Sodium in PDB 7jja: Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form

The structure of Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form, PDB code: 7jja was solved by Z.Luo, J.R.More, B.Kobe, C.A.Mcdevitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 1.01
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.166, 50.169, 87.783, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 13.9

The binding sites of Sodium atom in the Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form (pdb code 7jja). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form, PDB code: 7jja:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:40.7 occ:1.00 H A:ASP389 2.0 9.9 1.0 OD1 A:ASP389 2.2 12.2 0.5 O A:HOH746 2.3 30.2 1.0 O A:HOH937 2.5 40.8 1.0 CG A:ASP389 2.7 11.3 0.5 N A:ASP389 2.8 8.2 1.0 HB2 A:ASP389 2.9 12.2 0.5 HA A:THR388 2.9 8.3 1.0 O A:HOH804 3.1 12.7 0.9 HG1 A:THR388 3.2 9.4 1.0 OD2 A:ASP389 3.3 12.9 0.5 CB A:ASP389 3.5 10.2 0.5 HB3 A:ASP389 3.5 12.3 0.5 CB A:ASP389 3.5 10.2 0.5 CA A:THR388 3.6 6.9 1.0 C A:THR388 3.6 7.3 1.0 HE21 A:GLN404 3.7 20.5 1.0 CA A:ASP389 3.7 8.8 0.5 CA A:ASP389 3.7 8.8 0.5 HE22 A:GLN387 3.7 16.2 1.0 OG1 A:THR388 3.7 7.8 1.0 O A:HOH836 3.8 14.2 1.0 CG A:ASP389 3.9 11.3 0.5 H A:VAL390 4.0 8.5 1.0 OD2 A:ASP389 4.2 12.6 0.5 HG23 A:VAL390 4.2 10.3 1.0 CB A:THR388 4.3 7.1 1.0 HB2 A:ASP389 4.4 12.3 0.5 NE2 A:GLN387 4.4 13.5 1.0 NE2 A:GLN404 4.4 17.1 1.0 HB3 A:ASP389 4.4 12.2 0.5 OE1 A:GLN387 4.4 12.0 1.0 HA A:ASP389 4.5 10.6 1.0 O A:HOH881 4.5 27.4 1.0 C A:ASP389 4.5 8.6 1.0 N A:VAL390 4.5 7.1 1.0 OD1 A:ASP389 4.5 12.2 0.5 HE22 A:GLN404 4.6 20.5 1.0 HZ A:PHE466 4.7 19.1 1.0 HB A:THR388 4.7 8.5 1.0 N A:THR388 4.8 6.8 1.0 O A:THR388 4.8 7.9 1.0 CD A:GLN387 4.8 11.4 1.0 O A:HOH704 4.8 32.0 0.9 HG3 A:GLN404 4.9 18.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Zint-Like Domain of Streptococcus Pneumoniae Adca in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:20.0 occ:1.00 HD2 A:PHE465 2.6 13.8 1.0 HD2 A:PRO482 2.7 9.9 1.0 O A:HOH939 2.8 18.8 1.0 HA A:PHE465 2.8 10.2 1.0 HD3 A:PRO482 3.0 9.9 1.0 O A:ASN480 3.0 10.7 1.0 CD2 A:PHE465 3.1 11.5 1.0 O A:ILE464 3.2 10.6 1.0 CD A:PRO482 3.3 8.3 1.0 HG2 A:GLU477 3.3 14.8 1.0 HA A:TRP481 3.3 9.2 1.0 O A:HOH1014 3.5 49.5 1.0 CA A:PHE465 3.7 8.5 1.0 CE2 A:PHE465 3.7 12.8 1.0 O A:HOH850 3.7 20.0 1.0 CG A:PHE465 3.8 9.3 1.0 HE2 A:PHE465 3.8 15.3 1.0 HB3 A:PHE465 3.8 11.0 1.0 C A:ASN480 3.9 8.9 1.0 CB A:PHE465 4.0 9.1 1.0 HG2 A:PRO482 4.0 10.7 1.0 HG3 A:GLU477 4.0 14.8 1.0 OD1 A:ASN480 4.1 11.7 1.0 CG A:GLU477 4.1 12.3 1.0 O A:HOH769 4.1 32.2 1.0 C A:ILE464 4.1 8.1 1.0 CA A:TRP481 4.2 7.7 1.0 CG A:PRO482 4.2 8.9 1.0 H A:PHE466 4.3 10.3 1.0 N A:TRP481 4.3 7.5 1.0 HB3 A:ASN480 4.3 10.7 1.0 N A:PHE465 4.4 7.9 1.0 N A:PRO482 4.4 7.0 1.0 CG A:ASN480 4.6 9.4 1.0 HB3 A:GLU477 4.7 14.9 1.0 HG3 A:PRO482 4.7 10.7 1.0 CZ A:PHE465 4.7 11.7 1.0 CD1 A:PHE465 4.8 9.0 1.0 CB A:ASN480 4.8 8.9 1.0 C A:TRP481 4.8 6.9 1.0 C A:PHE465 4.8 8.1 1.0 N A:PHE466 4.9 8.6 1.0 HB2 A:PHE465 4.9 11.0 1.0 HB3 A:TRP481 5.0 9.6 1.0 CA A:ASN480 5.0 8.6 1.0

Z.Luo, J.R.Morey, E.Deplazes, V.G.Pederick, A.Motygullina, S.L.Begg, N.Eleftheriadis, M.Isselstein, J.C.Paton, T.Cordes, J.Harmer, B.Kobe, C.A.Mcdevitt. The Molecular Basis of Zinc Acquisition By Streptococcus Pneumoniae Adca To Be Published.