Zinc in PDB 6rxm: Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide

The structure of Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide, PDB code: 6rxm was solved by M.Spinck, R.Gasper, H.Neumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.47 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.300, 95.380, 168.830, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.3

The binding sites of Zinc atom in the Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide (pdb code 6rxm). 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 Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide, PDB code: 6rxm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide


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 Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:51.0 occ:1.00 SG A:CYS177 2.2 98.5 1.0 SG A:CYS176 2.3 45.0 1.0 SG A:CYS174 2.3 68.8 1.0 SG A:CYS155 2.3 47.5 1.0 CB A:CYS174 3.0 56.3 1.0 CB A:CYS177 3.1 78.2 1.0 CB A:CYS155 3.3 41.3 1.0 N A:CYS177 3.6 76.9 1.0 CB A:SER158 3.7 50.7 1.0 CB A:CYS176 3.8 64.1 1.0 C A:CYS176 3.9 78.0 1.0 CA A:CYS177 4.0 80.3 1.0 N A:CYS176 4.1 66.1 1.0 CA A:CYS176 4.2 70.5 1.0 CG A:GLN157 4.2 70.2 1.0 NE2 A:GLN157 4.3 82.0 1.0 N A:SER158 4.4 53.3 1.0 CA A:CYS174 4.4 50.1 1.0 OG A:SER158 4.5 57.0 1.0 O A:CYS176 4.6 78.6 1.0 CA A:CYS155 4.6 38.0 1.0 CB A:ALA181 4.7 56.2 1.0 CA A:SER158 4.7 55.2 1.0 O A:HOH543 4.7 47.9 1.0 C A:CYS174 4.8 60.8 1.0 CD A:GLN157 4.8 80.3 1.0 N A:ALA181 4.8 48.1 1.0 N A:HIS175 4.9 66.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide


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 Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:59.7 occ:1.00 SG B:CYS174 2.4 66.8 1.0 SG B:CYS176 2.5 55.8 1.0 SG B:CYS155 2.5 53.3 1.0 NE2 B:GLN157 2.6 68.0 1.0 CB B:CYS174 3.0 65.5 1.0 SG B:CYS177 3.0 77.2 1.0 N B:CYS177 3.5 72.7 1.0 CB B:CYS155 3.5 49.6 1.0 CB B:CYS177 3.6 77.5 1.0 CD B:GLN157 3.8 76.4 1.0 CB B:CYS176 3.8 69.7 1.0 C B:CYS176 3.9 80.1 1.0 N B:CYS176 3.9 72.2 1.0 OG B:SER158 4.0 58.3 1.0 CA B:CYS176 4.0 76.2 1.0 CG B:GLN157 4.1 65.7 1.0 CA B:CYS177 4.2 78.9 1.0 CA B:CYS174 4.4 71.7 1.0 CB B:SER158 4.4 59.6 1.0 O B:CYS176 4.7 80.4 1.0 N B:HIS175 4.8 76.6 1.0 C B:CYS174 4.8 74.6 1.0 N B:SER158 4.8 57.3 1.0 CB B:ALA181 4.8 60.8 1.0 CA B:CYS155 4.8 47.0 1.0 OE1 B:GLN157 4.8 76.3 1.0 N B:ALA181 4.8 75.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide


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 Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:41.6 occ:1.00 SG C:CYS174 2.2 39.0 1.0 SG C:CYS177 2.4 50.5 1.0 SG C:CYS176 2.4 44.5 1.0 SG C:CYS155 2.5 36.5 1.0 CB C:CYS174 3.1 43.8 1.0 N C:CYS177 3.3 48.5 1.0 CB C:CYS155 3.4 37.7 1.0 CB C:CYS177 3.4 54.1 1.0 CB C:CYS176 3.6 48.0 1.0 OG C:SER158 3.6 39.2 1.0 C C:CYS176 3.6 51.1 1.0 N C:CYS176 3.7 45.4 1.0 CA C:CYS176 3.8 43.9 1.0 CB C:SER158 3.9 38.5 1.0 CA C:CYS177 3.9 49.6 1.0 N C:SER158 4.4 41.3 1.0 O C:CYS176 4.4 45.0 1.0 CA C:CYS174 4.5 44.9 1.0 CB C:ALA181 4.7 41.7 1.0 N C:HIS175 4.7 45.9 1.0 CA C:CYS155 4.7 30.5 1.0 N C:ALA181 4.7 42.7 1.0 CA C:SER158 4.8 46.0 1.0 C C:CYS174 4.8 53.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide


