Magnesium 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 (Rb) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6u1e

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:36.3
occ:0.95
O1A A:ATP407 2.3 37.1 1.0
O2G A:ATP407 2.3 33.3 1.0
OD2 A:ASP270 2.4 49.6 1.0
O A:HOH579 2.4 34.3 1.0
OE2 A:GLU282 2.5 34.6 1.0
O3B A:ATP407 2.9 34.3 1.0
PG A:ATP407 3.2 35.3 1.0
O A:HOH573 3.4 41.0 1.0
CD A:GLU282 3.5 36.5 1.0
CG A:ASP270 3.6 52.8 1.0
PA A:ATP407 3.7 34.8 1.0
ND2 A:ASN281 3.8 33.9 1.0
PB A:ATP407 3.8 31.7 1.0
O2B A:ATP407 3.9 35.8 1.0
CG A:GLU282 3.9 34.4 1.0
O1G A:ATP407 4.0 32.3 1.0
NH1 A:ARG268 4.0 44.8 1.0
O3A A:ATP407 4.0 33.8 1.0
ND2 A:ASN284 4.2 40.7 1.0
MG A:MG404 4.2 32.1 1.0
CB A:ASP270 4.2 37.0 1.0
O3G A:ATP407 4.4 31.4 1.0
NZ A:LYS228 4.4 32.3 1.0
O5' A:ATP407 4.6 37.7 1.0
OD1 A:ASP270 4.6 55.9 1.0
OE1 A:GLU282 4.6 31.3 1.0
O3' A:ATP407 4.6 38.0 1.0
C5' A:ATP407 4.7 30.6 1.0
O2A A:ATP407 4.8 34.8 1.0
CG A:ASN281 5.0 35.2 1.0

Magnesium binding site 2 out of 4 in 6u1e

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg404

b:32.1
occ:1.00
O1G A:ATP407 1.9 32.3 1.0
O A:HOH585 2.0 27.8 1.0
OE2 A:GLU282 2.1 34.6 1.0
O2B A:ATP407 2.1 35.8 1.0
OD1 A:ASN284 2.1 31.3 1.0
OE1 A:GLU282 2.2 31.3 1.0
CD A:GLU282 2.4 36.5 1.0
PG A:ATP407 3.1 35.3 1.0
CG A:ASN284 3.1 36.3 1.0
PB A:ATP407 3.2 31.7 1.0
ND2 A:ASN284 3.4 40.7 1.0
O3B A:ATP407 3.4 34.3 1.0
RB A:RB405 3.6 37.9 0.8
O2G A:ATP407 3.6 33.3 1.0
NZ A:LYS116 3.9 33.7 1.0
CG A:GLU282 3.9 34.4 1.0
O1B A:ATP407 4.0 34.2 1.0
MG A:MG403 4.2 36.3 0.9
O A:THR157 4.2 32.0 1.0
O A:HOH595 4.3 38.5 1.0
O3G A:ATP407 4.4 31.4 1.0
CB A:ASN284 4.5 31.4 1.0
O A:HOH596 4.5 37.1 1.0
N A:DAL401 4.5 36.9 1.0
O3A A:ATP407 4.6 33.8 1.0
CA A:GLY158 4.6 32.2 1.0
O1A A:ATP407 4.7 37.1 1.0
CB A:GLU282 4.8 31.7 1.0

Magnesium binding site 3 out of 4 in 6u1e

Go back to Magnesium Binding Sites List in 6u1e
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:45.3
occ:1.00
O1A B:ATP407 2.2 43.1 1.0
O2G B:ATP407 2.3 39.6 1.0
OD2 B:ASP270 2.3 58.4 1.0
O B:HOH555 2.5 43.8 1.0
OE2 B:GLU282 2.5 40.5 1.0
O3B B:ATP407 3.0 44.5 1.0
PG B:ATP407 3.2 42.8 1.0
O B:HOH522 3.3 46.5 1.0
CD B:GLU282 3.5 44.6 1.0
CG B:ASP270 3.5 63.3 1.0
PA B:ATP407 3.6 41.5 1.0
ND2 B:ASN281 3.7 42.1 1.0
O2B B:ATP407 3.8 48.2 1.0
CG B:GLU282 3.8 40.9 1.0
PB B:ATP407 3.8 42.4 1.0
NH1 B:ARG268 3.9 45.6 1.0
O3A B:ATP407 4.0 45.2 1.0
O1G B:ATP407 4.0 43.9 1.0
CB B:ASP270 4.1 42.1 1.0
ND2 B:ASN284 4.2 45.3 1.0
MG B:MG404 4.3 39.4 1.0
O3G B:ATP407 4.4 39.9 1.0
O5' B:ATP407 4.4 47.1 1.0
OD1 B:ASP270 4.5 59.5 1.0
NZ B:LYS228 4.5 45.0 1.0
OE1 B:GLU282 4.6 36.2 1.0
C5' B:ATP407 4.6 48.6 1.0
O3' B:ATP407 4.7 46.6 1.0
O2A B:ATP407 4.7 43.1 1.0
CG B:ASN281 4.9 40.8 1.0
OE2 B:GLU199 4.9 64.7 1.0
C3' B:ATP407 5.0 45.1 1.0

Magnesium binding site 4 out of 4 in 6u1e

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg404

b:39.4
occ:1.00
O1G B:ATP407 1.9 43.9 1.0
O B:HOH574 2.0 32.6 1.0
OD1 B:ASN284 2.1 39.2 1.0
OE2 B:GLU282 2.1 40.5 1.0
O2B B:ATP407 2.2 48.2 1.0
OE1 B:GLU282 2.2 36.2 1.0
CD B:GLU282 2.4 44.6 1.0
CG B:ASN284 3.1 40.1 1.0
PG B:ATP407 3.1 42.8 1.0
PB B:ATP407 3.3 42.4 1.0
ND2 B:ASN284 3.5 45.3 1.0
O3B B:ATP407 3.6 44.5 1.0
RB B:RB405 3.6 41.0 0.8
O2G B:ATP407 3.6 39.6 1.0
NZ B:LYS116 3.9 41.0 1.0
CG B:GLU282 3.9 40.9 1.0
O1B B:ATP407 4.0 40.7 1.0
O B:THR157 4.2 39.7 1.0
O B:HOH583 4.3 43.0 1.0
MG B:MG403 4.3 45.3 1.0
O B:HOH569 4.3 46.2 1.0
O3G B:ATP407 4.4 39.9 1.0
CB B:ASN284 4.5 38.5 1.0
N B:DAL401 4.5 40.6 1.0
CA B:GLY158 4.6 43.7 1.0
O3A B:ATP407 4.6 45.2 1.0
O1A B:ATP407 4.6 43.1 1.0
CB B:GLU282 4.8 37.4 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: Tue Dec 15 00:59:02 2020

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