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Magnesium in PDB 6u1k: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+

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

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

Protein crystallography data

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+, PDB code: 6u1k 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) 43.58 / 1.67
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.909, 68.174, 90.641, 70.79, 79.22, 66.21
R / Rfree (%) 21.8 / 25.4

Other elements in 6u1k:

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

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ (pdb code 6u1k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+, PDB code: 6u1k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6u1k

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Magnesium binding site 1 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:11.5
occ:0.91
 O3B A:ADP406 2.0 11.9 1.0
O A:HOH616 2.0 12.3 1.0
O2 A:CO3407 2.0 14.9 1.0
OE1 A:GLU282 2.2 14.0 1.0
OD1 A:ASN284 2.2 17.7 1.0
OE2 A:GLU282 2.3 12.3 1.0
CD A:GLU282 2.5 14.7 1.0
C A:CO3407 3.0 15.1 1.0
CG A:ASN284 3.2 18.9 1.0
PB A:ADP406 3.2 12.4 1.0
O3 A:CO3407 3.3 12.7 1.0
O2B A:ADP406 3.5 13.7 1.0
ND2 A:ASN284 3.6 14.8 1.0
MG A:MG404 3.6 11.6 0.9
K A:K405 3.6 14.5 1.0
NZ A:LYS116 3.9 18.7 1.0
CG A:GLU282 4.1 14.1 1.0
CA A:GLY158 4.1 16.6 1.0
O1 A:CO3407 4.1 13.9 1.0
O A:THR157 4.2 15.0 1.0
O A:HOH564 4.3 13.7 1.0
O A:HOH622 4.3 23.8 1.0
N A:DAL401 4.3 14.3 1.0
O3A A:ADP406 4.3 14.7 1.0
O1B A:ADP406 4.3 10.1 1.0
O2A A:ADP406 4.6 13.9 1.0
CB A:ASN284 4.6 17.2 1.0
N A:SER159 4.7 13.5 1.0
O A:HOH513 4.9 14.5 1.0
CE A:LYS116 4.9 13.4 1.0
CB A:GLU282 4.9 13.7 1.0
O A:HOH525 5.0 15.0 1.0
C A:GLY158 5.0 13.4 1.0

Magnesium binding site 2 out of 8 in 6u1k

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Magnesium binding site 2 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:11.6
occ:0.88
 O3 A:CO3407 2.0 12.7 1.0
O2B A:ADP406 2.1 13.7 1.0
OE2 A:GLU282 2.1 12.3 1.0
O A:HOH513 2.1 14.5 1.0
O2A A:ADP406 2.1 13.9 1.0
O A:HOH583 2.1 13.4 1.0
C A:CO3407 2.9 15.1 1.0
PB A:ADP406 3.1 12.4 1.0
CD A:GLU282 3.1 14.7 1.0
PA A:ADP406 3.3 14.5 1.0
O3B A:ADP406 3.5 11.9 1.0
O2 A:CO3407 3.5 14.9 1.0
O3A A:ADP406 3.6 14.7 1.0
MG A:MG403 3.6 11.5 0.9
O A:HOH595 3.6 15.5 1.0
O1 A:CO3407 3.7 13.9 1.0
NZ A:LYS228 3.8 11.7 1.0
CG A:GLU282 3.9 14.1 1.0
C5' A:ADP406 4.0 8.0 1.0
OD2 A:ASP270 4.1 20.0 1.0
OE1 A:GLU282 4.1 14.0 1.0
O5' A:ADP406 4.1 13.6 1.0
ND2 A:ASN281 4.3 15.8 1.0
O3' A:ADP406 4.3 11.6 1.0
O A:HOH599 4.3 14.4 1.0
ND2 A:ASN284 4.4 14.8 1.0
O1B A:ADP406 4.5 10.1 1.0
O1A A:ADP406 4.6 14.8 1.0
NH1 A:ARG268 4.6 17.4 1.0
CE A:LYS228 4.7 10.7 1.0
C3' A:ADP406 4.8 15.6 1.0
OD1 A:ASN284 4.9 17.7 1.0
C4' A:ADP406 4.9 16.0 1.0
CG A:ASP270 5.0 23.1 1.0

