Sodium in PDB 7r8q: Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+

The structure of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+, PDB code: 7r8q 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)	36.89 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.868, 82.812, 107.782, 90, 131.06, 90
R / Rfree (%)	19.1 / 22

The structure of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ (pdb code 7r8q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+, PDB code: 7r8q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:32.3 occ:1.00 O6 A:CIT401 2.3 35.0 1.0 OD1 A:ASN303 2.4 28.1 1.0 OD2 A:ASP301 2.4 29.5 1.0 O A:HOH520 2.4 29.2 1.0 O2B A:ADP402 2.7 27.5 1.0 O3B A:ADP402 2.7 32.5 1.0 O2 A:CIT401 2.8 26.2 1.0 C6 A:CIT401 3.1 34.9 1.0 MG A:MG403 3.2 32.2 0.9 CG A:ASP301 3.2 30.9 1.0 PB A:ADP402 3.2 28.7 1.0 NA A:NA405 3.2 32.1 0.9 CG A:ASN303 3.2 28.5 1.0 OD1 A:ASP301 3.4 30.2 1.0 ND2 A:ASN303 3.5 29.8 1.0 O5 A:CIT401 3.6 37.0 1.0 NH2 A:ARG305 3.6 34.2 1.0 O7 A:CIT401 3.7 31.3 1.0 C1 A:CIT401 3.8 32.2 1.0 C3 A:CIT401 3.9 33.9 1.0 O1B A:ADP402 4.3 34.7 1.0 CA A:ALA181 4.4 29.9 1.0 O3A A:ADP402 4.4 31.8 1.0 O1A A:ADP402 4.5 27.6 1.0 C2 A:CIT401 4.5 28.9 1.0 CB A:ASN303 4.6 31.8 1.0 O1 A:CIT401 4.6 33.2 1.0 CB A:ASP301 4.6 33.5 1.0 O A:HOH661 4.7 33.7 1.0 CB A:ALA181 4.7 29.4 1.0 CZ A:ARG305 4.7 34.0 1.0 O A:THR180 4.7 29.2 1.0 OD2 A:ASP288 4.8 31.0 1.0 N A:GLY182 4.8 32.4 1.0 O A:HOH590 4.9 26.2 1.0

Sodium binding site 2 out of 6 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:32.1 occ:0.93 OD1 A:ASP301 2.3 30.2 1.0 O A:HOH661 2.4 33.7 1.0 O A:HOH629 2.4 31.6 1.0 OD1 A:ASN303 2.4 28.1 1.0 O A:HOH520 2.5 29.2 1.0 O A:LEU302 2.7 27.5 1.0 NA A:NA404 3.2 32.3 1.0 CG A:ASP301 3.3 30.9 1.0 CG A:ASN303 3.4 28.5 1.0 C A:LEU302 3.5 30.8 1.0 OD2 A:ASP301 3.6 29.5 1.0 CA A:ASN303 3.9 29.2 1.0 N A:ASN303 3.9 27.4 1.0 O A:HOH663 4.0 28.8 1.0 CB A:ASN303 4.1 31.8 1.0 N A:LEU302 4.2 29.4 1.0 NH2 A:ARG305 4.2 34.2 1.0 O3B A:ADP402 4.2 32.5 1.0 ND2 A:ASN303 4.3 29.8 1.0 CE A:LYS136 4.4 27.0 1.0 CA A:LEU302 4.5 30.7 1.0 OD1 A:ASN134 4.6 27.1 1.0 C A:ASP301 4.6 30.8 1.0 CB A:ASP301 4.6 33.5 1.0 O A:ASN134 4.7 29.8 1.0 O A:THR180 4.8 29.2 1.0 CA A:ASP301 4.9 27.4 1.0 CZ A:ARG305 5.0 34.0 1.0 CG A:LYS136 5.0 34.0 1.0 O A:HOH704 5.0 36.9 1.0

Sodium binding site 3 out of 6 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:31.8 occ:0.73 O A:HOH649 2.4 37.1 1.0 O A:HOH560 2.4 34.7 1.0 OG1 A:THR246 2.4 33.5 1.0 O A:HOH721 2.5 46.7 1.0 O A:HOH532 2.5 36.2 1.0 O A:THR246 2.5 31.8 1.0 C A:THR246 3.3 31.2 1.0 CB A:THR246 3.6 30.7 1.0 N A:THR246 3.7 32.2 1.0 CA A:THR246 3.7 32.0 1.0 O2' A:ADP402 4.0 30.1 1.0 O A:ASP247 4.1 37.5 1.0 OE2 A:GLU220 4.2 44.6 1.0 O A:HOH549 4.3 37.2 1.0 N A:ASP247 4.4 34.4 1.0 O A:HOH682 4.4 46.9 1.0 ND2 A:ASN223 4.4 34.0 1.0 C A:ASP247 4.7 35.0 1.0 CG2 A:THR246 4.7 30.7 1.0 O A:GLN244 4.8 31.9 1.0 CA A:ASP247 4.9 33.7 1.0 C A:LEU245 4.9 29.6 1.0

