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

Protein crystallography data

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

Zinc Binding Sites:

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 6rxm

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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 6rxm

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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 6rxm

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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 6rxm

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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 6rxm

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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 6rxm

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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

Reference:

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
Page generated: Wed Dec 16 12:43:42 2020

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