Zinc in PDB 6nl6: Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q)

The structure of Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q), PDB code: 6nl6 was solved by T.Huxford, S.Boguslaw, B.Maniaci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.38 / 1.40
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	48.292, 48.292, 83.341, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 21.4

The structure of Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) (pdb code 6nl6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q), PDB code: 6nl6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, 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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:16.8 occ:1.00 OE2 A:GLU19 1.9 13.8 1.0 O A:HOH242 2.0 10.7 1.0 O A:HOH245 2.3 8.8 1.0 CD A:GLU19 2.9 14.5 1.0 CG A:GLU19 3.3 16.6 1.0 OE1 A:GLU19 4.1 22.4 1.0 N A:MET1 4.6 17.4 1.0 CB A:GLU19 4.8 12.2 1.0 O A:ALA20 5.0 14.7 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, 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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:19.2 occ:1.00 CL B:CL104 2.0 21.0 1.0 OE1 A:GLU27 2.0 23.1 1.0 NE2 B:HIS36 2.1 22.4 0.6 NE2 B:HIS36 2.1 25.8 0.4 CE1 B:HIS36 2.2 24.7 0.4 O B:HOH248 2.3 12.3 1.0 NE2 B:HIS32 2.5 26.6 1.0 CD A:GLU27 2.9 16.0 1.0 OE2 A:GLU27 2.9 20.9 1.0 CD2 B:HIS36 3.0 12.0 0.6 CE1 B:HIS36 3.1 18.1 0.6 CE1 B:HIS32 3.3 21.0 1.0 CD2 B:HIS36 3.4 25.1 0.4 CD2 B:HIS32 3.5 30.0 1.0 ND1 B:HIS36 3.5 22.4 0.4 O D:HOH212 4.0 19.4 1.0 CG B:HIS36 4.0 21.8 0.4 CG B:HIS36 4.1 18.6 0.6 ND1 B:HIS36 4.2 19.8 0.6 O A:HOH238 4.2 19.0 1.0 ND1 B:HIS32 4.3 35.5 1.0 CG A:GLU27 4.3 15.3 1.0 CG B:HIS32 4.4 26.2 1.0 O A:HOH246 4.6 21.4 1.0 O A:HOH254 4.6 38.5 1.0 CB A:GLU27 4.8 12.3 1.0 O A:HOH207 4.9 30.1 1.0 O B:HOH230 4.9 52.0 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, 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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:19.3 occ:1.00 OE2 B:GLU19 1.9 16.8 1.0 O B:HOH236 1.9 13.8 1.0 O B:HOH249 2.3 10.3 1.0 CD B:GLU19 3.0 17.8 1.0 CG B:GLU19 3.3 18.8 1.0 OE1 B:GLU19 4.1 26.7 1.0 N B:MET1 4.7 16.6 1.0 CB B:GLU19 4.8 12.4 1.0 O B:ALA20 4.9 15.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, 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 Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:18.5 occ:1.00 CL B:CL105 2.0 19.6 1.0 OE1 B:GLU27 2.1 21.3 1.0 O B:HOH253 2.3 11.3 1.0 CD B:GLU27 2.9 15.2 1.0 OE2 B:GLU27 2.9 21.3 1.0 O B:HOH234 4.1 18.4 1.0 CG B:GLU27 4.3 13.7 1.0 O B:HOH252 4.4 38.1 1.0 O B:HOH251 4.5 23.0 1.0 CB B:GLU27 4.8 12.3 1.0 O B:HOH203 4.9 25.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:23.1 occ:1.00 NE2 C:HIS36 1.9 11.2 0.3 NE2 C:HIS36 2.1 12.0 0.7 NE2 C:HIS32 2.1 16.1 1.0 O C:HOH244 2.3 13.4 1.0 CL C:CL102 2.5 22.5 1.0 CE1 C:HIS36 2.5 10.5 0.3 CD2 C:HIS36 3.0 8.2 0.7 CE1 C:HIS32 3.1 15.2 1.0 CE1 C:HIS36 3.1 12.6 0.7 CD2 C:HIS32 3.1 15.1 1.0 CD2 C:HIS36 3.1 11.8 0.3 ND1 C:HIS36 3.8 12.4 0.3 CG C:HIS36 4.1 12.7 0.3 ND1 C:HIS32 4.1 14.6 1.0 ND1 C:HIS36 4.1 13.4 0.7 CG C:HIS36 4.2 14.0 0.7 CG C:HIS32 4.2 16.7 1.0 O A:HOH216 4.3 18.1 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mutant B1 Immunoglobulin-Binding Domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:20.4 occ:1.00 NE2 D:HIS36 1.9 14.8 0.3 NE2 D:HIS36 1.9 12.8 0.7 NE2 D:HIS32 2.1 12.7 1.0 O D:HOH247 2.2 12.2 1.0 CE1 D:HIS36 2.4 18.7 0.3 CL D:CL102 2.4 20.2 1.0 CE1 D:HIS36 2.9 14.4 0.7 CD2 D:HIS36 3.0 16.9 0.7 CE1 D:HIS32 3.1 12.2 1.0 CD2 D:HIS32 3.1 11.6 1.0 CD2 D:HIS36 3.2 22.0 0.3 ND1 D:HIS36 3.6 18.5 0.3 CG D:HIS36 4.0 16.2 0.3 ND1 D:HIS36 4.0 13.7 0.7 CG D:HIS36 4.1 15.1 0.7 O B:HOH216 4.1 18.4 1.0 ND1 D:HIS32 4.2 17.6 1.0 CG D:HIS32 4.2 16.0 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