Zinc in PDB 4d0y: Crystal Structure of Dacb From Streptococcus Pneumoniae D39

All present enzymatic activity of Crystal Structure of Dacb From Streptococcus Pneumoniae D39:
3.4.17.13;

The structure of Crystal Structure of Dacb From Streptococcus Pneumoniae D39, PDB code: 4d0y was solved by J.Gutierrez-Fernandez, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.84 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.950, 37.634, 102.837, 90.00, 97.98, 90.00
R / Rfree (%)	18.114 / 24.263

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39 (pdb code 4d0y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39, PDB code: 4d0y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


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 Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1239 b:15.0 occ:1.00 O4 A:PO41244 1.8 29.5 1.0 OD1 A:ASP160 2.0 15.3 1.0 NE2 A:HIS153 2.1 11.7 1.0 ND1 A:HIS207 2.1 12.2 1.0 CG A:ASP160 2.5 15.7 1.0 OD2 A:ASP160 2.8 13.4 1.0 CE1 A:HIS153 3.0 12.3 1.0 CE1 A:HIS207 3.0 11.5 1.0 CD2 A:HIS153 3.1 11.4 1.0 CG A:HIS207 3.2 12.2 1.0 P A:PO41244 3.3 33.2 1.0 O A:HOH2129 3.5 32.5 1.0 CB A:HIS207 3.5 12.6 1.0 O1 A:PO41244 3.8 43.0 1.0 OE1 A:GLU204 3.8 19.7 1.0 CB A:ASP160 4.1 16.1 1.0 O2 A:PO41244 4.1 26.9 1.0 O3 A:PO41244 4.1 23.3 1.0 ND1 A:HIS153 4.1 11.8 1.0 NE2 A:HIS207 4.2 12.1 1.0 CG A:HIS153 4.2 11.8 1.0 NE1 A:TRP206 4.2 16.2 1.0 CD2 A:HIS207 4.2 11.6 1.0 CA A:HIS207 4.3 12.4 1.0 O A:HOH2154 4.5 24.4 1.0 CD1 A:TRP206 4.6 15.9 1.0 O A:HOH2222 4.7 47.5 1.0 CA A:ASP160 4.8 17.7 1.0 N A:ASP160 4.8 17.3 1.0 O A:HOH2224 4.8 25.5 1.0 CD A:GLU204 5.0 21.9 1.0

Zinc binding site 2 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


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 Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1240 b:18.1 occ:0.80 O A:HOH2191 2.0 30.5 1.0 ND1 A:HIS181 2.0 23.4 1.0 OD2 A:ASP184 2.1 19.4 1.0 CE1 A:HIS181 2.3 23.7 1.0 O A:HOH2192 2.3 20.6 1.0 O A:HOH2188 2.4 27.1 1.0 CG A:ASP184 2.9 19.8 1.0 OD1 A:ASP184 3.1 19.0 1.0 CG A:HIS181 3.3 22.9 1.0 O A:HOH2197 3.6 26.9 1.0 NE2 A:HIS181 3.6 24.2 1.0 O A:HOH2190 3.9 26.0 1.0 O A:ASP180 3.9 17.2 1.0 CA A:HIS181 3.9 20.2 1.0 CB A:HIS181 4.0 22.5 1.0 CD2 A:HIS181 4.1 23.4 1.0 CB A:ASP184 4.4 20.4 1.0 O A:HOH2193 4.5 47.0 1.0 C A:ASP180 4.6 18.8 1.0 O A:HOH2126 4.6 39.3 1.0 O A:HOH2125 4.7 24.6 1.0 N A:HIS181 4.7 18.3 1.0 O A:HIS181 4.9 17.7 1.0 C A:HIS181 4.9 19.9 1.0

