Zinc in PDB 2wad: Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)

The structure of Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204), PDB code: 2wad was solved by C.Contreras-Martel, C.Dahout-Gonzalez, A.Dos-Santos-Martins, M.Kotnik, A.Dessen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 2.18
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	128.788, 128.788, 123.139, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 26.1

The binding sites of Zinc atom in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) (pdb code 2wad). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204), PDB code: 2wad:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:61.4 occ:1.00 OD2 A:ASP288 1.9 13.2 1.0 OD2 A:ASP292 2.0 23.6 1.0 ND1 A:HIS290 2.3 37.1 1.0 CG A:ASP288 2.8 24.2 1.0 OD1 A:ASP288 2.9 19.9 1.0 CG A:ASP292 2.9 26.2 1.0 CG A:HIS290 3.2 39.0 1.0 CB A:ASP292 3.2 29.1 1.0 CE1 A:HIS290 3.3 33.2 1.0 CB A:HIS290 3.4 38.9 1.0 OD1 A:ASP292 4.1 28.8 1.0 CB A:ASP288 4.2 30.8 1.0 CD2 A:HIS290 4.4 40.2 1.0 NE2 A:HIS290 4.4 37.3 1.0 N A:HIS290 4.4 43.0 1.0 N A:ASP292 4.4 33.3 1.0 CA A:HIS290 4.4 40.3 1.0 CA A:ASP292 4.5 31.9 1.0 C A:HIS290 5.0 39.3 1.0

Zinc binding site 2 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:57.2 occ:1.00 NE2 A:HIS653 2.0 38.0 1.0 O A:HOH2253 2.2 20.9 1.0 O A:HOH2254 2.2 36.2 1.0 CD2 A:HIS653 2.9 33.6 1.0 CE1 A:HIS653 3.0 35.5 1.0 CG A:HIS653 4.1 33.8 1.0 ND1 A:HIS653 4.1 37.9 1.0 OE2 A:GLU341 4.4 49.9 1.0 CG1 A:VAL383 4.5 45.2 1.0 OE1 A:GLU341 4.7 44.2 1.0 CD A:GLU341 4.8 45.4 1.0 CB A:PRO652 4.9 33.0 1.0 OD1 A:ASN631 4.9 49.5 1.0

Zinc binding site 3 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:99.7 occ:1.00 ND1 A:HIS676 2.4 58.2 1.0 O A:HOH2255 2.9 43.9 1.0 CG A:HIS676 3.2 55.3 1.0 CB A:HIS676 3.3 47.1 1.0 CE1 A:HIS676 3.5 55.9 1.0 O A:HOH2245 3.9 51.3 1.0 CA A:HIS676 3.9 48.2 1.0 CD2 A:HIS676 4.4 55.0 1.0 NE2 A:HIS676 4.5 53.9 1.0 CB A:ALA315 4.7 42.3 1.0 N A:HIS676 4.8 48.8 1.0 O A:HIS676 4.8 44.6 1.0 C A:HIS676 4.9 47.6 1.0

Zinc binding site 4 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:0.2 occ:1.00 O B:HOH2200 2.0 48.6 1.0 CB B:HIS290 3.4 71.8 1.0 OD2 B:ASP292 3.5 72.6 1.0 CG B:HIS290 3.7 70.8 1.0 ND1 B:HIS290 3.9 70.2 1.0 CG B:ASP292 4.2 74.8 1.0 OD1 B:ASP292 4.4 75.4 1.0 CD2 B:HIS290 4.4 71.1 1.0 CA B:HIS290 4.6 72.1 1.0 CE1 B:HIS290 4.7 71.5 1.0 NZ B:LYS87 4.8 55.9 1.0 O B:HIS290 4.8 71.7 1.0 C B:HIS290 4.9 72.0 1.0

