Zinc 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn101 b:9.0 occ:1.00 NE2 A:HIS25 2.0 9.5 1.0 CL A:CL107 2.2 10.4 1.0 CD2 A:HIS25 3.0 8.6 1.0 CE1 A:HIS25 3.0 10.5 1.0 O A:HOH273 4.0 38.7 1.0 CG A:HIS25 4.1 8.7 1.0 ND1 A:HIS25 4.1 9.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn102 b:14.9 occ:1.00 O A:ACT104 1.6 19.7 1.0 OD1 A:ASP46 1.9 14.3 1.0 OXT A:ACT103 2.0 30.6 1.0 OXT A:ACT104 2.0 22.1 1.0 C A:ACT104 2.1 31.0 1.0 O A:ACT103 2.4 16.2 1.0 C A:ACT103 2.5 18.6 1.0 CG A:ASP46 2.7 14.0 1.0 OD2 A:ASP46 3.0 17.0 1.0 CH3 A:ACT104 3.5 33.5 1.0 O B:HOH216 3.9 32.6 1.0 CH3 A:ACT103 4.0 27.1 1.0 N B:GLU42 4.0 11.4 1.0 CB A:ASP46 4.1 8.9 1.0 O A:HOH225 4.2 59.4 1.0 C B:GLY41 4.2 14.2 1.0 CB A:ALA48 4.3 11.6 1.0 CB B:GLU42 4.5 13.2 1.0 CA B:GLU42 4.5 10.3 1.0 CA B:GLY41 4.6 15.7 1.0 CA A:ASP46 4.6 7.2 1.0 O B:HOH239 4.7 43.1 1.0 O B:GLY41 4.7 13.3 1.0 N A:ALA48 4.7 9.3 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn102 b:14.4 occ:1.00 NE2 B:HIS21 2.0 13.9 1.0 O B:HOH246 2.1 18.1 1.0 OXT B:ACT105 2.1 16.0 1.0 ND1 B:HIS25 2.1 13.0 1.0 O B:ACT105 2.4 23.1 1.0 C B:ACT105 2.6 19.5 1.0 CD2 B:HIS21 3.0 16.3 1.0 CE1 B:HIS21 3.1 14.1 1.0 CE1 B:HIS25 3.1 20.4 1.0 CG B:HIS25 3.2 16.4 1.0 CB B:HIS25 3.5 13.8 1.0 CH3 B:ACT105 4.1 19.6 1.0 ND1 B:HIS21 4.2 17.2 1.0 CG B:HIS21 4.2 14.4 1.0 NE2 B:HIS25 4.3 21.5 1.0 CD2 B:HIS25 4.3 21.1 1.0 CA B:HIS25 4.3 12.8 1.0 O B:HOH209 4.7 35.3 1.0 OD1 B:ASP22 4.8 15.8 1.0 O B:HOH257 4.9 37.9 1.0 N B:HIS25 4.9 12.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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 B:Zn103 b:16.3 occ:1.00 OXT B:ACT106 1.7 17.7 1.0 OD1 B:ASP46 1.9 16.9 1.0 O B:ACT106 2.0 21.3 1.0 C B:ACT106 2.1 26.8 1.0 O B:ACT104 2.1 32.7 1.0 OXT B:ACT104 2.4 18.9 1.0 C B:ACT104 2.6 20.6 1.0 CG B:ASP46 2.7 15.1 1.0 OD2 B:ASP46 3.0 18.4 1.0 CH3 B:ACT106 3.5 31.4 1.0 O A:HOH210 3.9 30.2 1.0 N A:GLU42 4.1 10.4 1.0 CB B:ASP46 4.1 9.8 1.0 CH3 B:ACT104 4.1 30.0 1.0 CB B:ALA48 4.2 13.4 1.0 C A:GLY41 4.2 11.3 1.0 CA A:GLY41 4.5 12.8 1.0 CA A:GLU42 4.6 10.3 1.0 CB A:GLU42 4.6 11.8 1.0 CA B:ASP46 4.6 8.2 1.0 N B:ALA48 4.7 10.5 1.0 O A:GLY41 4.7 12.3 1.0 C B:ASP46 5.0 8.2 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