Sodium in PDB 6nla: Crystal Structure of De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc

The structure of Crystal Structure of De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc, PDB code: 6nla was solved by B.Maniaci, S.Boguslaw, T.Huxford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.58 / 1.34
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	63.155, 63.155, 39.610, 90.00, 90.00, 90.00
R / Rfree (%)	10.4 / 12.8

The structure of Crystal Structure of De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc (pdb code 6nla). 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 De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc, PDB code: 6nla:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc


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 De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:55.2 occ:1.00 O1 A:GOL105 2.0 51.4 1.0 O A:HOH217 2.6 58.6 1.0 O A:HOH213 3.0 35.5 1.0 C1 A:GOL105 3.3 39.9 1.0 C2 A:GOL105 3.7 46.0 1.0 CG2 A:THR25 3.7 20.3 1.0 O2 A:GOL105 3.9 53.6 1.0 O A:HOH307 4.3 44.7 1.0 O A:GLU19 4.3 17.2 1.0 CA A:ALA20 4.6 16.4 1.0 CB A:ALA20 4.7 17.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc


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 De Novo Designed Metal-Controlled Dimer of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:41.7 occ:1.00 OD1 A:ASP47 2.2 52.3 1.0 OH A:TYR45 2.6 21.9 1.0 O A:HOH222 2.6 36.0 1.0 O A:HOH287 3.1 74.3 1.0 CG A:ASP47 3.3 45.8 1.0 CZ A:TYR45 3.4 18.6 1.0 CE2 A:TYR45 3.5 21.0 1.0 O A:HOH208 3.8 56.5 1.0 CB A:ASP47 4.1 31.1 1.0 CA A:ASP47 4.2 25.9 1.0 OD2 A:ASP47 4.2 69.8 1.0 CB A:ALA23 4.2 22.0 1.0 O A:ASP47 4.3 27.9 1.0 O A:HOH261 4.5 33.2 1.0 CG A:LYS50 4.6 21.9 1.0 C A:ASP47 4.7 26.5 1.0 CE1 A:TYR45 4.7 19.0 1.0 CE2 A:TYR3 4.8 17.1 1.0 CD2 A:TYR45 4.8 20.9 1.0 OH A:TYR3 4.9 21.3 1.0

B.Maniaci, C.H.Lipper, D.L.Anipindi, H.Erlandsen, J.L.Cole, B.Stec, T.Huxford, J.J.Love. Design of High-Affinity Metal-Controlled Protein Dimers. Biochemistry V. 58 2199 2019.
ISSN: ISSN 0006-2960
PubMed: 30938154
DOI: 10.1021/ACS.BIOCHEM.9B00055