Magnesium binding site 3 out of 8 in 6u1k

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Magnesium binding site 3 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:19.0
occ:1.00
 O B:HOH508 1.9 18.1 1.0
O1A B:ADP406 2.0 18.6 1.0
O3B B:ADP406 2.1 15.3 1.0
OE2 B:GLU282 2.1 16.5 1.0
O2 B:CO3407 2.2 15.6 1.0
O B:HOH592 2.2 17.6 1.0
C B:CO3407 3.0 17.8 1.0
PB B:ADP406 3.2 19.2 1.0
CD B:GLU282 3.2 20.0 1.0
PA B:ADP406 3.3 20.6 1.0
O1B B:ADP406 3.4 16.9 1.0
O1 B:CO3407 3.5 18.3 1.0
O B:HOH535 3.5 17.5 1.0
MG B:MG404 3.5 15.4 1.0
O3A B:ADP406 3.7 16.5 1.0
NZ B:LYS228 3.9 16.2 1.0
OD2 B:ASP270 3.9 20.0 1.0
CG B:GLU282 3.9 17.2 1.0
O3 B:CO3407 3.9 21.2 1.0
ND2 B:ASN281 4.0 15.8 1.0
O B:HOH595 4.1 24.2 1.0
C5' B:ADP406 4.1 22.4 1.0
O5' B:ADP406 4.2 21.4 1.0
OE1 B:GLU282 4.2 15.1 1.0
O3' B:ADP406 4.3 22.2 1.0
ND2 B:ASN284 4.3 19.7 1.0
O2A B:ADP406 4.5 17.1 1.0
O2B B:ADP406 4.6 18.6 1.0
NH1 B:ARG268 4.6 23.0 1.0
CE B:LYS228 4.8 17.0 1.0
C3' B:ADP406 4.8 23.9 1.0
OD1 B:ASN284 4.8 13.8 1.0
CG B:ASP270 4.9 20.7 1.0

Magnesium binding site 4 out of 8 in 6u1k

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Magnesium binding site 4 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:15.4
occ:1.00
 O1B B:ADP406 2.0 16.9 1.0
O1 B:CO3407 2.0 18.3 1.0
OE2 B:GLU282 2.1 16.5 1.0
O B:HOH567 2.1 16.6 1.0
OD1 B:ASN284 2.2 13.8 1.0
OE1 B:GLU282 2.3 15.1 1.0
CD B:GLU282 2.5 20.0 1.0
C B:CO3407 3.0 17.8 1.0
CG B:ASN284 3.2 18.3 1.0
PB B:ADP406 3.2 19.2 1.0
O2 B:CO3407 3.4 15.6 1.0
ND2 B:ASN284 3.5 19.7 1.0
O3B B:ADP406 3.5 15.3 1.0
MG B:MG403 3.5 19.0 1.0
K B:K405 3.7 16.6 1.0
NZ B:LYS116 3.9 19.2 1.0
CG B:GLU282 4.1 17.2 1.0
CA B:GLY158 4.2 17.2 1.0
O3 B:CO3407 4.2 21.2 1.0
O B:THR157 4.2 17.1 1.0
O2B B:ADP406 4.2 18.6 1.0
O B:HOH591 4.2 18.0 1.0
O3A B:ADP406 4.3 16.5 1.0
N B:DAL401 4.3 14.4 1.0
O1A B:ADP406 4.4 18.6 1.0
CB B:ASN284 4.5 19.2 1.0
O B:HOH512 4.5 18.7 1.0
N B:SER159 4.8 16.8 1.0
O B:HOH508 4.8 18.1 1.0
CB B:GLU282 5.0 17.5 1.0
PA B:ADP406 5.0 20.6 1.0

