Zinc in PDB 2c5w: Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) From Streptococcus Pneumoniae

The structure of Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) From Streptococcus Pneumoniae, PDB code: 2c5w was solved by C.Contreras-Martel, V.Job, A.-M.Di Guilmi, T.Vernet, O.Dideberg, A.Dessen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.07 / 2.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	112.376, 183.373, 54.850, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 25.5

The structure of Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) From Streptococcus Pneumoniae also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) From Streptococcus Pneumoniae (pdb code 2c5w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) From Streptococcus Pneumoniae, PDB code: 2c5w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) 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 (Cefotaxime) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:63.8 occ:1.00 ND1 B:HIS309 2.4 56.2 1.0 O B:HOH2063 2.7 50.1 1.0 CE1 B:HIS309 3.3 52.0 1.0 CG B:HIS309 3.3 50.0 1.0 CB B:HIS309 3.6 48.4 1.0 CA B:HIS309 3.6 52.2 1.0 OD2 B:ASP312 3.8 68.1 1.0 OH B:TYR319 4.0 58.7 1.0 N B:HIS309 4.4 51.1 1.0 NE2 B:HIS309 4.4 52.1 1.0 CD2 B:HIS309 4.4 49.0 1.0 C B:HIS309 4.7 54.3 1.0 O B:HIS309 4.7 54.2 1.0 CZ B:TYR319 4.8 56.0 1.0 CG B:ASP312 4.8 63.0 1.0 CB B:ASP312 4.9 62.0 1.0

Zinc binding site 2 out of 5 in the Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) 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 (Cefotaxime) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:44.2 occ:1.00 ND1 B:HIS395 2.1 33.2 1.0 OE1 B:GLU435 2.4 77.3 1.0 OE2 B:GLU435 2.6 73.9 1.0 CD B:GLU435 2.7 68.3 1.0 CE1 B:HIS395 3.0 36.2 1.0 CG B:HIS395 3.2 31.6 1.0 CB B:HIS395 3.6 38.2 1.0 OE2 B:GLU397 3.8 56.0 1.0 CG B:GLU435 4.1 59.3 1.0 NE2 B:HIS395 4.1 37.2 1.0 O B:HOH2015 4.1 39.5 1.0 NZ B:LYS439 4.2 64.8 1.0 CD2 B:HIS395 4.2 33.9 1.0 CE B:LYS439 4.7 52.1 1.0 CA B:HIS395 4.9 38.8 1.0

Zinc binding site 3 out of 5 in the Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) 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 (Cefotaxime) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:37.0 occ:1.00 ND1 B:HIS460 2.3 34.5 1.0 O B:HOH2064 2.3 28.9 1.0 CE1 B:HIS460 3.0 34.5 1.0 CG B:HIS460 3.3 30.9 1.0 CB B:HIS460 3.8 35.8 1.0 NE2 B:HIS460 4.2 35.9 1.0 O B:HOH2032 4.3 35.4 1.0 CA B:HIS460 4.3 39.2 1.0 CD2 B:HIS460 4.3 33.2 1.0 O B:ILE459 4.7 41.3 1.0

Zinc binding site 4 out of 5 in the Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) 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 (Cefotaxime) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn704 b:58.0 occ:0.36 NE2 B:HIS503 2.4 68.4 1.0 CE1 B:HIS503 3.0 68.4 1.0 CD2 B:HIS503 3.6 64.2 1.0 O A:HOH2001 3.8 41.2 1.0 NZ B:LYS504 4.0 72.2 1.0 OD1 A:ASN60 4.0 72.3 1.0 ND2 A:ASN60 4.1 66.7 1.0 ND1 B:HIS503 4.3 66.3 1.0 CE B:LYS504 4.4 74.2 1.0 CG A:ASN60 4.5 70.6 1.0 CG B:HIS503 4.6 63.9 1.0

Zinc binding site 5 out of 5 in the Penicillin-Binding Protein 1A (Pbp-1A) Acyl-Enzyme Complex (Cefotaxime) 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 (Cefotaxime) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn705 b:64.6 occ:0.48 ND1 B:HIS349 2.5 64.8 1.0 CE1 B:HIS349 3.3 67.3 1.0 CG B:HIS349 3.4 64.6 1.0 CB B:HIS349 3.7 63.3 1.0 CA B:HIS349 4.2 62.4 1.0 NE2 B:HIS349 4.3 70.6 1.0 CD2 B:HIS349 4.4 68.7 1.0 O B:HIS349 4.6 66.2 1.0 C B:HIS349 4.8 67.4 1.0

C.Contreras-Martel, V.Job, A.-M.Di Guilmi, T.Vernet, O.Dideberg, A.Dessen. Crystal Structure of Penicillin-Binding Protein 1A (PBP1A) Reveals A Mutational Hotspot Implicated in Beta-Lactam Resistance in Streptococcus Pneumoniae. J.Mol.Biol. V. 355 684 2006.
ISSN: ISSN 0022-2836
PubMed: 16316661
DOI: 10.1016/J.JMB.2005.10.030