Zinc binding site 3 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


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 Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1241 b:17.1 occ:1.00 OD1 A:ASP85 1.9 22.0 1.0 OD1 A:ASP62 2.0 15.3 1.0 O A:HOH2016 2.3 37.9 1.0 CG A:ASP85 2.3 20.2 1.0 O A:HOH2064 2.4 17.3 1.0 OD2 A:ASP85 2.5 22.3 1.0 CG A:ASP62 2.9 15.1 1.0 ZN A:ZN1242 3.0 18.4 1.0 OD2 A:ASP62 3.2 15.0 1.0 OG A:SER83 3.4 21.9 1.0 CB A:ASP85 3.9 21.6 1.0 CB A:ASP62 4.2 14.1 1.0 O A:HOH2017 4.3 15.3 1.0 C A:ASP85 4.4 20.0 1.0 N A:TYR86 4.5 18.9 1.0 CB A:SER83 4.5 19.2 1.0 CA A:ASP62 4.5 13.1 1.0 CA A:ASP85 4.6 20.8 1.0 O A:ASP85 4.6 18.0 1.0 N A:ASP85 4.9 18.7 1.0 CA A:TYR86 4.9 17.1 1.0

Zinc binding site 4 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


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 Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1242 b:18.4 occ:1.00 OD2 A:ASP62 2.0 15.0 1.0 O A:HOH2017 2.1 15.3 1.0 O A:HOH2064 2.4 17.3 1.0 CG A:ASP62 3.0 15.1 1.0 ZN A:ZN1241 3.0 17.1 1.0 O A:HOH2252 3.1 23.2 1.0 OD1 A:ASP62 3.3 15.3 1.0 O A:HOH2039 4.0 45.5 1.0 O A:HOH2016 4.2 37.9 1.0 CB A:ASP62 4.3 14.1 1.0 N A:ASP62 4.6 13.2 1.0 OD2 A:ASP85 4.9 22.3 1.0 CA A:ASP62 4.9 13.1 1.0 OD1 A:ASP85 4.9 22.0 1.0

Zinc binding site 5 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


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 Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1243 b:46.7 occ:1.00 OE2 A:GLU205 2.1 29.4 1.0 O A:HOH2253 2.2 6.9 1.0 NE2 B:HIS115 2.2 33.9 1.0 CD2 B:HIS115 2.7 30.1 1.0 CD A:GLU205 3.2 20.4 1.0 OE1 A:GLU205 3.4 21.4 1.0 CE1 B:HIS115 3.4 29.9 1.0 NZ A:LYS193 3.5 30.5 1.0 CG B:HIS115 4.0 30.0 1.0 ND1 B:HIS115 4.3 31.5 1.0 CG A:GLU205 4.6 19.0 1.0 O A:HOH2167 4.6 32.8 1.0 O A:HOH2208 4.6 24.6 1.0 O B:HOH2100 4.7 36.0 1.0 CE A:LYS193 4.8 28.7 1.0

Zinc binding site 6 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


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 Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1239 b:17.5 occ:1.00 OD1 B:ASP160 2.0 20.4 1.0 O2 B:PO41247 2.0 35.5 1.0 NE2 B:HIS153 2.1 16.5 1.0 ND1 B:HIS207 2.1 14.8 1.0 CG B:ASP160 2.4 20.0 1.0 OD2 B:ASP160 2.6 25.1 1.0 P B:PO41247 2.6 40.3 1.0 CE1 B:HIS153 3.0 15.9 1.0 CE1 B:HIS207 3.0 13.4 1.0 O4 B:PO41247 3.1 38.0 1.0 O1 B:PO41247 3.1 32.8 1.0 CD2 B:HIS153 3.2 14.9 1.0 CG B:HIS207 3.2 14.8 1.0 CB B:HIS207 3.5 15.8 1.0 OE1 B:GLU204 3.9 47.5 1.0 CB B:ASP160 4.0 20.6 1.0 O3 B:PO41247 4.0 34.9 1.0 ND1 B:HIS153 4.1 16.3 1.0 NE2 B:HIS207 4.1 13.3 1.0 CD2 B:HIS207 4.2 14.0 1.0 CG B:HIS153 4.2 14.3 1.0 CA B:HIS207 4.3 15.6 1.0 NH2 B:ARG120 4.3 38.5 1.0 CA B:ASP160 4.7 20.6 1.0 N B:ASP160 4.7 17.8 1.0 O B:HOH2147 4.8 18.9 1.0 CD B:GLU204 5.0 41.2 1.0

