Zinc in PDB 4u10: Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans

The structure of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans, PDB code: 4u10 was solved by D.Varudharasu, R.Narayanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.48 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.240, 67.100, 101.010, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 22

The structure of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans (pdb code 4u10). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans, PDB code: 4u10:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.8 occ:1.00 O A:HOH551 1.9 6.2 1.0 OD1 A:ASP99 1.9 17.3 1.0 NE2 A:HIS173 2.1 13.1 1.0 NE2 A:HIS168 2.1 14.7 1.0 O A:HOH584 2.8 23.5 1.0 CG A:ASP99 2.9 17.5 1.0 CE1 A:HIS173 3.0 12.9 1.0 CD2 A:HIS173 3.0 13.6 1.0 CD2 A:HIS168 3.0 13.2 1.0 CE1 A:HIS168 3.1 14.2 1.0 OD2 A:ASP99 3.3 21.0 1.0 ZN A:ZN402 3.4 14.7 1.0 CB A:ASP98 4.0 15.0 1.0 ND1 A:HIS173 4.1 13.0 1.0 ND1 A:HIS168 4.2 13.1 1.0 CB A:ASP99 4.2 16.6 1.0 CG A:HIS168 4.2 12.7 1.0 CG A:HIS173 4.2 12.3 1.0 OD2 A:ASP98 4.4 12.6 1.0 CA A:PRO233 4.4 13.4 1.0 CD2 A:HIS34 4.4 15.1 1.0 CA A:ASP99 4.5 16.5 1.0 NE2 A:HIS34 4.5 16.9 1.0 N A:ASP99 4.6 15.2 1.0 CG A:ASP98 4.7 14.4 1.0 N A:TYR234 4.7 16.7 1.0 C A:ASP98 4.8 15.9 1.0 CB A:PRO233 5.0 13.5 1.0

Zinc binding site 2 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:14.7 occ:1.00 O A:HOH551 2.0 6.2 1.0 OD2 A:ASP98 2.1 12.6 1.0 NE2 A:HIS34 2.2 16.9 1.0 CL A:CL404 2.2 16.7 1.0 CG A:ASP98 3.1 14.4 1.0 CE1 A:HIS34 3.1 15.8 1.0 CD2 A:HIS34 3.1 15.1 1.0 CB A:ASP98 3.3 15.0 1.0 ZN A:ZN401 3.4 14.8 1.0 O A:HOH566 4.0 18.7 1.0 NE2 A:HIS168 4.1 14.7 1.0 CE1 A:HIS168 4.1 14.2 1.0 NH2 A:ARG271 4.1 13.7 1.0 ND1 A:HIS34 4.2 16.0 1.0 O A:HOH584 4.2 23.5 1.0 OD1 A:ASP99 4.2 17.3 1.0 OD1 A:ASP98 4.2 11.8 1.0 CG A:HIS34 4.2 15.4 1.0 N A:TYR234 4.4 16.7 1.0 O A:TRP232 4.7 11.8 1.0 CA A:ASP98 4.8 15.5 1.0 CA A:TYR234 5.0 16.4 1.0

Zinc binding site 3 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:15.0 occ:0.60 ZN A:ZN403 0.0 15.0 0.6 ZN A:ZN403 1.6 34.0 0.4 OD2 A:ASP67 1.9 26.4 1.0 NZ A:LYS66 2.5 31.1 1.0 CG A:ASP67 2.7 34.3 1.0 OD1 A:ASP67 2.7 33.5 1.0 CE A:LYS66 3.6 28.9 1.0 O A:HOH524 4.1 19.2 1.0 CB A:ASP67 4.2 32.7 1.0 O A:HOH532 4.2 33.1 1.0 O A:ASN63 4.2 25.9 1.0 CB A:ASN63 4.3 22.6 1.0 OD1 A:ASN63 4.3 21.1 1.0 CG A:ASN63 4.3 22.1 1.0 CG A:LYS66 4.5 28.6 1.0 CD A:LYS66 4.6 29.9 1.0 CA A:ASN63 4.6 23.3 1.0 C A:ASN63 4.8 23.3 1.0 ND2 A:ASN63 5.0 22.2 1.0

Zinc binding site 4 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:34.0 occ:0.40 ZN A:ZN403 0.0 34.0 0.4 ZN A:ZN403 1.6 15.0 0.6 NZ A:LYS66 2.1 31.1 1.0 O A:HOH532 2.8 33.1 1.0 CE A:LYS66 3.2 28.9 1.0 OD2 A:ASP67 3.5 26.4 1.0 OD1 A:ASN63 3.6 21.1 1.0 OD1 A:ASP67 3.9 33.5 1.0 CG A:ASN63 4.0 22.1 1.0 CG A:ASP67 4.1 34.3 1.0 CB A:ASN63 4.5 22.6 1.0 CD A:LYS66 4.5 29.9 1.0 ND2 A:ASN63 4.5 22.2 1.0 CG A:LYS66 4.9 28.6 1.0 CA A:ASN63 4.9 23.3 1.0