Zinc binding site 5 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:70.8 occ:1.00 NE2 B:HIS653 2.0 45.1 1.0 O B:HOH2201 2.3 24.4 1.0 CD2 B:HIS653 3.0 35.0 1.0 CE1 B:HIS653 3.0 41.6 1.0 ND1 B:HIS653 4.0 44.9 1.0 CG B:HIS653 4.1 42.7 1.0 CG1 B:VAL383 4.4 43.2 1.0 OE2 B:GLU341 4.5 52.5 1.0 OE1 B:GLU341 4.7 50.3 1.0 CD B:GLU341 4.9 43.1 1.0 CB B:PRO652 5.0 31.9 1.0

Zinc binding site 6 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:0.1 occ:1.00 ND1 B:HIS676 2.0 77.0 1.0 CE1 B:HIS676 2.6 76.4 1.0 O B:HOH2202 2.6 47.6 1.0 CG B:HIS676 3.1 67.3 1.0 NE2 B:HIS676 3.7 74.8 1.0 CB B:HIS676 3.7 58.8 1.0 CD2 B:HIS676 4.0 73.8 1.0 CA B:HIS676 4.1 58.0 1.0 CB B:ALA315 5.0 38.3 1.0 N B:HIS676 5.0 56.3 1.0

Zinc binding site 7 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn700 b:69.6 occ:1.00 OD2 C:ASP292 2.0 40.4 1.0 ND1 C:HIS290 2.2 40.2 1.0 OD2 C:ASP288 2.7 45.2 1.0 CE1 C:HIS290 3.2 33.3 1.0 CG C:ASP292 3.2 51.0 1.0 CG C:HIS290 3.2 36.6 1.0 CG C:ASP288 3.4 44.1 1.0 OD1 C:ASP288 3.5 45.5 1.0 CB C:HIS290 3.5 39.7 1.0 CB C:ASP292 3.9 52.3 1.0 OD1 C:ASP292 4.2 52.8 1.0 NE2 C:HIS290 4.3 37.6 1.0 CD2 C:HIS290 4.3 39.6 1.0 N C:HIS290 4.6 41.1 1.0 O C:HOH2004 4.6 62.5 1.0 CA C:HIS290 4.6 40.4 1.0 CB C:ASP288 4.7 43.3 1.0 N C:ASP292 5.0 49.3 1.0

Zinc binding site 8 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


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 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:83.0 occ:1.00 NE2 C:HIS653 1.8 49.4 1.0 O C:HOH2113 2.5 29.7 1.0 CE1 C:HIS653 2.7 50.8 1.0 CD2 C:HIS653 2.9 45.8 1.0 ND1 C:HIS653 3.8 49.7 1.0 CG C:HIS653 4.0 50.0 1.0 OE2 C:GLU341 4.3 48.8 1.0 CG1 C:VAL383 4.3 47.7 1.0 OE1 C:GLU341 4.7 52.1 1.0 CB C:PRO652 4.8 43.3 1.0 CD C:GLU341 4.8 48.0 1.0 OD1 C:ASN631 5.0 74.5 1.0

Zinc binding site 9 out of 9 in the Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Penicillin-Binding Protein 2B (Pbp-2B) From Streptococcus Pneumoniae (Strain 5204) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:0.1 occ:1.00 OD2 C:ASP313 2.3 45.2 1.0 NE2 C:HIS676 2.8 61.0 1.0 CE1 C:HIS676 2.9 61.4 1.0 CG C:ASP313 3.0 44.9 1.0 OD1 C:ASP313 3.3 44.3 1.0 CD2 C:HIS676 4.1 60.0 1.0 ND1 C:HIS676 4.2 64.2 1.0 O C:HOH2038 4.2 49.1 1.0 CB C:ASP313 4.3 42.4 1.0 CB C:SER67 4.4 53.3 1.0 CB C:ALA315 4.6 42.8 1.0 CG C:HIS676 4.8 59.6 1.0 OG C:SER67 4.9 57.2 1.0

C.Contreras-Martel, C.Dahout-Gonzalez, A.Dos-Santos-Martins, M.Kotnik, A.Dessen. Pbp Active Site Flexibility As the Key Mechanism For Beta-Lactam Resistance in Pneumococci J.Mol.Biol. V. 387 899 2009.
ISSN: ISSN 0022-2836
PubMed: 19233207
DOI: 10.1016/J.JMB.2009.02.024