Zinc binding site 7 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1240 b:16.1 occ:1.00 O B:HOH2014 1.8 27.7 1.0 OD1 B:ASP85 2.0 17.9 1.0 OD1 B:ASP62 2.0 15.4 1.0 O B:HOH2064 2.2 19.4 1.0 CG B:ASP85 2.3 16.4 1.0 OD2 B:ASP85 2.4 21.4 1.0 CG B:ASP62 2.9 14.8 1.0 ZN B:ZN1241 3.1 16.0 1.0 OD2 B:ASP62 3.3 14.4 1.0 OG B:SER83 3.6 24.2 1.0 O B:HOH2055 3.9 37.0 1.0 CB B:ASP85 3.9 16.9 1.0 CB B:ASP62 4.2 13.4 1.0 C B:ASP85 4.4 16.6 1.0 N B:TYR86 4.6 15.8 1.0 O B:ASP85 4.6 17.0 1.0 CA B:ASP62 4.6 12.0 1.0 CB B:SER83 4.6 18.5 1.0 CA B:ASP85 4.6 16.2 1.0 O B:HOH2225 4.9 36.1 1.0 CA B:TYR86 4.9 15.0 1.0

Zinc binding site 8 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1241 b:16.0 occ:1.00 OD2 B:ASP62 2.0 14.4 1.0 O B:HOH2064 2.4 19.4 1.0 O B:HOH2225 2.8 36.1 1.0 CG B:ASP62 3.0 14.8 1.0 ZN B:ZN1240 3.1 16.1 1.0 OD1 B:ASP62 3.4 15.4 1.0 O B:HOH2014 3.9 27.7 1.0 O B:HOH2015 4.3 32.9 1.0 CB B:ASP62 4.4 13.4 1.0 N B:ASP62 4.5 11.5 1.0 CA B:ASP62 4.9 12.0 1.0 OD2 B:ASP85 5.0 21.4 1.0

Zinc binding site 9 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1242 b:56.1 occ:0.70 NE2 B:HIS181 2.1 42.3 1.0 CD2 B:HIS181 3.0 38.5 1.0 CE1 B:HIS181 3.2 44.5 1.0 CG B:HIS181 4.2 36.1 1.0 ND1 B:HIS181 4.2 39.6 1.0 CB B:ASP180 4.3 30.5 1.0 OD2 B:ASP180 4.4 36.9 1.0 CG B:ASP180 4.8 31.4 1.0

Zinc binding site 10 out of 13 in the Crystal Structure of Dacb From Streptococcus Pneumoniae D39


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Dacb From Streptococcus Pneumoniae D39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1243 b:63.3 occ:1.00 ND1 B:HIS181 2.1 39.6 1.0 OD2 B:ASP184 2.1 35.4 1.0 CE1 B:HIS181 2.3 44.5 1.0 O B:HOH2167 2.8 41.7 1.0 CG B:ASP184 2.9 26.2 1.0 OD1 B:ASP184 3.1 31.1 1.0 CG B:HIS181 3.4 36.1 1.0 NE2 B:HIS181 3.6 42.3 1.0 O B:ASP180 4.0 25.7 1.0 CA B:HIS181 4.1 27.8 1.0 CD2 B:HIS181 4.1 38.5 1.0 CB B:HIS181 4.1 31.5 1.0 CB B:ASP184 4.4 24.7 1.0 C B:ASP180 4.7 25.5 1.0 N B:HIS181 4.9 25.8 1.0

M.R.Abdullah, J.Gutierrez-Fernandez, T.Pribyl, N.Gisch, M.Saleh, M.Rohde, L.Petruschka, G.Burchhardt, D.Schwudke, J.A.Hermoso, S.Hammerschmidt. Structure of the Pneumococcal L,D-Carboxypeptidase Dacb and Pathophysiological Effects of Disabled Cell Wall Hydrolases Daca and Dacb. Mol.Microbiol. V. 93 1183 2014.
ISSN: ISSN 0950-382X
PubMed: 25060741
DOI: 10.1111/MMI.12729