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Magnesium in PDB 6u1i: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+

Enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+

All present enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+:
6.3.2.4;

Protein crystallography data

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+, PDB code: 6u1i was solved by J.L.Pederick, J.B.Bruning, A.P.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.83 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.369, 68.453, 91.747, 69.50, 78.86, 66.05
R / Rfree (%) 23.8 / 28

Other elements in 6u1i:

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+ also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+ (pdb code 6u1i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+, PDB code: 6u1i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6u1i

Go back to Magnesium Binding Sites List in 6u1i
Magnesium binding site 1 out of 2 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+


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 Adp, Phosphorylated D-Cycloserine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:14.8
occ:0.87
 O9 C:DS0405 1.8 18.9 0.9
OE2 C:GLU282 2.1 18.9 1.0
O C:HOH514 2.1 16.7 1.0
O1A C:ADP404 2.2 19.4 0.9
O2B C:ADP404 2.2 15.5 0.9
O C:HOH502 2.4 19.8 1.0
P8 C:DS0405 3.1 15.6 0.9
CD C:GLU282 3.2 17.4 1.0
O11 C:DS0405 3.4 18.1 0.9
PB C:ADP404 3.4 14.4 0.9
MG C:MG402 3.5 14.9 1.0
PA C:ADP404 3.6 17.2 0.9
OD2 C:ASP270 3.6 12.5 1.0
O1B C:ADP404 3.6 12.2 0.9
CG C:GLU282 3.9 15.4 1.0
O3A C:ADP404 4.0 15.2 0.9
NZ C:LYS228 4.0 18.3 1.0
O10 C:DS0405 4.1 15.2 0.9
ND2 C:ASN284 4.1 15.1 1.0
OE1 C:GLU282 4.2 15.7 1.0
O7 C:DS0405 4.2 12.9 0.9
ND2 C:ASN281 4.3 15.7 1.0
C5' C:ADP404 4.4 19.0 0.9
O5' C:ADP404 4.4 18.2 0.9
NH1 C:ARG268 4.4 14.0 1.0
O C:HOH556 4.5 16.4 1.0
O3' C:ADP404 4.6 21.5 0.9
O3B C:ADP404 4.7 15.1 0.9
O2A C:ADP404 4.7 19.8 0.9
CG C:ASP270 4.7 13.4 1.0
OD1 C:ASN284 4.7 9.6 1.0
CE C:LYS228 4.8 20.5 1.0
CG C:ASN284 4.9 14.2 1.0

Magnesium binding site 2 out of 2 in 6u1i

Go back to Magnesium Binding Sites List in 6u1i
Magnesium binding site 2 out of 2 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+


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 Adp, Phosphorylated D-Cycloserine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:14.9
occ:1.00
 O11 C:DS0405 2.0 18.1 0.9
OE1 C:GLU282 2.2 15.7 1.0
OD1 C:ASN284 2.2 9.6 1.0
OE2 C:GLU282 2.3 18.9 1.0
O1B C:ADP404 2.3 12.2 0.9
O C:HOH540 2.4 17.0 1.0
CD C:GLU282 2.5 17.4 1.0
CG C:ASN284 3.1 14.2 1.0
P8 C:DS0405 3.3 15.6 0.9
PB C:ADP404 3.3 14.4 0.9
ND2 C:ASN284 3.4 15.1 1.0
O2B C:ADP404 3.5 15.5 0.9
MG C:MG401 3.5 14.8 0.9
O9 C:DS0405 3.6 18.9 0.9
K C:K403 3.7 9.5 0.7
NZ C:LYS116 4.0 14.6 1.0
O7 C:DS0405 4.0 12.9 0.9
CG C:GLU282 4.0 15.4 1.0
N6 C:DS0405 4.2 12.6 0.9
O C:THR157 4.2 20.4 1.0
O3B C:ADP404 4.3 15.1 0.9
CA C:GLY158 4.3 19.2 1.0
O1A C:ADP404 4.3 19.4 0.9
O C:HOH552 4.4 10.2 1.0
O10 C:DS0405 4.4 15.2 0.9
CB C:ASN284 4.5 11.6 1.0
O3A C:ADP404 4.6 15.2 0.9
C3 C:DS0405 4.6 13.9 0.9
O C:HOH548 4.7 19.1 1.0
CB C:GLU282 4.9 12.8 1.0
C4 C:DS0405 4.9 16.6 0.9
N C:SER159 4.9 19.3 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: Tue Oct 1 20:42:32 2024

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