Atomistry » Zinc » PDB 2z45-2zem » 2zc6
Atomistry »
  Zinc »
    PDB 2z45-2zem »
      2zc6 »

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

Protein crystallography data

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

Zinc Binding Sites:

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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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 2zc6

Go back to Zinc Binding Sites List in 2zc6
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

Reference:

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
Page generated: Wed Dec 16 04:04:50 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy