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Magnesium in PDB 6u1j: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+

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

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

Protein crystallography data

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+, PDB code: 6u1j 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) 34.85 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.613, 69.080, 93.792, 71.37, 80.24, 64.32
R / Rfree (%) 21.9 / 26.2

Other elements in 6u1j:

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

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+ (pdb code 6u1j). 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 Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+, PDB code: 6u1j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6u1j

Go back to Magnesium Binding Sites List in 6u1j
Magnesium binding site 1 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, 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, Phosphate, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:35.4
occ:0.95
 O4 A:PO4405 1.6 39.2 0.6
O2A A:ADP407 1.9 39.5 0.8
O A:HOH507 2.0 34.9 1.0
O A:HOH551 2.0 35.3 1.0
O2B A:ADP407 2.3 38.3 0.8
OE2 A:GLU282 2.4 41.4 1.0
P A:PO4405 3.1 45.4 0.6
PA A:ADP407 3.3 40.4 0.8
PB A:ADP407 3.4 38.7 0.8
CD A:GLU282 3.4 41.7 1.0
O A:HOH585 3.4 42.7 1.0
O3B A:ADP407 3.7 39.0 0.8
O1 A:PO4405 3.7 38.7 0.6
C5' A:ADP407 3.7 42.8 0.8
NZ A:LYS228 3.7 42.2 1.0
O3A A:ADP407 3.7 36.2 0.8
ND2 A:ASN281 3.8 36.3 1.0
OD2 A:ASP270 3.8 33.0 1.0
O5' A:ADP407 3.9 35.9 0.8
O2 A:PO4405 3.9 40.3 0.6
O3 A:PO4405 3.9 33.8 0.6
CG A:GLU282 3.9 34.2 1.0
MG A:MG404 4.1 39.3 0.7
O3' A:ADP407 4.3 40.8 0.8
O A:HOH521 4.4 41.3 1.0
OE1 A:GLU282 4.4 39.5 1.0
O1A A:ADP407 4.5 37.9 0.8
C3' A:ADP407 4.5 38.9 0.8
CE A:LYS228 4.6 46.0 1.0
C4' A:ADP407 4.7 42.6 0.8
O1B A:ADP407 4.7 38.2 0.8
ND2 A:ASN284 4.8 33.8 1.0
NH1 A:ARG268 4.9 34.9 1.0
CG A:ASP270 4.9 32.9 1.0
OD1 A:ASN284 4.9 38.5 1.0
CG A:ASN281 5.0 35.1 1.0

Magnesium binding site 2 out of 4 in 6u1j

Go back to Magnesium Binding Sites List in 6u1j
Magnesium binding site 2 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, 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, Phosphate, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:39.3
occ:0.66
 O3B A:ADP407 1.9 39.0 0.8
O A:HOH544 2.1 38.4 1.0
OE1 A:GLU282 2.2 39.5 1.0
OE2 A:GLU282 2.3 41.4 1.0
O3 A:PO4405 2.5 33.8 0.6
CD A:GLU282 2.5 41.7 1.0
OD1 A:ASN284 2.8 38.5 1.0
PB A:ADP407 3.2 38.7 0.8
K A:K406 3.3 27.9 0.7
O4 A:PO4405 3.5 39.2 0.6
P A:PO4405 3.6 45.4 0.6
O2B A:ADP407 3.6 38.3 0.8
NZ A:LYS116 3.7 41.3 1.0
O A:THR157 3.8 39.9 1.0
O A:HOH581 3.8 34.0 1.0
CG A:ASN284 3.9 37.7 1.0
O1B A:ADP407 4.0 38.2 0.8
O A:HOH587 4.0 44.2 1.0
CG A:GLU282 4.0 34.2 1.0
CA A:GLY158 4.1 37.9 1.0
MG A:MG403 4.1 35.4 0.9
O2A A:ADP407 4.3 39.5 0.8
O3A A:ADP407 4.4 36.2 0.8
O1 A:PO4405 4.4 38.7 0.6
ND2 A:ASN284 4.5 33.8 1.0
CE A:LYS116 4.6 39.2 1.0
C A:THR157 4.7 45.0 1.0
O2 A:PO4405 4.7 40.3 0.6
CB A:GLU282 4.8 38.5 1.0
PA A:ADP407 4.9 40.4 0.8
N A:GLY158 4.9 46.6 1.0
N A:SER159 4.9 40.0 1.0
N A:DAL401 5.0 42.2 0.8

