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Magnesium in PDB 5f48: Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A

Protein crystallography data

The structure of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A, PDB code: 5f48 was solved by Z.Xu, T.Skarina, P.J.Stogios, V.Yim, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.62 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.133, 80.187, 53.926, 90.00, 91.97, 90.00
R / Rfree (%) 19 / 23.5

Other elements in 5f48:

The structure of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A (pdb code 5f48). 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 An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A, PDB code: 5f48:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5f48

Go back to Magnesium Binding Sites List in 5f48
Magnesium binding site 1 out of 3 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A


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 An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:30.4
occ:0.99
O A:HOH361 2.1 45.9 1.0
OE2 A:GLU14 2.1 40.5 1.0
O A:HOH346 2.2 36.2 1.0
OD2 A:ASP20 2.2 20.1 1.0
OD1 A:ASP20 2.4 22.3 1.0
CG A:ASP20 2.6 21.1 1.0
CD A:GLU14 3.3 39.0 1.0
NZ A:LYS23 4.0 27.9 1.0
O A:HOH460 4.1 56.1 1.0
CB A:ASP20 4.1 19.7 1.0
OE1 A:GLU14 4.1 40.4 1.0
CG A:GLU14 4.3 35.2 1.0
N A:ALA17 4.5 25.1 1.0
OD1 A:ASN19 4.5 34.4 1.0
CD A:LYS23 4.5 23.0 1.0
CE A:LYS23 4.7 27.0 1.0
CB A:ALA17 4.8 28.4 1.0
CA A:LEU16 4.9 19.8 1.0
CD2 A:LEU16 5.0 17.3 1.0

Magnesium binding site 2 out of 3 in 5f48

Go back to Magnesium Binding Sites List in 5f48
Magnesium binding site 2 out of 3 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A


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 An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:30.0
occ:1.00
O8A B:COA201 2.4 46.7 1.0
O2B B:COA201 2.6 37.4 1.0
P3B B:COA201 3.3 47.0 1.0
O3B B:COA201 3.4 39.7 1.0
O7A B:COA201 3.6 46.9 1.0
C2B B:COA201 3.7 37.5 1.0
O B:HOH308 3.8 38.5 1.0
C3B B:COA201 4.1 38.2 1.0
O B:HOH426 4.4 48.7 1.0
O9A B:COA201 4.7 46.0 1.0
NH1 A:ARG100 4.7 55.1 1.0

Magnesium binding site 3 out of 3 in 5f48

Go back to Magnesium Binding Sites List in 5f48
Magnesium binding site 3 out of 3 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A


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 An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:11.9
occ:1.00
O B:HOH398 2.1 30.6 1.0
OE2 B:GLU14 2.2 33.4 1.0
O B:HOH377 2.2 30.8 1.0
O B:HOH409 2.2 28.8 1.0
OD2 B:ASP20 2.2 24.8 1.0
OD1 B:ASP20 2.5 24.5 1.0
CG B:ASP20 2.7 24.4 1.0
CD B:GLU14 3.3 32.5 1.0
CG B:GLU14 4.2 28.6 1.0
OE1 B:GLU14 4.2 34.3 1.0
CB B:ASP20 4.2 21.8 1.0
NZ B:LYS23 4.3 27.7 1.0
O B:HOH442 4.4 43.6 1.0
OD1 B:ASN19 4.7 27.9 1.0
N B:ALA17 4.7 22.9 1.0
CD B:LYS23 4.9 26.1 1.0
O B:ARG15 4.9 26.7 1.0
CB B:ALA17 5.0 24.6 1.0

Reference:

Z.Xu, P.J.Stogios, A.T.Quaile, K.J.Forsberg, S.Patel, T.Skarina, S.Houliston, C.Arrowsmith, G.Dantas, A.Savchenko. Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes. Acs Infect Dis V. 3 653 2017.
ISSN: ESSN 2373-8227
PubMed: 28756664
DOI: 10.1021/ACSINFECDIS.7B00068
Page generated: Sun Sep 29 04:03:18 2024

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