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Magnesium in PDB 6u1h: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, MG2+ and K+

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

All present enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, 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, MG2+ and K+, PDB code: 6u1h 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) 42.43 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.291, 68.616, 91.646, 69.55, 78.97, 66.10
R / Rfree (%) 21.8 / 26.5

Other elements in 6u1h:

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, 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, MG2+ and K+ (pdb code 6u1h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, MG2+ and K+, PDB code: 6u1h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6u1h

Go back to Magnesium Binding Sites List in 6u1h
Magnesium binding site 1 out of 5 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, 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, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:32.1
occ:0.87
 O1B A:ADP405 2.0 22.7 1.0
O A:HOH567 2.0 33.1 1.0
OE1 A:GLU282 2.2 28.2 1.0
O3 A:PO4403 2.3 27.6 0.7
OE2 A:GLU282 2.3 25.4 1.0
OD1 A:ASN284 2.5 26.2 1.0
CD A:GLU282 2.5 32.9 1.0
PB A:ADP405 3.2 29.8 1.0
O3B A:ADP405 3.5 34.8 1.0
P A:PO4403 3.5 33.8 0.7
CG A:ASN284 3.6 32.2 1.0
O2 A:PO4403 3.6 30.1 0.7
K A:K404 3.6 27.4 0.7
MG A:MG402 3.7 29.6 1.0
NZ A:LYS116 3.9 32.1 1.0
CG A:GLU282 3.9 25.6 1.0
ND2 A:ASN284 4.0 27.6 1.0
O A:THR157 4.0 34.4 1.0
O2B A:ADP405 4.1 30.9 1.0
CA A:GLY158 4.2 36.4 1.0
O A:HOH558 4.3 35.6 1.0
O3A A:ADP405 4.4 38.1 1.0
O4 A:PO4403 4.4 28.1 0.7
O1 A:PO4403 4.5 29.0 0.7
O1A A:ADP405 4.5 32.9 1.0
CB A:GLU282 4.8 20.8 1.0
N A:SER159 4.8 38.1 1.0
CB A:ASN284 4.9 24.9 1.0
C A:THR157 4.9 37.5 1.0
CE A:LYS116 5.0 30.0 1.0
PA A:ADP405 5.0 31.4 1.0

Magnesium binding site 2 out of 5 in 6u1h

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Magnesium binding site 2 out of 5 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, 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, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:29.6
occ:0.98
 O2 A:PO4403 2.0 30.1 0.7
O A:HOH503 2.0 24.3 1.0
O1A A:ADP405 2.1 32.9 1.0
O3B A:ADP405 2.1 34.8 1.0
OE2 A:GLU282 2.1 25.4 1.0
O A:HOH550 2.1 30.6 1.0
PB A:ADP405 3.2 29.8 1.0
P A:PO4403 3.3 33.8 0.7
CD A:GLU282 3.3 32.9 1.0
O A:HOH535 3.3 32.5 1.0
PA A:ADP405 3.4 31.4 1.0
O1B A:ADP405 3.5 22.7 1.0
NZ A:LYS228 3.6 39.6 1.0
O3 A:PO4403 3.7 27.6 0.7
MG A:MG401 3.7 32.1 0.9
O3A A:ADP405 3.7 38.1 1.0
OD2 A:ASP270 3.8 27.6 1.0
O4 A:PO4403 3.8 28.1 0.7
CG A:GLU282 4.0 25.6 1.0
ND2 A:ASN281 4.1 28.6 1.0
C5' A:ADP405 4.2 33.5 1.0
OE1 A:GLU282 4.3 28.2 1.0
O5' A:ADP405 4.3 26.8 1.0
O3' A:ADP405 4.4 38.0 1.0
O1 A:PO4403 4.4 29.0 0.7
O2B A:ADP405 4.5 30.9 1.0
ND2 A:ASN284 4.5 27.6 1.0
CE A:LYS228 4.6 37.1 1.0
O2A A:ADP405 4.6 30.5 1.0
C3' A:ADP405 4.8 33.0 1.0
NH1 A:ARG268 4.9 26.6 1.0
OD1 A:ASN284 4.9 26.2 1.0
CG A:ASP270 4.9 27.9 1.0

