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:
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+
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_01.jpg) Mono view
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_01_stereo.jpg) 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+
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_02.jpg) Mono view
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_02_stereo.jpg) 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+
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_03.jpg) Mono view
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_03_stereo.jpg) 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+
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_04.jpg) Mono view
![](/pictures/RB/pdb/u1/6u1e-RB-sphere_04_stereo.jpg) 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: Wed Dec 16 02:07:15 2020
|