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

Protein crystallography data

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

Other elements in 5u08:

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

Calcium Binding Sites:

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 5u08

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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 5u08

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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 5u08

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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 5u08

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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 5u08

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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

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: Sat Dec 12 05:45:09 2020

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