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Magnesium in PDB 6u1f: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+

Enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+

All present enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+:
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 Cs+, PDB code: 6u1f 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) 47.72 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.431, 95.431, 192.075, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.6

Other elements in 6u1f:

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Alanine-D-Alanine, MG2+ and Cs+ also contains other interesting chemical elements:

Caesium (Cs) 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 Cs+ (pdb code 6u1f). 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 Cs+, PDB code: 6u1f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6u1f

Go back to Magnesium Binding Sites List in 6u1f
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 Cs+


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 Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:45.4
occ:1.00
 O1A A:ATP407 2.2 40.9 1.0
O A:HOH553 2.2 44.5 1.0
O1G A:ATP407 2.3 47.1 1.0
OE2 A:GLU282 2.4 46.8 1.0
O3B A:ATP407 2.5 40.0 1.0
OD2 A:ASP270 2.5 57.3 1.0
PG A:ATP407 3.0 44.5 1.0
CD A:GLU282 3.3 47.0 1.0
PA A:ATP407 3.5 42.9 1.0
O A:HOH556 3.6 50.0 1.0
PB A:ATP407 3.7 47.2 1.0
CG A:GLU282 3.7 46.6 1.0
CG A:ASP270 3.7 58.4 1.0
O3G A:ATP407 3.8 49.0 1.0
ND2 A:ASN281 3.8 45.2 1.0
O2B A:ATP407 3.9 47.0 1.0
O3A A:ATP407 3.9 40.8 1.0
NH1 A:ARG268 4.1 50.9 1.0
MG A:MG404 4.1 43.6 1.0
ND2 A:ASN284 4.2 45.6 1.0
O2G A:ATP407 4.2 46.1 1.0
OE1 A:GLU282 4.3 44.9 1.0
NZ A:LYS228 4.3 48.0 1.0
CB A:ASP270 4.4 36.5 1.0
O5' A:ATP407 4.5 50.6 1.0
O2A A:ATP407 4.5 50.9 1.0
C5' A:ATP407 4.7 47.8 1.0
O3' A:ATP407 4.7 50.9 1.0
OD1 A:ASP270 4.7 54.1 1.0
OD1 A:ASN284 5.0 46.9 1.0
O1B A:ATP407 5.0 46.0 1.0
CG A:ASN281 5.0 43.3 1.0
OE2 A:GLU199 5.0 56.5 1.0

Magnesium binding site 2 out of 4 in 6u1f

Go back to Magnesium Binding Sites List in 6u1f
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 Cs+


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 Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:43.6
occ:1.00
 O3G A:ATP407 1.8 49.0 1.0
OE1 A:GLU282 2.1 44.9 1.0
O A:HOH504 2.2 45.4 1.0
OE2 A:GLU282 2.2 46.8 1.0
OD1 A:ASN284 2.2 46.9 1.0
O2B A:ATP407 2.3 47.0 1.0
CD A:GLU282 2.5 47.0 1.0
PG A:ATP407 3.1 44.5 1.0
CG A:ASN284 3.3 43.4 1.0
PB A:ATP407 3.3 47.2 1.0
O3B A:ATP407 3.4 40.0 1.0
CS A:CS405 3.5 47.4 0.7
ND2 A:ASN284 3.7 45.6 1.0
O1G A:ATP407 3.7 47.1 1.0
NZ A:LYS116 3.8 45.7 1.0
CG A:GLU282 4.0 46.6 1.0
O A:THR157 4.0 50.4 1.0
MG A:MG403 4.1 45.4 1.0
O1B A:ATP407 4.1 46.0 1.0
O2G A:ATP407 4.3 46.1 1.0
O A:HOH526 4.3 48.3 1.0
O A:HOH518 4.4 45.8 1.0
CA A:GLY158 4.5 47.1 1.0
N A:DAL401 4.5 49.7 1.0
CB A:ASN284 4.6 39.6 1.0
O3A A:ATP407 4.6 40.8 1.0
CB A:GLU282 4.7 40.2 1.0
O1A A:ATP407 4.8 40.9 1.0
CE A:LYS116 4.9 45.6 1.0
C A:THR157 5.0 48.9 1.0

Magnesium binding site 3 out of 4 in 6u1f

Go back to Magnesium Binding Sites List in 6u1f
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 Cs+


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 Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:38.9
occ:1.00
 O B:HOH542 1.9 34.2 1.0
O3G B:ATP407 1.9 36.6 1.0
OE1 B:GLU282 2.0 34.9 1.0
OD1 B:ASN284 2.0 36.0 1.0
OE2 B:GLU282 2.3 38.5 1.0
O2B B:ATP407 2.3 38.0 1.0
CD B:GLU282 2.4 40.2 1.0
CG B:ASN284 3.1 39.8 1.0
PG B:ATP407 3.2 40.8 1.0
PB B:ATP407 3.4 35.2 1.0
ND2 B:ASN284 3.4 42.2 1.0
O3B B:ATP407 3.5 38.5 1.0
CS B:CS405 3.5 45.0 0.9
O1G B:ATP407 3.8 34.0 1.0
CG B:GLU282 3.9 38.1 1.0
NZ B:LYS116 4.0 37.8 1.0
O B:THR157 4.1 39.9 1.0
MG B:MG404 4.2 39.5 0.9
O1B B:ATP407 4.3 38.5 1.0
O B:HOH561 4.3 40.2 1.0
O2G B:ATP407 4.4 32.3 1.0
O B:HOH532 4.4 43.0 1.0
CB B:ASN284 4.4 36.4 1.0
CA B:GLY158 4.5 33.8 1.0
N B:DAL401 4.6 33.7 1.0
CB B:GLU282 4.7 36.6 1.0
O3A B:ATP407 4.7 42.1 1.0
O1A B:ATP407 4.7 42.4 1.0

Magnesium binding site 4 out of 4 in 6u1f

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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 Cs+


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 Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:39.5
occ:0.92
 O1A B:ATP407 2.2 42.4 1.0
OE2 B:GLU282 2.2 38.5 1.0
O B:HOH560 2.3 39.3 1.0
O1G B:ATP407 2.4 34.0 1.0
OD2 B:ASP270 2.4 51.8 1.0
O3B B:ATP407 2.7 38.5 1.0
PG B:ATP407 3.1 40.8 1.0
CD B:GLU282 3.3 40.2 1.0
O B:HOH540 3.5 41.2 1.0
PA B:ATP407 3.6 35.1 1.0
CG B:ASP270 3.6 48.1 1.0
ND2 B:ASN281 3.7 42.2 1.0
CG B:GLU282 3.8 38.1 1.0
PB B:ATP407 3.8 35.2 1.0
O3G B:ATP407 3.9 36.6 1.0
NH1 B:ARG268 4.0 40.3 1.0
O3A B:ATP407 4.0 42.1 1.0
O2B B:ATP407 4.1 38.0 1.0
CB B:ASP270 4.2 37.3 1.0
MG B:MG403 4.2 38.9 1.0
O2G B:ATP407 4.4 32.3 1.0
ND2 B:ASN284 4.4 42.2 1.0
NZ B:LYS228 4.4 37.6 1.0
OE1 B:GLU282 4.4 34.9 1.0
O5' B:ATP407 4.5 40.8 1.0
O3' B:ATP407 4.5 35.6 1.0
C5' B:ATP407 4.6 37.1 1.0
OD1 B:ASP270 4.6 47.0 1.0
O2A B:ATP407 4.7 37.0 1.0
CG B:ASN281 4.9 41.9 1.0
C3' B:ATP407 5.0 38.3 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 Aug 13 18:21:28 2025

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