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Zinc in PDB 2c6w: Penicillin-Binding Protein 1A (Pbp-1A) From Streptococcus Pneumoniae

Protein crystallography data

The structure of Penicillin-Binding Protein 1A (Pbp-1A) From Streptococcus Pneumoniae, PDB code: 2c6w 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) 44.99 / 2.61
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 109.782, 187.256, 51.303, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27.6

Other elements in 2c6w:

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

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Penicillin-Binding Protein 1A (Pbp-1A) From Streptococcus Pneumoniae (pdb code 2c6w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Penicillin-Binding Protein 1A (Pbp-1A) From Streptococcus Pneumoniae, PDB code: 2c6w:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2c6w

Go back to Zinc Binding Sites List in 2c6w
Zinc binding site 1 out of 3 in the Penicillin-Binding Protein 1A (Pbp-1A) 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) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:0.7
occ:1.00
ND1 B:HIS309 2.5 0.8 1.0
CE1 B:HIS309 3.2 0.9 1.0
CG B:HIS309 3.4 0.8 1.0
OH B:TYR319 3.6 97.2 1.0
CA B:HIS309 3.7 82.3 1.0
CB B:HIS309 3.8 93.4 1.0
OD2 B:ASP312 3.9 87.6 0.5
NE2 B:HIS309 4.2 0.4 1.0
N B:HIS309 4.3 76.9 1.0
CD2 B:HIS309 4.4 0.9 1.0
CZ B:TYR319 4.7 97.0 1.0
C B:LYS308 4.8 72.9 1.0
O B:LYS308 4.9 69.3 1.0
C B:HIS309 4.9 80.0 1.0
CG B:ASP312 4.9 86.8 1.0

Zinc binding site 2 out of 3 in 2c6w

Go back to Zinc Binding Sites List in 2c6w
Zinc binding site 2 out of 3 in the Penicillin-Binding Protein 1A (Pbp-1A) 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) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:51.3
occ:1.00
ND1 B:HIS395 2.1 39.3 1.0
OE1 B:GLU435 2.1 66.1 1.0
CD B:GLU435 2.9 59.5 1.0
CE1 B:HIS395 3.0 46.3 1.0
OE2 B:GLU435 3.0 68.9 1.0
CG B:HIS395 3.2 43.0 1.0
CB B:HIS395 3.6 40.9 1.0
OE2 B:GLU397 3.7 58.8 1.0
NE2 B:HIS395 4.2 45.4 1.0
CD2 B:HIS395 4.3 40.6 1.0
NZ B:LYS439 4.3 51.5 1.0
CG B:GLU435 4.3 57.7 1.0
CA B:HIS395 4.9 47.7 1.0
CD B:GLU397 4.9 51.2 1.0

Zinc binding site 3 out of 3 in 2c6w

Go back to Zinc Binding Sites List in 2c6w
Zinc binding site 3 out of 3 in the Penicillin-Binding Protein 1A (Pbp-1A) 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) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:61.4
occ:1.00
O B:HOH2035 2.0 26.1 1.0
ND1 B:HIS460 2.0 50.5 1.0
CE1 B:HIS460 2.9 50.4 1.0
CG B:HIS460 3.1 47.4 1.0
CB B:HIS460 3.6 40.0 1.0
NE2 B:HIS460 4.1 50.7 1.0
CD2 B:HIS460 4.2 44.4 1.0
CA B:HIS460 4.3 43.7 1.0
O B:ILE459 4.8 49.2 1.0
O B:HOH2017 4.8 40.9 1.0

Reference:

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
Page generated: Wed Dec 16 03:19:06 2020

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