Sodium in PDB 6nl7: Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)

The structure of Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q), PDB code: 6nl7 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)	40.06 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.903, 63.057, 53.225, 90.00, 103.31, 90.00
R / Rfree (%)	11.3 / 15.8

The structure of Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) (pdb code 6nl7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q), PDB code: 6nl7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)


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 B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:19.1 occ:1.00 O A:HOH211 1.8 32.8 1.0 OE1 A:GLU56 1.9 25.7 0.7 OE1 A:GLU56 2.0 21.3 0.3 O A:HOH259 2.1 34.7 1.0 O A:HOH248 2.3 16.9 1.0 CD A:GLU56 2.5 26.1 0.7 OE2 A:GLU56 2.5 27.7 0.7 OE2 A:GLU56 2.6 24.1 0.3 CD A:GLU56 2.6 19.2 0.3 N A:LYS10 3.8 21.6 1.0 CB A:LYS10 3.8 30.0 1.0 CG A:LYS10 3.9 38.3 1.0 CG A:GLU56 4.0 22.3 0.7 O A:HOH295 4.0 60.2 1.0 CG A:GLU56 4.1 18.7 0.3 O A:HOH241 4.2 28.9 1.0 O A:HOH203 4.3 25.3 1.0 CD A:LYS10 4.4 48.8 1.0 CA A:LYS10 4.4 22.8 1.0 CB A:GLU56 4.6 19.0 0.7 CB A:GLU56 4.6 17.4 0.3 N A:THR11 4.6 22.8 1.0 CE A:LYS10 4.7 53.8 1.0 O A:GLY38 4.7 16.6 1.0 CA A:GLY9 4.7 18.8 1.0 C A:GLY9 4.8 19.8 1.0 CG2 A:VAL39 5.0 16.3 1.0 OG1 A:THR11 5.0 32.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)


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 B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:20.6 occ:1.00 O B:HOH201 1.4 33.7 1.0 O A:HOH223 1.6 35.4 1.0 O A:HOH256 2.2 30.6 1.0 OE1 A:GLU27 2.2 16.9 0.7 O A:HOH224 2.3 34.0 1.0 NA B:NA107 2.5 17.9 1.0 O1 B:PO4108 2.6 38.5 1.0 OE2 A:GLU27 2.8 17.1 0.3 CD A:GLU27 2.9 14.1 0.7 O4 A:PO4108 3.0 36.4 1.0 OE2 A:GLU27 3.0 16.0 0.7 CD A:GLU27 3.2 11.5 0.3 OE1 A:GLU27 3.3 13.1 0.3 OE1 B:GLU27 3.9 17.2 0.6 P B:PO4108 3.9 51.5 1.0 O3 B:PO4108 3.9 34.7 1.0 OE1 B:GLU27 3.9 18.4 0.4 O B:HOH206 4.0 28.6 1.0 O A:HOH268 4.1 15.1 1.0 O3 A:PO4108 4.2 45.0 1.0 P A:PO4108 4.3 45.5 1.0 CG A:GLU27 4.3 10.7 0.7 CG A:GLU27 4.4 10.0 0.3 O B:HOH210 4.4 45.6 1.0 OE2 B:GLU27 4.5 20.9 0.4 CD B:GLU27 4.6 13.8 0.4 O2 B:PO4108 4.6 45.7 1.0 CD B:GLU27 4.6 16.6 0.6 OE2 B:GLU27 4.6 18.5 0.6 CB A:GLU27 5.0 8.8 0.7 CB A:GLU27 5.0 8.9 0.3

Sodium binding site 3 out of 4 in the Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)


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 B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na107 b:17.9 occ:1.00 O A:HOH223 1.6 35.4 1.0 O4 A:PO4108 1.8 36.4 1.0 OE1 B:GLU27 2.1 17.2 0.6 OE2 B:GLU27 2.1 20.9 0.4 O B:HOH201 2.2 33.7 1.0 O B:HOH210 2.3 45.6 1.0 OE2 B:GLU27 2.4 18.5 0.6 NA A:NA106 2.5 20.6 1.0 CD B:GLU27 2.5 16.6 0.6 CD B:GLU27 2.6 13.8 0.4 OE1 B:GLU27 2.6 18.4 0.4 P A:PO4108 3.1 45.5 1.0 O1 B:PO4108 3.3 38.5 1.0 O2 A:PO4108 3.4 50.3 1.0 O A:HOH224 3.7 34.0 1.0 OE1 A:GLU27 3.7 16.9 0.7 O3 A:PO4108 3.7 45.0 1.0 OE1 A:GLU27 3.9 13.1 0.3 CG B:GLU27 3.9 12.4 0.4 O B:HOH245 4.0 25.8 1.0 CG B:GLU27 4.0 13.3 0.6 O B:HOH220 4.2 25.8 1.0 OE2 A:GLU27 4.3 17.1 0.3 O1 A:PO4108 4.4 43.2 1.0 OE2 A:GLU27 4.4 16.0 0.7 CD A:GLU27 4.4 14.1 0.7 O5 B:DPO101 4.5 30.9 1.0 CD A:GLU27 4.5 11.5 0.3 O3 B:PO4108 4.5 34.7 1.0 O A:HOH256 4.6 30.6 1.0 P B:PO4108 4.6 51.5 1.0 NE B:ARG31 4.7 20.0 1.0 CB B:GLU27 4.8 12.3 0.4 CB B:GLU27 4.8 12.6 0.6 O4 B:DPO101 4.8 32.3 1.0 O7 B:DPO101 4.8 29.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)


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 B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na103 b:27.3 occ:1.00 O D:HOH204 1.3 42.6 1.0 OE1 C:GLU42 2.1 39.5 0.7 O C:HOH249 2.2 51.7 1.0 O D:HOH251 2.2 33.1 1.0 OE2 D:GLU27 2.3 26.0 1.0 CD C:GLU42 2.9 35.6 0.7 OE2 C:GLU42 2.9 59.2 0.7 O D:HOH221 3.1 42.3 1.0 CD D:GLU27 3.1 23.2 1.0 OE1 D:GLU27 3.2 25.5 1.0 O D:HOH257 4.0 19.4 1.0 NE D:ARG31 4.1 18.8 1.0 CG C:GLU42 4.4 32.2 0.7 CG D:GLU27 4.4 14.6 1.0 NH1 D:ARG31 4.5 31.7 1.0 CZ D:ARG31 4.6 26.0 1.0 OXT C:ACT101 4.8 36.6 1.0 O D:HOH222 4.9 15.8 1.0 CD D:ARG31 4.9 16.4 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