Magnesium binding site 5 out of 8 in 6u1k

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Magnesium binding site 5 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, 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, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:14.3
occ:1.00
 O3B C:ADP406 2.0 11.4 1.0
O1A C:ADP406 2.0 14.9 1.0
OE2 C:GLU282 2.1 18.3 1.0
O C:HOH585 2.2 14.0 1.0
O C:HOH525 2.2 13.8 1.0
O1 C:CO3407 2.2 12.4 1.0
C C:CO3407 3.1 13.7 1.0
PB C:ADP406 3.1 12.1 1.0
CD C:GLU282 3.2 14.7 1.0
PA C:ADP406 3.2 16.5 1.0
O1B C:ADP406 3.4 13.7 1.0
O3A C:ADP406 3.4 12.1 1.0
MG C:MG404 3.6 12.3 1.0
O2 C:CO3407 3.6 19.0 1.0
O C:HOH547 3.7 16.4 1.0
NZ C:LYS228 3.7 11.2 1.0
CG C:GLU282 3.8 14.5 1.0
O3 C:CO3407 3.9 17.9 1.0
C5' C:ADP406 3.9 10.9 1.0
O5' C:ADP406 4.1 13.0 1.0
OD2 C:ASP270 4.2 18.9 1.0
ND2 C:ASN281 4.2 16.0 1.0
OE1 C:GLU282 4.2 14.3 1.0
O3' C:ADP406 4.3 17.3 1.0
O C:HOH594 4.3 17.8 1.0
O2B C:ADP406 4.4 12.5 1.0
ND2 C:ASN284 4.4 19.3 1.0
O2A C:ADP406 4.4 14.0 1.0
C3' C:ADP406 4.7 18.1 1.0
CE C:LYS228 4.7 10.5 1.0
NH1 C:ARG268 4.8 20.8 1.0
OD1 C:ASN284 4.8 14.4 1.0
C4' C:ADP406 4.9 16.6 1.0

Magnesium binding site 6 out of 8 in 6u1k

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Magnesium binding site 6 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:12.3
occ:1.00
 O1B C:ADP406 2.0 13.7 1.0
O2 C:CO3407 2.1 19.0 1.0
OD1 C:ASN284 2.1 14.4 1.0
O C:HOH558 2.1 12.1 1.0
OE2 C:GLU282 2.2 18.3 1.0
OE1 C:GLU282 2.3 14.3 1.0
CD C:GLU282 2.5 14.7 1.0
C C:CO3407 3.1 13.7 1.0
CG C:ASN284 3.1 20.6 1.0
PB C:ADP406 3.2 12.1 1.0
O1 C:CO3407 3.4 12.4 1.0
O3B C:ADP406 3.5 11.4 1.0
ND2 C:ASN284 3.5 19.3 1.0
MG C:MG403 3.6 14.3 1.0
K C:K405 3.7 15.7 1.0
CG C:GLU282 4.0 14.5 1.0
CA C:GLY158 4.1 15.4 1.0
NZ C:LYS116 4.1 19.1 1.0
O C:THR157 4.1 12.9 1.0
O3 C:CO3407 4.2 17.9 1.0
O3A C:ADP406 4.2 12.1 1.0
N C:DAL401 4.3 15.8 1.0
O C:HOH564 4.3 16.4 1.0
O2B C:ADP406 4.3 12.5 1.0
CB C:ASN284 4.5 13.3 1.0
O C:HOH537 4.5 21.5 1.0
O1A C:ADP406 4.6 14.9 1.0
N C:SER159 4.7 13.1 1.0
CB C:GLU282 4.9 15.0 1.0
O C:HOH525 4.9 13.8 1.0
C C:GLY158 4.9 12.0 1.0
C C:THR157 5.0 14.9 1.0

