Atomistry » Rubidium » PDB 5aw4-7w49 » 6u1d
Atomistry »
  Rubidium »
    PDB 5aw4-7w49 »
      6u1d »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy