Calcium in PDB 5u08: Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin

The structure of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin, PDB code: 5u08 was solved by Z.Xu, T.Skarina, Z.Wawrzak, P.J.Stogios, V.Yim, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.55 / 1.52
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.295, 53.035, 78.676, 71.76, 75.61, 88.69
R / Rfree (%)	16.6 / 20

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

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin (pdb code 5u08). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin, PDB code: 5u08:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:24.6 occ:1.00 OD2 A:ASP44 2.3 33.6 1.0 O D:PHE40 2.3 22.9 1.0 O A:HOH471 2.4 30.6 1.0 O D:HOH355 2.4 29.1 1.0 O B:HOH469 2.5 26.3 1.0 OE2 B:GLU83 2.5 22.3 1.0 OE1 B:GLU83 2.6 25.9 1.0 CD B:GLU83 2.9 24.3 1.0 CG A:ASP44 3.4 36.4 1.0 C D:PHE40 3.5 23.4 1.0 O A:HOH364 3.8 33.2 1.0 CB A:ASP44 4.0 22.1 1.0 N D:PHE40 4.2 22.8 1.0 O B:HOH310 4.2 37.9 1.0 OD1 A:ASP44 4.3 39.6 1.0 O D:HOH326 4.3 27.1 1.0 N D:SER41 4.4 23.8 1.0 O A:HOH481 4.4 41.9 1.0 CA D:PHE40 4.4 23.4 1.0 CG B:GLU83 4.4 22.7 1.0 O A:HOH373 4.4 43.8 1.0 O B:HOH530 4.4 45.4 1.0 CA D:SER41 4.5 22.9 1.0 OE1 D:GLU32 4.5 30.6 1.0 O A:HOH499 4.6 42.2 1.0 C D:ASN39 4.6 23.3 1.0 OG D:SER41 4.7 25.6 1.0 CA D:ASN39 5.0 25.4 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:26.2 occ:0.74 O C:HOH324 2.2 22.0 1.0 O C:HOH427 2.2 29.7 1.0 OD1 D:ASP44 2.3 65.4 1.0 OE1 C:GLU83 2.3 25.4 1.0 O A:HOH361 2.4 36.3 1.0 O A:PHE40 2.4 20.6 1.0 OE2 C:GLU83 2.7 31.5 1.0 CD C:GLU83 2.8 34.3 1.0 CG D:ASP44 3.4 61.2 1.0 C A:PHE40 3.6 18.8 1.0 O D:HOH377 3.7 34.5 1.0 O C:HOH301 3.8 33.6 1.0 O D:HOH481 4.1 33.5 1.0 OD2 D:ASP44 4.1 66.2 1.0 N A:PHE40 4.2 20.7 1.0 CB D:ASP44 4.3 35.8 1.0 CG C:GLU83 4.4 29.4 1.0 OE1 A:GLU32 4.4 27.1 1.0 N A:SER41 4.5 20.7 1.0 CA A:PHE40 4.5 18.9 1.0 O D:HOH482 4.5 50.2 1.0 O A:HOH345 4.5 22.8 1.0 CA A:SER41 4.6 21.6 1.0 C A:ASN39 4.7 21.9 1.0 OG A:SER41 5.0 26.0 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:20.5 occ:0.94 OE2 B:GLU14 2.2 27.6 1.0 O B:HOH345 2.3 24.3 1.0 O B:HOH439 2.4 31.6 1.0 O B:HOH394 2.4 21.8 1.0 OD2 B:ASP20 2.5 19.1 1.0 OD1 B:ASP20 2.7 23.9 1.0 CG B:ASP20 2.9 21.3 1.0 CD B:GLU14 3.4 29.2 1.0 CG B:GLU14 4.1 24.6 1.0 NZ B:LYS23 4.2 29.6 1.0 OE1 B:GLU14 4.2 35.3 1.0 CB B:ASP20 4.4 21.1 1.0 OD1 B:ASN19 4.5 23.7 1.0 N B:ALA17 4.8 17.6 1.0 O B:ARG15 4.8 19.9 1.0 CD B:LYS23 5.0 18.7 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:18.8 occ:0.77 OE2 C:GLU14 2.3 30.9 1.0 O C:HOH397 2.3 30.7 1.0 O C:HOH400 2.4 22.7 1.0 OD2 C:ASP20 2.5 20.7 1.0 OD1 C:ASP20 2.5 22.1 1.0 CG C:ASP20 2.8 20.3 1.0 CD C:GLU14 3.5 27.8 1.0 O C:HOH456 3.9 51.2 1.0 NZ C:LYS23 4.2 34.0 1.0 CG C:GLU14 4.2 25.1 1.0 OE1 C:GLU14 4.3 34.7 1.0 CB C:ASP20 4.3 19.2 1.0 OD1 C:ASN19 4.6 21.2 1.0 N C:ALA17 4.8 19.7 1.0 CD C:LYS23 4.9 27.7 1.0 O C:ARG15 4.9 21.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Aminoglycoside Acetyltransferase Meta-AAC0020 From An Uncultured Soil Metagenomic Sample in Complex with Sisomicin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:24.7 occ:0.50 OE1 C:GLU18 2.2 37.0 1.0 O C:HOH409 2.3 49.9 1.0 O C:HOH439 2.4 48.6 1.0 O C:ASN53 2.4 21.5 1.0 O C:HOH391 2.4 41.2 1.0 O C:HOH398 2.6 49.4 1.0 CD C:GLU18 3.3 26.0 1.0 C C:ASN53 3.5 17.9 1.0 O C:HOH403 3.7 25.6 1.0 OE2 C:GLU18 3.8 27.4 1.0 CA C:ASN53 4.0 17.9 1.0 O C:HOH449 4.0 50.7 1.0 CB C:ASN53 4.2 19.5 1.0 CG C:GLU18 4.5 24.7 1.0 N C:GLN54 4.6 21.0 1.0 O C:HOH463 4.6 46.9 1.0 C C:GLN54 4.7 23.1 1.0 O C:HOH471 4.7 43.5 1.0 N C:ASN55 4.8 21.6 1.0 O C:GLN54 4.9 22.9 1.0 CA C:GLN54 5.0 20.7 1.0

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