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Magnesium in PDB 6u1g: 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: 6u1g 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) 47.85 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.692, 95.692, 192.402, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.3

Other elements in 6u1g:

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 6u1g). 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: 6u1g:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6u1g

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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 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:Mg405

b:48.8
occ:1.00
 O1A A:ATP407 2.2 42.3 1.0
OE2 A:GLU282 2.4 48.8 1.0
O3B A:ATP407 2.4 42.4 1.0
O3G A:ATP407 2.4 49.3 1.0
O A:HOH549 2.5 58.5 1.0
OD2 A:ASP270 2.6 61.2 1.0
PG A:ATP407 3.0 43.5 1.0
CD A:GLU282 3.4 49.4 1.0
PA A:ATP407 3.5 43.7 1.0
PB A:ATP407 3.6 43.5 1.0
O3A A:ATP407 3.8 47.8 1.0
CG A:ASP270 3.8 59.3 1.0
CG A:GLU282 3.9 46.6 1.0
O2G A:ATP407 3.9 43.7 1.0
ND2 A:ASN281 3.9 42.0 1.0
O2B A:ATP407 3.9 45.2 1.0
NZ A:LYS228 4.0 47.8 1.0
MG A:MG406 4.1 44.4 0.8
O1G A:ATP407 4.1 45.1 1.0
NH1 A:ARG268 4.2 45.6 1.0
ND2 A:ASN284 4.3 42.4 1.0
O5' A:ATP407 4.4 49.9 1.0
CB A:ASP270 4.5 40.0 1.0
OE1 A:GLU282 4.5 47.4 1.0
O3' A:ATP407 4.6 57.1 1.0
O2A A:ATP407 4.6 48.0 1.0
C5' A:ATP407 4.7 42.3 1.0
OD1 A:ASP270 4.8 54.8 1.0
O1B A:ATP407 4.9 43.9 1.0
CE A:LYS228 4.9 48.7 1.0
OE2 A:GLU199 5.0 57.6 1.0
C3' A:ATP407 5.0 48.8 1.0

Magnesium binding site 2 out of 4 in 6u1g

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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 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:Mg406

b:44.4
occ:0.81
 O2G A:ATP407 1.9 43.7 1.0
O A:HOH512 1.9 39.5 1.0
OD1 A:ASN284 2.0 47.6 1.0
OE1 A:GLU282 2.0 47.4 1.0
OE2 A:GLU282 2.1 48.8 1.0
CD A:GLU282 2.3 49.4 1.0
O2B A:ATP407 2.5 45.2 1.0
CG A:ASN284 3.0 42.9 1.0
PG A:ATP407 3.0 43.5 1.0
ND2 A:ASN284 3.4 42.4 1.0
O3B A:ATP407 3.4 42.4 1.0
PB A:ATP407 3.4 43.5 1.0
CS A:CS403 3.5 45.0 0.7
O3G A:ATP407 3.5 49.3 1.0
CG A:GLU282 3.8 46.6 1.0
NZ A:LYS116 4.0 47.0 1.0
MG A:MG405 4.1 48.8 1.0
O A:THR157 4.2 52.3 1.0
O1B A:ATP407 4.3 43.9 1.0
O A:HOH544 4.3 43.8 1.0
O1G A:ATP407 4.3 45.1 1.0
CB A:ASN284 4.3 39.5 1.0
N A:DAL401 4.4 46.4 1.0
O A:HOH514 4.5 50.7 1.0
CB A:GLU282 4.6 34.6 1.0
CA A:GLY158 4.7 42.5 1.0
O1A A:ATP407 4.7 42.3 1.0
O3A A:ATP407 4.8 47.8 1.0
CE A:LYS116 5.0 38.6 1.0
CA A:ASN284 5.0 37.2 1.0

Magnesium binding site 3 out of 4 in 6u1g

Go back to Magnesium Binding Sites List in 6u1g
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:Mg405

b:37.2
occ:0.96
 O B:HOH519 1.9 44.2 1.0
O1G B:ATP407 1.9 37.5 1.0
OE1 B:GLU282 2.0 36.2 1.0
OD1 B:ASN284 2.0 43.6 1.0
O2B B:ATP407 2.4 38.6 1.0
OE2 B:GLU282 2.6 36.9 1.0
CD B:GLU282 2.6 44.0 1.0
CG B:ASN284 3.0 41.1 1.0
PG B:ATP407 3.2 35.6 1.0
ND2 B:ASN284 3.4 45.9 1.0
CS B:CS403 3.4 44.3 0.8
PB B:ATP407 3.4 32.6 1.0
O3B B:ATP407 3.7 37.9 1.0
O2G B:ATP407 3.7 37.1 1.0
O B:HOH569 3.9 44.9 1.0
NZ B:LYS116 3.9 36.9 1.0
CG B:GLU282 4.1 38.2 1.0
O1B B:ATP407 4.1 39.0 1.0
O B:THR157 4.1 36.9 1.0
CB B:ASN284 4.4 39.3 1.0
O3G B:ATP407 4.4 32.7 1.0
MG B:MG406 4.4 32.1 0.9
N B:DAL401 4.5 37.2 1.0
O B:HOH558 4.5 42.2 1.0
CA B:GLY158 4.5 30.5 1.0
CB B:GLU282 4.7 34.4 1.0
O3A B:ATP407 4.8 47.9 1.0
O1A B:ATP407 4.9 43.3 1.0
CE B:LYS116 5.0 41.8 1.0

Magnesium binding site 4 out of 4 in 6u1g

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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:Mg406

b:32.1
occ:0.86
 OE2 B:GLU282 2.2 36.9 1.0
O2G B:ATP407 2.2 37.1 1.0
O1A B:ATP407 2.3 43.3 1.0
O B:HOH548 2.4 42.4 1.0
OD2 B:ASP270 2.4 55.1 1.0
O3B B:ATP407 2.9 37.9 1.0
PG B:ATP407 3.1 35.6 1.0
CD B:GLU282 3.3 44.0 1.0
CG B:ASP270 3.6 55.3 1.0
PA B:ATP407 3.7 35.0 1.0
CG B:GLU282 3.8 38.2 1.0
ND2 B:ASN281 3.8 41.0 1.0
PB B:ATP407 3.9 32.6 1.0
NH1 B:ARG268 3.9 44.6 1.0
O2B B:ATP407 3.9 38.6 1.0
O1G B:ATP407 4.0 37.5 1.0
O3A B:ATP407 4.1 47.9 1.0
ND2 B:ASN284 4.2 45.9 1.0
CB B:ASP270 4.2 37.5 1.0
O3G B:ATP407 4.3 32.7 1.0
NZ B:LYS228 4.3 33.7 1.0
OE1 B:GLU282 4.4 36.2 1.0
MG B:MG405 4.4 37.2 1.0
O5' B:ATP407 4.6 43.4 1.0
OD1 B:ASP270 4.6 48.1 1.0
O3' B:ATP407 4.7 38.3 1.0
C5' B:ATP407 4.7 32.2 1.0
O2A B:ATP407 4.8 37.3 1.0
CG B:ASN281 5.0 41.2 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 20:42:12 2024

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