Zinc in PDB 2zc5: Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae

The structure of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae, PDB code: 2zc5 was solved by M.Yamada, T.Watanabe, Y.Takeuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	185.704, 50.665, 110.784, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 27.6

The binding sites of Zinc atom in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae (pdb code 2zc5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae, PDB code: 2zc5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:55.2 occ:1.00 ND1 B:HIS309 2.1 56.0 1.0 OH B:TYR319 2.5 60.8 1.0 CE1 B:HIS309 2.8 55.6 1.0 CG B:HIS309 3.2 56.2 1.0 CZ B:TYR319 3.4 61.0 1.0 CB B:HIS309 3.7 56.4 1.0 ZN B:ZN804 3.8 83.7 1.0 CE1 B:TYR319 3.8 61.1 1.0 CA B:HIS309 3.9 56.5 1.0 OD2 B:ASP312 4.0 56.6 1.0 NE2 B:HIS309 4.0 55.8 1.0 CD2 B:HIS309 4.2 55.8 1.0 CE2 B:TYR319 4.4 61.1 1.0 CB B:ASP312 4.4 56.2 1.0 O B:HIS309 4.7 56.5 1.0 CG B:ASP312 4.7 56.3 1.0 CD1 B:TYR624 4.8 59.2 1.0 CE1 B:TYR624 4.8 59.4 1.0 C B:HIS309 4.8 56.4 1.0 N B:HIS309 4.9 56.7 1.0

Zinc binding site 2 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:35.5 occ:1.00 OE1 B:GLU435 1.9 44.9 1.0 ND1 B:HIS395 2.1 44.3 1.0 CD B:GLU435 2.6 44.0 1.0 OE2 B:GLU435 2.8 45.1 1.0 CG B:HIS395 3.0 43.8 1.0 CE1 B:HIS395 3.1 44.5 1.0 CB B:HIS395 3.3 43.8 1.0 OE2 B:GLU397 3.8 38.9 1.0 CG B:GLU435 4.1 43.4 1.0 CD2 B:HIS395 4.2 44.0 1.0 NE2 B:HIS395 4.2 43.8 1.0 CA B:HIS395 4.6 43.8 1.0 N B:HIS395 4.9 44.2 1.0 O B:HIS395 5.0 43.3 1.0

Zinc binding site 3 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:44.3 occ:1.00 ND1 B:HIS460 2.0 43.0 1.0 CE1 B:HIS460 2.9 43.5 1.0 CG B:HIS460 3.1 42.8 1.0 CB B:HIS460 3.6 42.5 1.0 NE2 B:HIS460 4.1 43.7 1.0 CA B:HIS460 4.1 42.4 1.0 CD2 B:HIS460 4.2 42.8 1.0 O B:ILE459 4.6 42.9 1.0

Zinc binding site 4 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn804 b:83.7 occ:1.00 OH B:TYR319 2.5 60.8 1.0 OE2 B:GLU318 2.6 58.6 1.0 OE1 B:GLU318 2.6 59.2 1.0 CD B:GLU318 2.9 59.3 1.0 CZ B:TYR319 3.5 61.0 1.0 ZN B:ZN801 3.8 55.2 1.0 CE1 B:TYR319 3.9 61.1 1.0 CG B:GLU318 4.3 59.1 1.0 OD2 B:ASP312 4.3 56.6 1.0 CE2 B:TYR319 4.6 61.1 1.0

Zinc binding site 5 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn805 b:44.8 occ:1.00 ND1 D:HIS309 2.2 49.3 1.0 CE1 D:HIS309 3.1 50.0 1.0 CG D:HIS309 3.2 48.9 1.0 OD2 D:ASP312 3.4 47.7 1.0 CB D:HIS309 3.6 48.5 1.0 OH D:TYR319 3.6 48.6 1.0 CA D:HIS309 3.7 48.5 1.0 NE2 D:HIS309 4.2 50.0 1.0 CG D:ASP312 4.3 47.9 1.0 CD2 D:HIS309 4.3 49.5 1.0 N D:HIS309 4.4 48.5 1.0 CB D:ASP312 4.6 47.9 1.0 CZ D:TYR319 4.6 48.5 1.0 CE1 D:TYR624 4.8 51.6 1.0 C D:HIS309 4.9 48.3 1.0 O D:LYS308 4.9 48.7 1.0 C D:LYS308 4.9 48.8 1.0 CE1 D:TYR319 5.0 48.8 1.0 O D:HIS309 5.0 48.3 1.0

Zinc binding site 6 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn806 b:41.9 occ:1.00 OE2 D:GLU435 1.8 38.1 1.0 ND1 D:HIS395 2.0 40.2 1.0 CD D:GLU435 2.6 36.9 1.0 OE1 D:GLU435 2.8 38.2 1.0 CE1 D:HIS395 2.9 40.6 1.0 CG D:HIS395 3.1 40.0 1.0 CB D:HIS395 3.5 40.1 1.0 OE2 D:GLU397 3.9 39.0 1.0 CG D:GLU435 4.0 36.6 1.0 NE2 D:HIS395 4.0 40.4 1.0 CD2 D:HIS395 4.1 39.9 1.0 NZ D:LYS439 4.6 38.6 1.0 CA D:HIS395 4.8 40.0 1.0 N D:HIS395 5.0 40.2 1.0

Zinc binding site 7 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn807 b:45.0 occ:1.00 ND1 D:HIS460 2.2 37.4 1.0 CE1 D:HIS460 2.9 38.0 1.0 CG D:HIS460 3.3 37.1 1.0 CB D:HIS460 3.8 37.0 1.0 NE2 D:HIS460 4.1 38.3 1.0 CA D:HIS460 4.2 37.0 1.0 CD2 D:HIS460 4.3 37.3 1.0 O D:ILE459 4.6 36.1 1.0

Zinc binding site 8 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Biapenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn808 b:63.9 occ:1.00 OH D:TYR319 2.2 48.6 1.0 OE2 D:GLU318 2.3 49.9 1.0 CZ D:TYR319 3.0 48.5 1.0 CD D:GLU318 3.0 50.2 1.0 OE1 D:GLU318 3.0 50.5 1.0 CE2 D:TYR319 3.4 48.1 1.0 CE1 D:TYR319 4.0 48.8 1.0 CG D:GLU318 4.5 49.8 1.0 CD2 D:TYR319 4.6 48.2 1.0 CE1 D:HIS309 4.8 50.0 1.0

M.Yamada, T.Watanabe, N.Baba, Y.Takeuchi, F.Ohsawa, S.Gomi. Crystal Structures of Biapenem and Tebipenem Complexed with Penicillin-Binding Proteins 2X and 1A From Streptococcus Pneumoniae Antimicrob.Agents Chemother. V. 52 2053 2008.
ISSN: ISSN 0066-4804
PubMed: 18391040
DOI: 10.1128/AAC.01456-07