Sodium in PDB 6nl9: Crystal Structure of De Novo Designed Metal-Controlled Dimer of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-Apo

The structure of Crystal Structure of De Novo Designed Metal-Controlled Dimer of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-Apo, PDB code: 6nl9 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)	45.64 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.817, 52.027, 50.148, 90.00, 114.48, 90.00
R / Rfree (%)	18.6 / 22.4

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

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of De Novo Designed Metal-Controlled Dimer of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-Apo (pdb code 6nl9). 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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-Apo, PDB code: 6nl9:
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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-Apo


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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-Apo within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:37.9 occ:1.00 O D:HOH222 2.2 22.2 1.0 N D:VAL21 4.1 15.8 1.0 CA D:ALA20 4.1 16.6 1.0 O D:HOH209 4.1 35.1 1.0 O D:GLU19 4.2 16.7 1.0 C D:ALA20 4.4 16.3 1.0 N D:ALA20 4.5 16.0 1.0 C D:GLU19 4.5 17.5 1.0 CG D:GLU19 4.5 19.8 1.0 OE2 D:GLU19 4.8 21.8 1.0 CB D:VAL21 4.9 18.3 1.0 CA D:VAL21 4.9 16.9 1.0

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


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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-Apo within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:40.0 occ:1.00 O D:HOH221 2.3 21.2 1.0 O D:HOH214 2.3 36.9 1.0 OE2 D:GLU27 3.3 27.9 1.0 O D:TRP43 4.0 24.2 1.0 CB D:TRP43 4.2 25.0 1.0 C D:TRP43 4.5 24.8 1.0 CD D:GLU27 4.6 23.8 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