Zinc in PDB 2zc6: Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) From Streptococcus Pneumoniae

The structure of Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) From Streptococcus Pneumoniae, PDB code: 2zc6 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)	29.88 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	185.755, 50.277, 109.535, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 27.1

The binding sites of Zinc atom in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) From Streptococcus Pneumoniae (pdb code 2zc6). 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 (Tebipenem) From Streptococcus Pneumoniae, PDB code: 2zc6:
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 (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:47.6 occ:1.00 ND1 B:HIS309 2.2 36.9 1.0 OH B:TYR319 2.3 42.1 1.0 CE1 B:HIS309 3.0 36.8 1.0 CG B:HIS309 3.3 37.5 1.0 CZ B:TYR319 3.3 42.7 1.0 ZN B:ZN804 3.3 56.5 1.0 OD2 B:ASP312 3.6 40.1 1.0 CB B:HIS309 3.7 38.4 1.0 CE1 B:TYR319 4.0 43.0 1.0 CA B:HIS309 4.0 38.5 1.0 CE2 B:TYR319 4.2 42.6 1.0 NE2 B:HIS309 4.2 36.5 1.0 CD2 B:HIS309 4.4 36.4 1.0 CB B:ASP312 4.4 39.5 1.0 CG B:ASP312 4.4 40.0 1.0 CE1 B:TYR624 4.6 47.7 1.0 CD1 B:TYR624 4.6 47.4 1.0 O B:HIS309 4.8 38.2 1.0 OE2 B:GLU318 4.9 43.4 1.0 C B:HIS309 4.9 38.4 1.0

Zinc binding site 2 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:35.6 occ:1.00 OE1 B:GLU435 1.9 35.8 1.0 ND1 B:HIS395 2.3 37.4 1.0 CD B:GLU435 2.6 34.7 1.0 OE2 B:GLU435 2.7 35.0 1.0 CG B:HIS395 3.2 36.5 1.0 CE1 B:HIS395 3.3 36.5 1.0 CB B:HIS395 3.4 36.4 1.0 OE2 B:GLU397 3.5 33.2 1.0 CG B:GLU435 4.1 34.4 1.0 CD2 B:HIS395 4.3 36.8 1.0 NE2 B:HIS395 4.4 36.9 1.0 CD B:GLU397 4.6 34.1 1.0 CA B:HIS395 4.7 36.6 1.0 NZ B:LYS439 4.9 38.0 1.0

Zinc binding site 3 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:39.3 occ:1.00 ND1 B:HIS460 2.1 38.4 1.0 CE1 B:HIS460 3.0 38.9 1.0 CG B:HIS460 3.1 38.0 1.0 CB B:HIS460 3.5 37.8 1.0 CA B:HIS460 4.1 37.7 1.0 NE2 B:HIS460 4.2 38.6 1.0 CD2 B:HIS460 4.2 38.2 1.0 O B:ILE459 4.4 37.5 1.0

Zinc binding site 4 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn804 b:56.5 occ:1.00 OH B:TYR319 2.3 42.1 1.0 OE1 B:GLU318 2.6 43.7 1.0 OE2 B:GLU318 2.8 43.4 1.0 CD B:GLU318 3.0 42.7 1.0 ZN B:ZN801 3.3 47.6 1.0 CZ B:TYR319 3.4 42.7 1.0 OD2 B:ASP312 3.5 40.1 1.0 CE1 B:TYR319 3.8 43.0 1.0 CG B:ASP312 4.3 40.0 1.0 CE2 B:TYR319 4.4 42.6 1.0 CG B:GLU318 4.5 42.2 1.0 CB B:ASP312 4.6 39.5 1.0 CB B:GLU318 5.0 42.1 1.0

Zinc binding site 5 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn805 b:38.2 occ:1.00 ND1 D:HIS309 2.0 36.2 1.0 CE1 D:HIS309 2.8 36.4 1.0 CG D:HIS309 3.0 36.0 1.0 OD2 D:ASP312 3.3 41.8 1.0 CB D:HIS309 3.5 36.4 1.0 CA D:HIS309 3.6 36.5 1.0 OH D:TYR319 3.7 40.4 1.0 NE2 D:HIS309 3.9 36.2 1.0 CD2 D:HIS309 4.1 36.4 1.0 CG D:ASP312 4.3 40.2 1.0 CB D:ASP312 4.4 39.0 1.0 N D:HIS309 4.5 37.1 1.0 CZ D:TYR319 4.6 39.6 1.0 O D:HIS309 4.7 36.2 1.0 C D:HIS309 4.7 36.4 1.0 CE1 D:TYR624 4.9 40.8 1.0 ZN D:ZN808 5.0 46.2 1.0

Zinc binding site 6 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn806 b:42.9 occ:1.00 OE1 D:GLU435 2.1 34.4 1.0 ND1 D:HIS395 2.2 44.1 1.0 OE2 D:GLU435 2.4 34.8 1.0 CD D:GLU435 2.5 33.9 1.0 CG D:HIS395 3.1 43.0 1.0 CE1 D:HIS395 3.2 43.9 1.0 CB D:HIS395 3.3 42.6 1.0 CG D:GLU435 4.0 34.1 1.0 OE2 D:GLU397 4.0 38.7 1.0 CD2 D:HIS395 4.2 43.5 1.0 NE2 D:HIS395 4.2 43.8 1.0 NZ D:LYS439 4.3 38.2 1.0 CA D:HIS395 4.7 42.5 1.0 O D:HIS395 4.9 42.2 1.0 CD D:GLU397 4.9 39.3 1.0 N D:HIS395 5.0 42.8 1.0

Zinc binding site 7 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn807 b:44.2 occ:1.00 ND1 D:HIS460 1.9 34.1 1.0 CE1 D:HIS460 2.8 35.0 1.0 CG D:HIS460 3.0 33.9 1.0 CB D:HIS460 3.4 33.2 1.0 NE2 D:HIS460 4.0 35.6 1.0 CA D:HIS460 4.0 33.2 1.0 CD2 D:HIS460 4.1 34.6 1.0 O D:ILE459 4.5 32.3 1.0 N D:HIS460 4.9 32.6 1.0

Zinc binding site 8 out of 8 in the Penicillin-Binding Protein 1A (Pbp 1A) Acyl-Enzyme Complex (Tebipenem) 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 (Tebipenem) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn808 b:46.2 occ:1.00 OE2 D:GLU318 2.0 37.3 1.0 OH D:TYR319 2.1 40.4 1.0 CD D:GLU318 2.9 37.6 1.0 CZ D:TYR319 2.9 39.6 1.0 OE1 D:GLU318 3.2 36.4 1.0 CE2 D:TYR319 3.4 39.5 1.0 CE1 D:TYR319 3.9 39.6 1.0 CG D:GLU318 4.2 37.7 1.0 CE1 D:HIS309 4.6 36.4 1.0 CD2 D:TYR319 4.6 39.2 1.0 ZN D:ZN805 5.0 38.2 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