Magnesium binding site 3 out of 4 in 6u1j

Go back to Magnesium Binding Sites List in 6u1j
Magnesium binding site 3 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+


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 Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:34.2
occ:0.64
 O4 C:PO4405 1.7 34.8 0.7
O1A C:ADP407 1.8 39.3 0.9
O3B C:ADP407 2.0 32.4 0.9
OE2 C:GLU282 2.1 36.7 1.0
O C:HOH515 2.2 35.8 1.0
O C:HOH523 2.2 33.5 1.0
P C:PO4405 3.1 37.6 0.7
PA C:ADP407 3.2 37.4 0.9
PB C:ADP407 3.2 33.7 0.9
CD C:GLU282 3.2 35.0 1.0
O3A C:ADP407 3.6 34.4 0.9
O1B C:ADP407 3.6 34.3 0.9
MG C:MG404 3.7 32.2 0.7
O3 C:PO4405 3.7 28.6 0.7
O C:HOH573 3.7 36.9 1.0
OD1 C:ASN281 3.8 42.0 1.0
NZ C:LYS228 3.8 35.5 1.0
CG C:GLU282 3.8 32.1 1.0
O5' C:ADP407 3.9 38.9 0.9
O2 C:PO4405 3.9 34.9 0.7
OD2 C:ASP270 4.0 29.9 1.0
C5' C:ADP407 4.0 38.3 0.9
O1 C:PO4405 4.0 44.8 0.7
OE1 C:GLU282 4.2 35.8 1.0
O3' C:ADP407 4.2 33.3 0.9
O2A C:ADP407 4.4 34.4 0.9
O C:HOH524 4.5 39.6 1.0
O2B C:ADP407 4.5 36.0 0.9
C3' C:ADP407 4.5 35.6 0.9
CE C:LYS228 4.7 39.8 1.0
ND2 C:ASN284 4.7 33.7 1.0
NH1 C:ARG268 4.8 31.6 1.0
C4' C:ADP407 4.8 36.3 0.9
CG C:ASN281 5.0 35.8 1.0

Magnesium binding site 4 out of 4 in 6u1j

Go back to Magnesium Binding Sites List in 6u1j
Magnesium binding site 4 out of 4 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+


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 Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:32.2
occ:0.71
 O3 C:PO4405 1.9 28.6 0.7
O1B C:ADP407 2.1 34.3 0.9
OE1 C:GLU282 2.1 35.8 1.0
OE2 C:GLU282 2.2 36.7 1.0
O C:HOH535 2.2 37.4 1.0
CD C:GLU282 2.4 35.0 1.0
OD1 C:ASN284 2.4 36.8 1.0
P C:PO4405 3.1 37.6 0.7
O4 C:PO4405 3.2 34.8 0.7
PB C:ADP407 3.2 33.7 0.9
O3B C:ADP407 3.4 32.4 0.9
CG C:ASN284 3.4 36.1 1.0
K C:K406 3.5 29.0 0.8
MG C:MG403 3.7 34.2 0.6
NZ C:LYS116 3.7 37.3 1.0
ND2 C:ASN284 3.7 33.7 1.0
O1 C:PO4405 3.8 44.8 0.7
CG C:GLU282 3.9 32.1 1.0
O C:THR157 4.1 39.2 1.0
O2 C:PO4405 4.2 34.9 0.7
O C:HOH545 4.2 39.6 1.0
CA C:GLY158 4.2 33.6 1.0
O1A C:ADP407 4.3 39.3 0.9
O2B C:ADP407 4.3 36.0 0.9
O C:HOH556 4.3 33.2 1.0
O3A C:ADP407 4.3 34.4 0.9
N C:DAL401 4.7 38.7 0.9
CB C:GLU282 4.7 37.4 1.0
CB C:ASN284 4.8 28.7 1.0
CE C:LYS116 4.8 35.2 1.0
PA C:ADP407 4.9 37.4 0.9
N C:SER159 4.9 37.4 1.0
C C:THR157 5.0 37.6 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 18:22:23 2025

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