Magnesium binding site 3 out of 5 in 6u1h

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Magnesium binding site 3 out of 5 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, 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, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:44.6
occ:1.00
 O2B B:ADP402 1.9 36.2 1.0
OE2 B:GLU282 2.1 44.0 1.0
O2A B:ADP402 2.1 34.8 1.0
O B:HOH506 2.3 26.9 1.0
O B:HOH551 2.4 24.9 1.0
PB B:ADP402 3.3 39.5 1.0
CD B:GLU282 3.3 39.1 1.0
PA B:ADP402 3.5 37.4 1.0
O3A B:ADP402 3.8 37.9 1.0
OD2 B:ASP270 3.9 31.4 1.0
O3B B:ADP402 4.0 48.3 1.0
OE1 B:GLU282 4.2 40.0 1.0
CG B:GLU282 4.2 34.2 1.0
C5' B:ADP402 4.2 28.8 1.0
O5' B:ADP402 4.2 28.8 1.0
ND2 B:ASN281 4.3 37.5 1.0
O1B B:ADP402 4.4 37.2 1.0
O3' B:ADP402 4.5 44.1 1.0
NH2 B:ARG268 4.6 31.0 1.0
ND2 B:ASN284 4.7 34.8 1.0
O1A B:ADP402 4.7 33.0 1.0
OD1 B:ASN284 4.7 41.6 1.0
C3' B:ADP402 4.8 38.3 1.0

Magnesium binding site 4 out of 5 in 6u1h

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Magnesium binding site 4 out of 5 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, 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, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:39.0
occ:1.00
 O3B C:ADP405 1.9 36.0 1.0
O2 C:PO4403 2.0 25.4 0.8
OE2 C:GLU282 2.0 31.6 1.0
O1A C:ADP405 2.1 34.0 1.0
O C:HOH528 2.1 35.3 1.0
O C:HOH506 2.2 27.6 1.0
PB C:ADP405 3.1 38.5 1.0
P C:PO4403 3.2 41.6 0.8
CD C:GLU282 3.2 32.8 1.0
PA C:ADP405 3.4 36.5 1.0
O1B C:ADP405 3.5 39.1 1.0
MG C:MG402 3.5 40.5 1.0
NZ C:LYS228 3.6 46.5 1.0
O4 C:PO4403 3.7 34.1 0.8
O3A C:ADP405 3.7 30.2 1.0
O3 C:PO4403 3.7 36.2 0.8
OD2 C:ASP270 3.9 34.3 1.0
O C:HOH560 4.0 44.4 1.0
CG C:GLU282 4.1 25.7 1.0
OE1 C:GLU282 4.1 34.2 1.0
C5' C:ADP405 4.2 32.4 1.0
O5' C:ADP405 4.3 33.8 1.0
ND2 C:ASN281 4.3 28.5 1.0
O2B C:ADP405 4.4 32.3 1.0
O1 C:PO4403 4.5 44.0 0.8
CE C:LYS228 4.5 41.9 1.0
O2A C:ADP405 4.6 33.6 1.0
O3' C:ADP405 4.6 32.3 1.0
NH1 C:ARG268 4.6 30.4 1.0
ND2 C:ASN284 4.6 35.4 1.0
OD1 C:ASN284 4.8 37.5 1.0
C3' C:ADP405 4.9 34.5 1.0

Magnesium binding site 5 out of 5 in 6u1h

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Magnesium binding site 5 out of 5 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:40.5
occ:1.00
 O3 C:PO4403 2.1 36.2 0.8
O1B C:ADP405 2.2 39.1 1.0
O C:HOH520 2.2 34.7 1.0
OE1 C:GLU282 2.3 34.2 1.0
OE2 C:GLU282 2.4 31.6 1.0
OD1 C:ASN284 2.5 37.5 1.0
CD C:GLU282 2.7 32.8 1.0
PB C:ADP405 3.1 38.5 1.0
P C:PO4403 3.2 41.6 0.8
O2 C:PO4403 3.3 25.4 0.8
O3B C:ADP405 3.3 36.0 1.0
MG C:MG401 3.5 39.0 1.0
CG C:ASN284 3.6 35.1 1.0
K C:K404 3.8 29.1 0.8
O C:HOH525 4.0 33.6 1.0
O2B C:ADP405 4.0 32.3 1.0
O C:HOH531 4.0 39.3 1.0
CA C:GLY158 4.1 41.2 1.0
ND2 C:ASN284 4.1 35.4 1.0
O C:THR157 4.1 39.9 1.0
O4 C:PO4403 4.1 34.1 0.8
CG C:GLU282 4.2 25.7 1.0
NZ C:LYS116 4.2 37.1 1.0
O1 C:PO4403 4.3 44.0 0.8
O C:HOH559 4.4 35.5 1.0
O3A C:ADP405 4.4 30.2 1.0
O1A C:ADP405 4.5 34.0 1.0
N C:SER159 4.6 41.8 1.0
C C:GLY158 4.9 40.2 1.0
CB C:ASN284 4.9 30.1 1.0
CB C:GLU282 4.9 24.6 1.0
C C:THR157 5.0 38.9 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 20:42:21 2024

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