 out of 4 in 6u1d

Go back to Rubidium Binding Sites List in 6u1d
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:59.5
occ:0.50
 O A:HOH699 2.9 55.9 1.0
O A:TRP133 2.9 34.0 1.0
O A:HOH724 3.1 58.2 1.0
O A:HOH692 3.3 44.9 1.0
CE2 A:TRP133 3.4 33.2 1.0
CZ2 A:TRP133 3.4 35.8 1.0
CH2 A:TRP133 3.5 37.0 1.0
CD2 A:TRP133 3.6 34.1 1.0
CZ3 A:TRP133 3.6 34.9 1.0
CE3 A:TRP133 3.7 35.8 1.0
O A:HOH510 4.0 48.7 1.0
C A:TRP133 4.0 35.8 1.0
NE1 A:TRP133 4.1 33.1 1.0
O A:HOH688 4.3 54.8 1.0
CG A:TRP133 4.3 30.2 1.0
NE2 B:GLN125 4.5 44.7 1.0
O A:HOH745 4.5 55.5 1.0
CD1 A:TRP133 4.6 32.3 1.0
O B:HOH628 4.7 61.8 1.0
CA A:VAL134 4.8 29.8 1.0
N A:TRP133 4.8 32.6 1.0
O A:HOH681 4.8 42.2 1.0
N A:VAL134 4.8 32.4 1.0
CA A:TRP133 4.9 33.1 1.0

Rubidium binding site 3 out of 4 in 6u1d

Go back to Rubidium Binding Sites List in 6u1d
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:29.9
occ:0.72
 OE1 B:GLU282 2.9 33.3 1.0
O B:LEU283 2.9 35.2 1.0
O B:CYS113 2.9 36.0 1.0
O B:HOH554 3.1 32.5 1.0
O B:HOH570 3.2 42.4 1.0
OD1 B:ASN284 3.2 35.2 1.0
O B:HOH598 3.2 33.7 1.0
MG B:MG404 3.7 36.9 1.0
SD B:MET114 3.9 46.2 1.0
C B:CYS113 3.9 35.3 1.0
C B:LEU283 3.9 33.8 1.0
O B:HOH604 3.9 37.4 1.0
CD B:GLU282 3.9 40.4 1.0
CG B:ASN284 4.0 36.1 1.0
CA B:MET114 4.0 37.1 1.0
CA B:ASN284 4.1 32.6 1.0
N B:MET114 4.4 33.9 1.0
N B:ASN284 4.4 35.3 1.0
CE B:MET114 4.5 43.6 1.0
CB B:ASN284 4.6 33.3 1.0
NZ B:LYS116 4.6 38.4 1.0
CB B:GLU282 4.6 35.4 1.0
C B:MET114 4.7 43.8 1.0
O B:MET114 4.7 42.8 1.0
OE2 B:GLU282 4.7 32.3 1.0
N B:LEU283 4.8 35.8 1.0
CG B:GLU282 4.8 36.2 1.0
ND2 B:ASN284 4.8 37.1 1.0
OE2 B:GLU87 4.8 36.4 1.0
O B:THR157 4.9 40.2 1.0
O1B B:ATP407 5.0 39.7 1.0
O B:HOH578 5.0 33.5 1.0
CG B:MET114 5.0 44.4 1.0

Rubidium binding site 4 out of 4 in 6u1d

Go back to Rubidium Binding Sites List in 6u1d
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:64.6
occ:0.51
 O B:TRP133 2.8 44.8 1.0
O A:HOH686 2.9 59.8 1.0
O B:HOH665 3.0 48.3 1.0
O A:HOH717 3.4 73.2 1.0
CZ3 B:TRP133 3.5 44.6 1.0
CE3 B:TRP133 3.5 47.2 1.0
CH2 B:TRP133 3.5 47.9 1.0
CD2 B:TRP133 3.6 44.0 1.0
CE2 B:TRP133 3.6 43.5 1.0
CZ2 B:TRP133 3.6 41.2 1.0
O B:HOH645 3.8 56.6 1.0
C B:TRP133 3.9 43.0 1.0
CG B:TRP133 4.3 45.8 1.0
NE1 B:TRP133 4.4 47.8 1.0
NE2 A:GLN125 4.4 47.1 1.0
N B:TRP133 4.4 42.4 1.0
CA B:TRP133 4.7 41.9 1.0
CD1 B:TRP133 4.8 42.2 1.0
O A:HOH638 4.8 50.4 1.0
N B:VAL134 4.8 39.9 1.0
CA B:VAL134 4.9 49.1 1.0
O B:HOH635 4.9 54.8 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 12:15:22 2024

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