Zinc binding site 5 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.6 occ:1.00 O B:HOH543 1.9 10.0 1.0 OD1 B:ASP99 2.0 16.8 1.0 NE2 B:HIS173 2.1 9.8 1.0 NE2 B:HIS168 2.1 14.6 1.0 CG B:ASP99 3.0 17.7 1.0 CD2 B:HIS168 3.0 15.4 1.0 CE1 B:HIS173 3.1 10.3 1.0 CE1 B:HIS168 3.1 15.7 1.0 CD2 B:HIS173 3.1 10.7 1.0 O B:HOH596 3.3 28.5 1.0 OD2 B:ASP99 3.4 18.9 1.0 ZN B:ZN402 3.4 14.6 1.0 CB B:ASP98 4.0 12.8 1.0 O B:HOH602 4.2 30.7 1.0 ND1 B:HIS168 4.2 15.4 1.0 ND1 B:HIS173 4.2 11.4 1.0 CG B:HIS168 4.2 14.8 1.0 CG B:HIS173 4.2 11.3 1.0 CA B:PRO233 4.3 15.2 1.0 CB B:ASP99 4.3 16.6 1.0 OD2 B:ASP98 4.3 13.8 1.0 CD2 B:HIS34 4.4 11.6 1.0 NE2 B:HIS34 4.5 11.2 1.0 CA B:ASP99 4.5 15.5 1.0 CG B:ASP98 4.6 13.0 1.0 N B:TYR234 4.6 16.7 1.0 N B:ASP99 4.7 13.5 1.0 CB B:PRO233 4.7 15.8 1.0 C B:ASP98 4.8 14.0 1.0

Zinc binding site 6 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:14.6 occ:1.00 O B:HOH543 1.8 10.0 1.0 NE2 B:HIS34 2.1 11.2 1.0 OD2 B:ASP98 2.1 13.8 1.0 CL B:CL405 2.2 17.1 1.0 CE1 B:HIS34 3.0 10.2 1.0 CG B:ASP98 3.1 13.0 1.0 CD2 B:HIS34 3.1 11.6 1.0 CB B:ASP98 3.3 12.8 1.0 ZN B:ZN401 3.4 14.6 1.0 O B:HOH602 3.8 30.7 1.0 NH2 B:ARG271 4.0 14.9 1.0 NE2 B:HIS168 4.1 14.6 1.0 ND1 B:HIS34 4.1 11.1 1.0 O B:HOH571 4.1 21.6 1.0 CE1 B:HIS168 4.1 15.7 1.0 CG B:HIS34 4.2 12.4 1.0 OD1 B:ASP98 4.2 11.7 1.0 OD1 B:ASP99 4.3 16.8 1.0 N B:TYR234 4.4 16.7 1.0 O B:HOH596 4.6 28.5 1.0 O B:TRP232 4.7 14.8 1.0 CA B:ASP98 4.8 13.3 1.0 CA B:TYR234 4.9 15.6 1.0

Zinc binding site 7 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:7.8 occ:0.70 ZN B:ZN403 0.0 7.8 0.7 ZN B:ZN403 1.8 19.6 0.3 OD2 B:ASP39 2.0 14.5 1.0 OE2 B:GLU45 2.0 21.5 1.0 OD1 B:ASP39 2.2 14.5 1.0 OE1 B:GLU45 2.4 22.0 1.0 CG B:ASP39 2.4 14.7 1.0 CD B:GLU45 2.5 25.9 1.0 CB B:ASP39 3.9 14.7 1.0 CG B:GLU45 4.0 24.1 1.0 O B:HOH566 4.2 20.4 1.0 CG2 B:THR40 4.8 18.6 1.0 CA B:ASP39 4.9 16.9 1.0 N B:THR40 4.9 16.2 1.0 CB B:GLU45 5.0 26.6 1.0

Zinc binding site 8 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:19.6 occ:0.30 ZN B:ZN403 0.0 19.6 0.3 ZN B:ZN403 1.8 7.8 0.7 OE2 B:GLU45 2.8 21.5 1.0 OE1 B:GLU45 3.0 22.0 1.0 OD1 B:ASP39 3.0 14.5 1.0 CD B:GLU45 3.2 25.9 1.0 OD2 B:ASP39 3.7 14.5 1.0 CG B:ASP39 3.8 14.7 1.0 CG2 B:THR40 4.2 18.6 1.0 CG B:GLU45 4.6 24.1 1.0

Zinc binding site 9 out of 9 in the Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:18.1 occ:0.50 OE2 B:GLU82 1.7 40.1 1.0 NE2 B:HIS252 2.2 26.1 1.0 CD B:GLU82 2.8 40.4 1.0 CD2 B:HIS252 3.1 24.1 1.0 CE1 B:HIS252 3.2 25.8 1.0 OE1 B:GLU82 3.4 42.6 1.0 CG B:GLU82 4.1 35.0 1.0 CD1 B:ILE79 4.1 21.7 1.0 CG B:HIS252 4.3 25.5 1.0 ND1 B:HIS252 4.3 29.6 1.0 OG1 B:THR251 4.6 34.9 1.0

D.Varudharsu, R.Narayanan. Probing the Structure and Mechanism of De-N-Acetylase From Aggregatibacter Actinomycetemcomitans To Be Published.