Magnesium binding site 7 out of 8 in 6u1k

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Magnesium binding site 7 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:19.4
occ:1.00
 O2B D:ADP406 2.0 20.1 1.0
O2A D:ADP406 2.0 21.1 1.0
O2 D:CO3407 2.1 15.7 1.0
O D:HOH588 2.1 18.4 1.0
OE2 D:GLU282 2.1 19.8 1.0
O D:HOH512 2.2 18.2 1.0
C D:CO3407 2.9 18.6 1.0
PB D:ADP406 3.1 21.2 1.0
CD D:GLU282 3.2 17.3 1.0
PA D:ADP406 3.3 22.6 1.0
O3B D:ADP406 3.4 17.9 1.0
O3 D:CO3407 3.5 19.5 1.0
MG D:MG404 3.6 16.8 1.0
O3A D:ADP406 3.6 19.9 1.0
O D:HOH548 3.6 19.8 1.0
O1 D:CO3407 3.8 21.6 1.0
NZ D:LYS228 3.8 15.3 1.0
OD2 D:ASP270 3.9 17.2 1.0
CG D:GLU282 3.9 17.7 1.0
C5' D:ADP406 4.0 19.2 1.0
O D:HOH572 4.1 23.3 1.0
O5' D:ADP406 4.1 20.6 1.0
ND2 D:ASN281 4.2 17.9 1.0
OE1 D:GLU282 4.2 16.6 1.0
O3' D:ADP406 4.3 23.0 1.0
ND2 D:ASN284 4.4 19.6 1.0
O1B D:ADP406 4.5 19.0 1.0
O1A D:ADP406 4.5 20.2 1.0
CE D:LYS228 4.7 21.7 1.0
NH1 D:ARG268 4.7 24.0 1.0
C3' D:ADP406 4.8 22.1 1.0
OD1 D:ASN284 4.8 19.2 1.0
CG D:ASP270 4.9 22.5 1.0
C4' D:ADP406 4.9 24.3 1.0

Magnesium binding site 8 out of 8 in 6u1k

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Magnesium binding site 8 out of 8 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Carbonate, D-Alanine-D-Alanine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:16.8
occ:1.00
 O3 D:CO3407 2.0 19.5 1.0
O3B D:ADP406 2.1 17.9 1.0
O D:HOH567 2.1 16.5 1.0
OD1 D:ASN284 2.1 19.2 1.0
OE2 D:GLU282 2.2 19.8 1.0
OE1 D:GLU282 2.3 16.6 1.0
CD D:GLU282 2.6 17.3 1.0
C D:CO3407 3.0 18.6 1.0
CG D:ASN284 3.1 20.1 1.0
PB D:ADP406 3.3 21.2 1.0
O2 D:CO3407 3.4 15.7 1.0
ND2 D:ASN284 3.5 19.6 1.0
O2B D:ADP406 3.5 20.1 1.0
MG D:MG403 3.6 19.4 1.0
K D:K405 3.6 14.7 0.8
NZ D:LYS116 4.0 19.0 1.0
O D:HOH613 4.0 20.2 1.0
CG D:GLU282 4.1 17.7 1.0
CA D:GLY158 4.1 18.5 1.0
O1 D:CO3407 4.1 21.6 1.0
O D:THR157 4.1 22.2 1.0
O1B D:ADP406 4.3 19.0 1.0
N D:DAL401 4.3 18.9 1.0
O3A D:ADP406 4.4 19.9 1.0
O D:HOH523 4.5 19.6 1.0
CB D:ASN284 4.5 17.1 1.0
O2A D:ADP406 4.5 21.1 1.0
N D:SER159 4.8 20.0 1.0
CB D:GLU282 4.9 18.2 1.0
C D:THR157 5.0 20.6 1.0
O D:HOH564 5.0 18.2 1.0
C D:GLY158 5.0 20.1 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 20:49:07 2024

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