Magnesium in PDB 6xxq: Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin

Enzymatic activity of Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin

All present enzymatic activity of Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin:
2.7.7.47;

Protein crystallography data

The structure of Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin, PDB code: 6xxq was solved by S.Kanchugal P, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.89 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.532, 69.312, 94.517, 90.00, 135.00, 90.00
R / Rfree (%) 24 / 27.1

Other elements in 6xxq:

The structure of Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin (pdb code 6xxq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin, PDB code: 6xxq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6xxq

Go back to Magnesium Binding Sites List in 6xxq
Magnesium binding site 1 out of 3 in the Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:33.8
occ:1.00
 OD1 A:ASP46 2.1 39.2 1.0
O2B A:ATP304 2.3 37.0 1.0
O3G A:ATP304 2.6 34.9 1.0
OD2 A:ASP48 2.7 37.6 1.0
O A:ASP46 2.9 39.9 1.0
O2A A:ATP304 3.1 38.3 1.0
CG A:ASP46 3.3 38.3 1.0
CG A:ASP48 3.3 37.4 1.0
N A:SER35 3.4 41.1 1.0
C A:ASP46 3.6 37.1 1.0
OG A:SER45 3.6 48.6 1.0
PB A:ATP304 3.7 35.1 1.0
OD1 A:ASP48 3.7 38.9 1.0
CB A:SER35 3.8 41.8 1.0
N A:ASP46 3.9 35.1 1.0
PG A:ATP304 3.9 37.9 1.0
OG A:SER35 3.9 41.5 1.0
OD2 A:ASP46 4.0 36.5 1.0
O3B A:ATP304 4.1 36.8 1.0
CA A:ASP46 4.1 34.9 1.0
CA A:GLY34 4.1 33.2 1.0
CA A:SER35 4.2 42.3 1.0
CB A:ASP48 4.3 33.1 1.0
C A:GLY34 4.3 42.4 1.0
CB A:ASP46 4.3 34.9 1.0
PA A:ATP304 4.4 39.2 1.0
N A:ASP48 4.4 35.5 1.0
O3A A:ATP304 4.4 35.3 1.0
O1G A:ATP304 4.4 40.0 1.0
N A:LEU47 4.5 36.7 1.0
O1B A:ATP304 4.8 36.5 1.0
CA A:LEU47 4.8 36.0 1.0
O A:PHE33 4.9 37.6 1.0
N A:GLY36 4.9 45.5 1.0
MG A:MG303 4.9 35.1 1.0
C A:LEU47 5.0 35.5 1.0
CB A:SER45 5.0 41.7 1.0
CA A:ASP48 5.0 33.8 1.0

Magnesium binding site 2 out of 3 in 6xxq

Go back to Magnesium Binding Sites List in 6xxq
Magnesium binding site 2 out of 3 in the Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:35.1
occ:1.00
 O1A A:ATP304 2.3 41.1 1.0
OD2 A:ASP46 2.4 36.5 1.0
O2B A:SCM305 2.5 40.0 1.0
O2A A:ATP304 2.9 38.3 1.0
PA A:ATP304 3.1 39.2 1.0
CG A:ASP46 3.1 38.3 1.0
C6 A:SCM305 3.1 39.0 1.0
O11 A:SCM305 3.2 36.3 1.0
OD1 A:ASP46 3.5 39.2 1.0
C12 A:SCM305 3.6 38.0 1.0
O1 A:SCM305 3.7 41.1 1.0
O3G A:ATP304 3.7 34.9 1.0
C11 A:SCM305 3.8 36.0 1.0
O2G A:ATP304 4.1 39.9 1.0
CB A:ASP46 4.1 34.9 1.0
O3A A:ATP304 4.2 35.3 1.0
NZ A:LYS203 4.2 37.5 1.0
O5' A:ATP304 4.3 38.4 1.0
OE1 A:GLU86 4.4 41.3 1.0
C5 A:SCM305 4.5 38.8 1.0
PG A:ATP304 4.5 37.9 1.0
OD1 A:ASP48 4.7 38.9 1.0
O A:HOH405 4.7 32.6 1.0
O5 A:SCM305 4.7 42.1 1.0
C2 A:SCM305 4.8 38.2 1.0
C7 A:SCM305 4.8 39.6 1.0
OD2 A:ASP48 4.9 37.6 1.0
MG A:MG302 4.9 33.8 1.0
O2B A:ATP304 4.9 37.0 1.0

Magnesium binding site 3 out of 3 in 6xxq

Go back to Magnesium Binding Sites List in 6xxq
Magnesium binding site 3 out of 3 in the Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Spectinomycin Adenyltransferase Aad(9) From Enterococcus Faecialis with Atp and Spectinomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:33.5
occ:1.00
 OD1 B:ASP46 1.9 39.0 1.0
O2B B:ATP303 2.1 35.6 1.0
OD2 B:ASP48 2.2 39.0 1.0
O2G B:ATP303 2.3 39.2 1.0
O2A B:ATP303 2.6 42.5 1.0
CG B:ASP48 3.0 36.8 1.0
CG B:ASP46 3.1 40.1 1.0
O B:ASP46 3.4 35.6 1.0
N B:SER35 3.4 45.6 1.0
PB B:ATP303 3.5 37.0 1.0
OD1 B:ASP48 3.5 36.5 1.0
PG B:ATP303 3.7 39.9 1.0
OD2 B:ASP46 3.7 39.3 1.0
CB B:SER35 3.9 44.9 1.0
PA B:ATP303 3.9 37.2 1.0
O3B B:ATP303 3.9 37.1 1.0
C B:ASP46 3.9 36.1 1.0
O3A B:ATP303 4.0 35.8 1.0
CB B:ASP48 4.0 35.3 1.0
CA B:GLY34 4.1 39.0 1.0
N B:ASP46 4.1 33.9 1.0
CA B:SER35 4.3 45.1 1.0
CB B:ASP46 4.3 33.8 1.0
C B:GLY34 4.3 44.8 1.0
CA B:ASP46 4.3 33.4 1.0
N B:ASP48 4.4 34.6 1.0
O3G B:ATP303 4.5 42.6 1.0
O1B B:ATP303 4.6 40.7 1.0
O1G B:ATP303 4.7 38.1 1.0
O1A B:ATP303 4.8 40.2 1.0
N B:LEU47 4.8 35.8 1.0
CA B:ASP48 4.8 33.8 1.0
O5' B:ATP303 4.9 35.4 1.0

Reference:

S.Kanchugal P, M.Selmer. Structural Recognition of Spectinomycin By Resistance Enzyme Ant(9) Fromenterococcus Faecalis. Antimicrob.Agents Chemother. 2020.
ISSN: ESSN 1098-6596
PubMed: 32253216
DOI: 10.1128/AAC.00371-20
Page generated: Tue Dec 15 01:43:46 2020

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