Atomistry » Magnesium » PDB 6u1j-6uey » 6u1k
Atomistry »
  Magnesium »
    PDB 6u1j-6uey »
      6u1k »

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

Go back to Magnesium Binding Sites List in 6u1k
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

Go back to Magnesium Binding Sites List in 6u1k
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

Go back to Magnesium Binding Sites List in 6u1k
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

Go back to Magnesium Binding Sites List in 6u1k
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

Go back to Magnesium Binding Sites List in 6u1k
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

Go back to Magnesium Binding Sites List in 6u1k
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

Go back to Magnesium Binding Sites List in 6u1k
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

Go back to Magnesium Binding Sites List in 6u1k
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy