Sodium in PDB 7jjb: Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca

The structure of Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca, PDB code: 7jjb 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)	19.72 / 1.10
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.251, 50.091, 87.215, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.7

The structure of Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca (pdb code 7jjb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca, PDB code: 7jjb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca


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 Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:27.5 occ:1.00 H A:THR101 2.1 21.8 1.0 HA A:LEU100 2.8 17.7 1.0 O A:HOH541 2.8 40.5 1.0 N A:THR101 3.0 18.1 1.0 HD23 A:LEU100 3.4 19.2 1.0 HB A:THR101 3.4 25.3 1.0 HD22 A:LEU100 3.6 19.2 1.0 CA A:LEU100 3.6 14.8 1.0 C A:LEU100 3.7 16.0 1.0 O A:THR101 3.8 23.6 1.0 HB3 A:LEU100 3.8 17.7 1.0 O A:HOH367 3.8 24.2 1.0 CD2 A:LEU100 3.9 16.0 1.0 CA A:THR101 3.9 20.1 1.0 CB A:THR101 4.0 21.1 1.0 CB A:LEU100 4.2 14.7 1.0 O A:ILE99 4.3 14.4 1.0 C A:THR101 4.3 22.3 1.0 OG1 A:THR101 4.3 21.9 1.0 HE3 A:LYS98 4.6 17.8 1.0 CG A:LEU100 4.7 15.4 1.0 HD21 A:LEU100 4.7 19.2 1.0 HG1 A:THR101 4.7 26.2 1.0 N A:LEU100 4.7 14.1 1.0 O A:HOH360 4.7 36.3 1.0 HA A:THR101 4.8 24.2 1.0 O A:LEU100 5.0 15.4 1.0 C A:ILE99 5.0 13.8 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca


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 Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:31.4 occ:1.00 H A:ASP68 2.0 10.7 0.5 H A:ASP68 2.0 9.1 0.5 OD1 A:ASP68 2.2 17.0 0.5 CG A:ASP68 2.6 16.2 0.5 O A:HOH525 2.7 31.0 1.0 N A:ASP68 2.8 8.9 0.5 N A:ASP68 2.9 7.6 0.5 HG1 A:THR67 2.9 9.5 1.0 HB2 A:ASP68 2.9 11.3 0.5 O A:HOH410 3.0 12.4 1.0 HA A:THR67 3.0 8.1 1.0 OD2 A:ASP68 3.2 19.5 0.5 CB A:ASP68 3.4 13.4 0.5 HB3 A:ASP68 3.5 16.1 0.5 OG1 A:THR67 3.5 7.9 1.0 CA A:ASP68 3.6 10.7 0.5 CB A:ASP68 3.6 9.4 0.5 HG23 A:VAL69 3.7 10.8 1.0 H A:VAL69 3.7 8.7 0.5 CA A:ASP68 3.7 8.4 0.5 CA A:THR67 3.7 6.8 1.0 C A:THR67 3.7 7.2 1.0 H A:VAL69 3.8 8.7 0.5 O A:HOH377 3.9 29.1 1.0 OE1 A:GLN83 3.9 26.8 1.0 O A:HOH393 4.0 11.5 1.0 CG A:ASP68 4.1 10.5 0.5 HE22 A:GLN66 4.1 15.4 1.0 N A:VAL69 4.2 7.2 1.0 C A:ASP68 4.2 9.0 0.5 CB A:THR67 4.2 7.2 1.0 OD2 A:ASP68 4.3 12.6 0.5 HB2 A:ASP68 4.3 16.1 0.5 C A:ASP68 4.3 7.7 0.5 HZ A:PHE145 4.3 17.1 1.0 HA A:ASP68 4.4 12.8 0.5 HB3 A:ASP68 4.5 11.3 0.5 HG3 A:GLN83 4.5 25.9 1.0 HA A:ASP68 4.5 10.1 0.5 CG2 A:VAL69 4.7 9.0 1.0 HB A:THR67 4.7 8.6 1.0 O A:HOH508 4.7 32.2 1.0 OD1 A:ASP68 4.8 11.7 0.5 NE2 A:GLN66 4.8 12.9 1.0 OE1 A:GLN66 4.9 11.5 1.0 O A:THR67 4.9 7.8 1.0 CD A:GLN83 4.9 24.1 1.0 N A:THR67 5.0 6.8 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:12.7 occ:1.00 H A:ASP130 2.1 8.1 1.0 HA A:SER129 2.6 9.7 0.2 HA A:SER129 2.6 8.6 0.8 O A:VAL109 2.7 9.5 1.0 O A:ASN132 2.8 8.8 1.0 N A:ASP130 2.9 6.7 1.0 O A:HOH365 2.9 7.9 1.0 OD1 A:ASP130 3.0 7.8 1.0 H A:ASN132 3.2 10.5 0.3 HE2 A:PHE111 3.2 11.2 1.0 H A:HIS131 3.2 9.8 0.3 HD2 A:PHE111 3.2 10.8 1.0 H A:ASN132 3.2 10.5 0.7 H A:HIS131 3.2 9.5 0.7 CA A:SER129 3.4 8.0 0.2 CA A:SER129 3.5 7.2 0.8 O A:HOH482 3.5 9.0 1.0 O A:HOH347 3.5 11.1 1.0 HH12 A:ARG17 3.6 9.7 1.0 C A:SER129 3.7 7.0 1.0 N A:HIS131 3.7 8.2 0.3 N A:HIS131 3.7 7.9 0.7 HG A:SER129 3.8 14.8 0.8 HB A:VAL109 3.8 11.8 1.0 N A:ASN132 3.8 8.7 1.0 CE2 A:PHE111 3.8 9.3 1.0 HH11 A:ARG17 3.9 9.7 1.0 HB2 A:SER129 3.9 12.3 0.2 C A:VAL109 3.9 8.8 1.0 CD2 A:PHE111 3.9 9.0 1.0 C A:ASN132 3.9 9.0 1.0 CA A:ASP130 3.9 7.3 1.0 O A:PHE128 4.0 7.8 1.0 H A:VAL109 4.0 11.6 1.0 CG A:ASP130 4.1 7.6 1.0 C A:ASP130 4.1 7.9 1.0 NH1 A:ARG17 4.1 8.1 1.0 CB A:SER129 4.2 10.2 0.2 HA A:ARG110 4.2 12.2 1.0 OG A:SER129 4.4 12.3 0.8 CB A:SER129 4.4 8.8 0.8 CA A:ASN132 4.4 8.4 1.0 HA A:HIS131 4.4 10.7 0.3 HH A:TYR22 4.4 9.9 1.0 N A:SER129 4.4 6.9 1.0 CA A:HIS131 4.5 8.9 0.3 CB A:ASP130 4.5 8.1 1.0 HB3 A:SER129 4.5 12.3 0.2 C A:HIS131 4.5 9.8 0.7 CA A:HIS131 4.5 9.5 0.7 HB2 A:ASN132 4.6 10.4 1.0 CB A:VAL109 4.6 9.8 1.0 CA A:VAL109 4.6 9.4 1.0 C A:PHE128 4.6 6.7 1.0 HB2 A:SER129 4.6 10.6 0.8 C A:HIS131 4.6 8.9 0.3 HA A:HIS131 4.6 11.4 0.7 HB3 A:ASP130 4.6 9.7 1.0 N A:VAL109 4.6 9.7 1.0 HA A:ASP130 4.8 8.8 1.0 HA A:ILE133 4.8 11.8 1.0 N A:ARG110 4.8 9.0 1.0 HG12 A:VAL109 4.8 12.5 1.0 O A:SER129 4.9 8.4 1.0 H A:PHE111 4.9 9.8 1.0 CA A:ARG110 5.0 10.1 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:13.2 occ:1.00 HB3 A:TYR30 2.6 7.8 1.0 HG23 A:THR67 2.7 9.2 1.0 OG A:SER28 2.8 6.2 1.0 O A:HOH600 2.8 19.7 1.0 HD3 A:PRO31 2.9 9.4 1.0 O A:THR67 2.9 7.8 1.0 HB3 A:SER28 3.1 7.3 1.0 HG22 A:THR67 3.2 9.2 1.0 HD2 A:TYR30 3.2 9.3 1.0 CB A:SER28 3.3 6.1 1.0 HG A:SER28 3.4 7.5 1.0 CG2 A:THR67 3.4 7.7 1.0 HA A:THR70 3.4 9.0 1.0 HG22 A:THR70 3.4 13.8 1.0 HB2 A:SER28 3.5 7.3 1.0 CB A:TYR30 3.5 6.5 1.0 HB2 A:TYR30 3.7 7.8 1.0 CD A:PRO31 3.9 7.8 1.0 HG21 A:THR67 3.9 9.2 1.0 C A:THR67 3.9 7.2 1.0 CD2 A:TYR30 4.0 7.8 1.0 HG3 A:PRO31 4.0 11.9 1.0 H A:THR67 4.0 8.2 1.0 H A:TYR30 4.0 6.9 1.0 O A:VAL69 4.1 7.0 1.0 HA A:ASP68 4.2 10.1 0.5 CG A:TYR30 4.2 6.6 1.0 O A:HOH467 4.3 15.5 1.0 CG2 A:THR70 4.3 11.5 1.0 CA A:THR70 4.3 7.5 1.0 HD2 A:PRO31 4.4 9.4 1.0 HA A:ASP68 4.4 12.8 0.5 CG A:PRO31 4.4 10.0 1.0 HG23 A:THR70 4.4 13.8 1.0 C A:VAL69 4.6 6.9 1.0 CA A:TYR30 4.6 5.9 1.0 CB A:THR67 4.6 7.2 1.0 N A:THR67 4.6 6.8 1.0 N A:TYR30 4.6 5.8 1.0 CA A:THR67 4.6 6.8 1.0 O A:HOH558 4.6 30.5 1.0 HG2 A:PRO31 4.7 11.9 1.0 N A:PRO31 4.7 7.1 1.0 N A:THR70 4.7 7.0 1.0 N A:ASP68 4.7 7.6 0.5 H A:VAL69 4.7 8.7 0.5 CA A:SER28 4.8 5.8 1.0 N A:ASP68 4.8 8.9 0.5 CA A:ASP68 4.8 8.4 0.5 H A:VAL69 4.8 8.7 0.5 C A:ASP68 4.8 7.7 0.5 CB A:THR70 4.9 9.6 1.0 N A:VAL69 4.9 7.2 1.0 CA A:ASP68 4.9 10.7 0.5 C A:ASP68 5.0 9.0 0.5 C A:TYR30 5.0 6.6 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:22.3 occ:1.00 O A:HOH604 2.7 17.4 1.0 O A:ALA13 2.7 14.6 1.0 O A:HOH633 2.9 22.9 1.0 O A:HOH610 2.9 26.5 1.0 HB2 A:ALA134 3.2 13.6 1.0 HA A:ALA13 3.2 18.5 1.0 HB1 A:ALA13 3.3 19.0 1.0 HG2 A:LYS15 3.3 22.6 1.0 HG3 A:LYS15 3.4 22.6 1.0 HB1 A:ALA134 3.5 13.6 1.0 C A:ALA13 3.6 14.5 1.0 HB3 A:ALA134 3.6 13.6 1.0 CB A:ALA134 3.6 11.3 1.0 CA A:ALA13 3.7 15.4 1.0 CG A:LYS15 3.8 18.8 1.0 CB A:ALA13 4.0 15.9 1.0 HB2 A:LYS15 4.3 19.3 1.0 HB2 A:ALA13 4.4 19.0 1.0 HE2 A:LYS15 4.4 28.4 1.0 HG13 A:ILE133 4.5 14.1 1.0 HE3 A:LYS15 4.6 28.4 1.0 CB A:LYS15 4.7 16.1 1.0 HB3 A:ALA13 4.7 19.0 1.0 N A:VAL14 4.8 14.0 1.0 CE A:LYS15 4.8 23.6 1.0 HD11 A:ILE133 4.9 15.1 1.0 O A:HOH433 4.9 15.2 1.0 CD A:LYS15 4.9 21.3 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Zn(II)-Bound Zint-Like Domain of Streptococcus Pneumoniae Adca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:29.4 occ:0.50 O A:HOH484 2.3 24.5 1.0 H A:LYS89 2.8 11.1 1.0 O A:HOH457 2.8 17.5 0.5 HA A:LYS88 3.0 11.2 0.5 HA A:LYS88 3.0 11.2 0.5 HB3 A:LYS89 3.3 11.9 1.0 O A:SER87 3.3 11.7 1.0 N A:LYS89 3.3 9.2 1.0 HB2 A:LYS89 3.7 11.9 1.0 CA A:LYS88 3.7 9.3 0.5 CA A:LYS88 3.7 9.4 0.5 CB A:LYS89 3.8 9.9 1.0 C A:SER87 3.9 10.0 1.0 C A:LYS88 3.9 8.9 0.5 C A:LYS88 3.9 8.4 0.5 N A:LYS88 4.1 9.2 0.5 N A:LYS88 4.1 9.2 0.5 HD3 A:LYS88 4.2 20.4 0.5 CA A:LYS89 4.2 9.1 1.0 O A:HOH375 4.3 20.1 1.0 HB2 A:SER87 4.4 16.3 1.0 HB3 A:SER87 4.5 16.3 1.0 O A:LYS89 4.6 9.7 1.0 HG3 A:GLU80 4.7 13.4 1.0 H A:LYS88 4.8 11.1 0.5 H A:LYS88 4.8 11.1 0.5 CB A:SER87 4.9 13.6 1.0 C A:LYS89 4.9 8.5 1.0 HA A:LYS89 5.0 10.9 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.