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 Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:40.9 occ:1.00 SG D:CYS174 2.2 41.6 1.0 SG D:CYS155 2.3 40.7 1.0 SG D:CYS177 2.4 42.5 1.0 SG D:CYS176 2.4 45.1 1.0 CB D:CYS174 3.0 41.9 1.0 N D:CYS177 3.3 42.7 1.0 CB D:CYS177 3.3 45.8 1.0 CB D:CYS155 3.3 39.2 1.0 C D:CYS176 3.7 46.5 1.0 CB D:CYS176 3.7 45.4 1.0 OG D:SER158 3.7 48.4 1.0 N D:CYS176 3.9 48.3 1.0 CA D:CYS177 3.9 47.2 1.0 CA D:CYS176 3.9 44.3 1.0 CB D:SER158 4.0 42.1 1.0 N D:SER158 4.4 47.9 1.0 O D:CYS176 4.4 40.3 1.0 CA D:CYS174 4.4 43.9 1.0 CB D:ALA181 4.6 43.0 1.0 CA D:CYS155 4.7 42.0 1.0 C D:CYS174 4.8 45.0 1.0 CA D:SER158 4.9 49.5 1.0 N D:HIS175 4.9 46.6 1.0 N D:ALA181 4.9 44.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide


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 Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:28.4 occ:1.00 SG E:CYS174 2.3 29.3 1.0 SG E:CYS176 2.3 27.1 1.0 SG E:CYS177 2.4 28.1 1.0 SG E:CYS155 2.4 29.8 1.0 CB E:CYS174 3.1 30.1 1.0 N E:CYS177 3.3 30.9 1.0 CB E:CYS177 3.3 28.6 1.0 CB E:CYS155 3.4 32.3 1.0 C E:CYS176 3.6 28.3 1.0 CB E:CYS176 3.6 30.7 1.0 OG E:SER158 3.7 37.5 1.0 N E:CYS176 3.8 26.4 1.0 CA E:CYS177 3.9 35.5 1.0 CA E:CYS176 3.9 27.9 1.0 CB E:SER158 4.0 38.4 1.0 O E:CYS176 4.2 29.7 1.0 N E:SER158 4.4 32.1 1.0 CA E:CYS174 4.6 28.7 1.0 CB E:ALA181 4.6 35.9 1.0 CB E:GLN157 4.7 34.1 1.0 CA E:CYS155 4.7 22.4 1.0 N E:ALA181 4.7 28.2 1.0 CA E:SER158 4.9 30.6 1.0 C E:CYS174 4.9 36.3 1.0 N E:HIS175 4.9 34.4 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide


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 Cobb AC2 (A76G, I131C, V162G) in Complex with H4K16-Acetyl Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:54.4 occ:1.00 SG F:CYS176 2.2 61.5 1.0 SG F:CYS174 2.3 67.0 1.0 SG F:CYS155 2.5 50.3 1.0 SG F:CYS177 2.5 82.5 1.0 CB F:CYS174 3.0 59.2 1.0 CB F:CYS155 3.3 45.9 1.0 CB F:CYS177 3.4 65.5 1.0 N F:CYS177 3.4 66.0 1.0 OG F:SER158 3.5 63.9 1.0 CB F:CYS176 3.6 78.5 1.0 C F:CYS176 3.8 73.6 1.0 CB F:SER158 3.9 67.7 1.0 N F:CYS176 3.9 62.5 1.0 CA F:CYS176 4.0 69.0 1.0 CA F:CYS177 4.1 69.3 1.0 CA F:CYS174 4.4 62.4 1.0 CG F:GLN157 4.4 76.3 1.0 OE1 F:GLN160 4.4 77.7 1.0 OE1 F:GLN157 4.5 83.0 1.0 O F:CYS176 4.6 68.1 1.0 N F:HIS175 4.6 69.7 1.0 C F:CYS174 4.6 64.4 1.0 N F:SER158 4.7 65.3 1.0 CA F:CYS155 4.7 48.1 1.0 CD F:GLN157 4.8 82.3 1.0 CA F:SER158 5.0 62.3 1.0 CB F:ALA181 5.0 55.2 1.0

M.Spinck, P.Neumann-Staubitz, M.Ecke, R.Gasper, H.Neumann. Evolved, Selective Erasers of Distinct Lysine Acylations. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32187803
DOI: 10.1002/ANIE.202002899