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Magnesium 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:

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

Magnesium binding site 1 out of 4 in 6u1d

Go back to Magnesium Binding Sites List in 6u1d
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:32.2
occ:1.00
 O A:HOH570 2.3 30.8 1.0
O1A A:ATP407 2.4 32.5 1.0
O2G A:ATP407 2.4 30.8 1.0
OD2 A:ASP270 2.5 39.6 1.0
OE2 A:GLU282 2.5 30.7 1.0
O3B A:ATP407 2.7 29.2 1.0
PG A:ATP407 3.2 31.1 1.0
CD A:GLU282 3.5 33.2 1.0
O A:HOH537 3.6 34.8 1.0
CG A:ASP270 3.6 41.1 1.0
PA A:ATP407 3.7 31.8 1.0
PB A:ATP407 3.9 30.2 1.0
ND2 A:ASN281 3.9 29.9 1.0
CG A:GLU282 3.9 30.1 1.0
NH1 A:ARG268 3.9 33.0 1.0
O1G A:ATP407 4.0 29.9 1.0
O3A A:ATP407 4.0 33.8 1.0
MG A:MG404 4.0 29.0 1.0
O A:HOH517 4.1 48.4 1.0
O2B A:ATP407 4.1 29.4 1.0
CB A:ASP270 4.2 32.8 1.0
ND2 A:ASN284 4.2 33.5 1.0
NZ A:LYS228 4.3 32.7 1.0
O3G A:ATP407 4.4 30.4 1.0
O3' A:ATP407 4.5 32.6 1.0
O5' A:ATP407 4.6 31.4 1.0
OE1 A:GLU282 4.6 28.8 1.0
OD1 A:ASP270 4.6 41.3 1.0
C5' A:ATP407 4.7 33.2 1.0
O2A A:ATP407 4.8 31.3 1.0

Magnesium binding site 2 out of 4 in 6u1d

Go back to Magnesium Binding Sites List in 6u1d
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:29.0
occ:1.00
 O1G A:ATP407 1.9 29.9 1.0
O A:HOH594 2.0 28.6 1.0
OE2 A:GLU282 2.0 30.7 1.0
O2B A:ATP407 2.1 29.4 1.0
OE1 A:GLU282 2.1 28.8 1.0
OD1 A:ASN284 2.2 28.8 1.0
CD A:GLU282 2.4 33.2 1.0
PG A:ATP407 3.1 31.1 1.0
CG A:ASN284 3.1 35.5 1.0
PB A:ATP407 3.2 30.2 1.0
O3B A:ATP407 3.2 29.2 1.0
ND2 A:ASN284 3.5 33.5 1.0
RB A:RB405 3.7 28.8 0.8
O2G A:ATP407 3.7 30.8 1.0
CG A:GLU282 3.9 30.1 1.0
NZ A:LYS116 3.9 29.1 1.0
MG A:MG403 4.0 32.2 1.0
O1B A:ATP407 4.1 31.6 1.0
O A:THR157 4.2 29.8 1.0
O3G A:ATP407 4.4 30.4 1.0
N A:DAL401 4.4 31.5 1.0
O A:HOH606 4.4 34.4 1.0
CA A:GLY158 4.4 30.1 1.0
O3A A:ATP407 4.5 33.8 1.0
O A:HOH568 4.5 34.5 1.0
CB A:ASN284 4.5 27.0 1.0
O1A A:ATP407 4.7 32.5 1.0
CB A:GLU282 4.8 29.9 1.0

Magnesium binding site 3 out of 4 in 6u1d

Go back to Magnesium Binding Sites List in 6u1d
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:39.1
occ:1.00
 O1A B:ATP407 2.3 38.3 1.0
O3G B:ATP407 2.4 33.4 1.0
OE2 B:GLU282 2.4 32.3 1.0
OD2 B:ASP270 2.4 49.8 1.0
O B:HOH602 2.5 37.9 1.0
O3B B:ATP407 2.7 38.2 1.0
PG B:ATP407 3.2 38.8 1.0
CD B:GLU282 3.4 40.4 1.0
O B:HOH515 3.4 41.5 1.0
CG B:ASP270 3.6 51.7 1.0
PA B:ATP407 3.6 38.9 1.0
CG B:GLU282 3.8 36.2 1.0
ND2 B:ASN281 3.8 38.4 1.0
PB B:ATP407 3.8 38.4 1.0
O3A B:ATP407 3.9 36.8 1.0
NH1 B:ARG268 3.9 36.8 1.0
O1G B:ATP407 4.0 38.5 1.0
MG B:MG404 4.0 36.9 1.0
O1B B:ATP407 4.1 39.7 1.0
CB B:ASP270 4.1 40.5 1.0
ND2 B:ASN284 4.1 37.1 1.0
O2G B:ATP407 4.4 38.6 1.0
NZ B:LYS228 4.5 44.5 1.0
OE1 B:GLU282 4.5 33.3 1.0
O5' B:ATP407 4.6 42.5 1.0
OD1 B:ASP270 4.6 46.4 1.0
C5' B:ATP407 4.6 41.8 1.0
O3' B:ATP407 4.7 42.8 1.0
O2A B:ATP407 4.7 39.0 1.0
CG B:ASN281 4.9 38.5 1.0
OE2 B:GLU199 5.0 48.6 1.0

Magnesium binding site 4 out of 4 in 6u1d

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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:36.9
occ:1.00
 O1G B:ATP407 1.9 38.5 1.0
O B:HOH598 2.1 33.7 1.0
OE2 B:GLU282 2.1 32.3 1.0
O1B B:ATP407 2.1 39.7 1.0
OD1 B:ASN284 2.1 35.2 1.0
OE1 B:GLU282 2.2 33.3 1.0
CD B:GLU282 2.5 40.4 1.0
PG B:ATP407 3.0 38.8 1.0
CG B:ASN284 3.1 36.1 1.0
PB B:ATP407 3.1 38.4 1.0
O3B B:ATP407 3.1 38.2 1.0
ND2 B:ASN284 3.4 37.1 1.0
O3G B:ATP407 3.7 33.4 1.0
RB B:RB405 3.7 29.9 0.7
NZ B:LYS116 4.0 38.4 1.0
CG B:GLU282 4.0 36.2 1.0
MG B:MG403 4.0 39.1 1.0
O2B B:ATP407 4.1 37.3 1.0
O B:THR157 4.2 40.2 1.0
O2G B:ATP407 4.3 38.6 1.0
O B:HOH633 4.3 40.0 1.0
CA B:GLY158 4.3 37.4 1.0
N B:DAL401 4.3 38.5 1.0
O3A B:ATP407 4.4 36.8 1.0
CB B:ASN284 4.5 33.3 1.0
O B:HOH570 4.6 42.4 1.0
O1A B:ATP407 4.8 38.3 1.0
CB B:GLU282 4.9 35.4 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 Oct 1 20:39:38 2024

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