Sodium binding site 4 out of 6 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:34.2 occ:1.00 OD1 B:ASP301 2.4 31.5 1.0 O B:HOH553 2.4 37.0 1.0 O B:HOH517 2.4 31.9 1.0 O B:HOH546 2.4 32.5 1.0 OD1 B:ASN303 2.5 32.2 1.0 O B:LEU302 2.6 32.6 1.0 CG B:ASN303 3.4 31.6 1.0 C B:LEU302 3.4 29.9 1.0 CG B:ASP301 3.4 32.3 1.0 NA B:NA407 3.5 30.3 0.9 OD2 B:ASP301 3.9 30.2 1.0 CA B:ASN303 3.9 33.4 1.0 O B:HOH619 3.9 37.1 1.0 N B:ASN303 4.0 29.8 1.0 NH2 B:ARG305 4.1 36.7 1.0 CB B:ASN303 4.2 32.9 1.0 N B:LEU302 4.2 31.8 1.0 ND2 B:ASN303 4.2 28.7 1.0 O B:HOH671 4.3 39.6 1.0 O1B B:ADP402 4.3 35.5 1.0 O B:HOH625 4.5 43.5 1.0 CA B:LEU302 4.5 34.2 1.0 OD1 B:ASN134 4.5 32.2 1.0 O B:ASN134 4.5 34.1 1.0 CE B:LYS136 4.5 40.4 1.0 O B:THR180 4.7 37.0 1.0 C B:ASP301 4.7 31.1 1.0 CB B:ASP301 4.7 31.6 1.0 CZ B:ARG305 4.9 38.0 1.0

Sodium binding site 5 out of 6 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:30.3 occ:0.87 OD1 B:ASN303 2.4 32.2 1.0 O B:HOH517 2.4 31.9 1.0 OD2 B:ASP301 2.4 30.2 1.0 O5 B:CIT401 2.5 31.1 1.0 O3B B:ADP402 2.6 27.1 1.0 O1 B:CIT401 2.7 29.4 1.0 O1B B:ADP402 2.9 35.5 1.0 C6 B:CIT401 3.0 33.1 1.0 MG B:MG405 3.1 27.1 0.8 CG B:ASP301 3.2 32.3 1.0 PB B:ADP402 3.2 33.1 1.0 CG B:ASN303 3.2 31.6 1.0 OD1 B:ASP301 3.3 31.5 1.0 ND2 B:ASN303 3.4 28.7 1.0 NA B:NA406 3.5 34.2 1.0 O6 B:CIT401 3.5 37.9 1.0 O7 B:CIT401 3.6 32.7 1.0 NH2 B:ARG305 3.7 36.7 1.0 C1 B:CIT401 3.8 31.5 1.0 C3 B:CIT401 3.9 31.1 1.0 O2B B:ADP402 4.2 37.1 1.0 CA B:ALA181 4.4 31.8 1.0 O3A B:ADP402 4.4 34.8 1.0 O2A B:ADP402 4.5 31.5 1.0 C2 B:CIT401 4.5 29.7 1.0 OD2 B:ASP288 4.6 30.7 1.0 CB B:ASP301 4.6 31.6 1.0 CB B:ASN303 4.6 32.9 1.0 O2 B:CIT401 4.7 26.4 1.0 N B:GLY182 4.7 31.2 1.0 O B:HOH512 4.7 28.4 1.0 CZ B:ARG305 4.7 38.0 1.0 O B:THR180 4.8 37.0 1.0 CB B:ALA181 4.8 32.5 1.0

Sodium binding site 6 out of 6 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:42.3 occ:0.62 O B:HOH689 2.4 44.7 1.0 O B:HOH586 2.4 39.8 1.0 O B:HOH534 2.4 42.3 1.0 O B:HOH637 2.4 42.2 1.0 OG1 B:THR246 2.5 34.4 1.0 O B:THR246 2.6 38.8 1.0 C B:THR246 3.4 40.6 1.0 CB B:THR246 3.7 36.4 1.0 CA B:THR246 3.8 34.1 1.0 N B:THR246 3.8 33.6 1.0 O B:ASP247 3.9 41.4 1.0 O2' B:ADP402 4.0 27.7 1.0 O B:HOH502 4.3 38.1 1.0 OE1 B:GLU220 4.4 47.0 1.0 N B:ASP247 4.5 41.8 1.0 C B:ASP247 4.6 44.2 1.0 ND2 B:ASN223 4.7 33.6 1.0 CG2 B:THR246 4.8 32.3 1.0 O B:HOH695 4.8 50.6 1.0 CA B:ASP247 4.9 40.9 1.0 O B:GLN244 5.0 36.2 1.0

J.L.Pederick, A.J.Horsfall, B.Jovcevski, J.Klose, A.D.Abell, T.L.Pukala, J.B.Bruning. Discovery of An ʟ-Amino Acid Ligase Implicated in Staphylococcal Sulfur Amino Acid Metabolism. J.Biol.Chem. V. 298 02392 2022.
ISSN: ESSN 1083-351X
PubMed: 35988643
DOI: 10.1016/J.JBC.2022.102392