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Zinc in PDB 6h8l: Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis

Protein crystallography data

The structure of Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis, PDB code: 6h8l was solved by M.A.Sainz-Polo, L.Grifoll-Romero, D.Albesa-Jove, A.Planas, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.07 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.346, 61.916, 132.226, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis (pdb code 6h8l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis, PDB code: 6h8l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6h8l

Go back to Zinc Binding Sites List in 6h8l
Zinc binding site 1 out of 2 in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:14.5
occ:1.00
O11 A:TLA502 1.9 14.9 1.0
OD1 A:ASP286 2.0 15.5 1.0
NE2 A:HIS340 2.0 17.5 1.0
NE2 A:HIS336 2.1 13.9 1.0
C1 A:TLA502 2.6 13.9 1.0
O1 A:TLA502 2.6 14.9 1.0
CG A:ASP286 2.9 13.8 1.0
CD2 A:HIS340 2.9 16.0 1.0
CD2 A:HIS336 3.0 14.8 1.0
CE1 A:HIS340 3.0 20.0 1.0
CE1 A:HIS336 3.1 13.2 1.0
OD2 A:ASP286 3.2 17.6 1.0
O41 A:TLA502 3.9 18.3 1.0
NH1 B:ARG471 3.9 16.9 1.0
C2 A:TLA502 4.1 17.3 1.0
CG A:HIS340 4.1 18.5 1.0
ND1 A:HIS340 4.1 17.6 1.0
CG A:HIS336 4.2 13.3 1.0
ND1 A:HIS336 4.2 12.9 1.0
C4 A:TLA502 4.3 19.6 1.0
CB A:ASP286 4.3 12.1 1.0
CB A:ASP285 4.4 11.9 1.0
CD2 A:HIS427 4.4 18.2 1.0
O2 A:TLA502 4.5 15.5 1.0
NE2 A:HIS427 4.5 19.2 1.0
CA A:ASP286 4.6 11.2 1.0
N A:ASP286 4.7 10.8 1.0
O4 A:TLA502 4.8 17.8 1.0
C3 A:TLA502 4.8 14.6 1.0
CZ B:ARG471 5.0 17.7 1.0
C A:ASP285 5.0 12.8 1.0
CA A:PRO376 5.0 15.6 1.0
OD2 A:ASP285 5.0 17.4 1.0

Zinc binding site 2 out of 2 in 6h8l

Go back to Zinc Binding Sites List in 6h8l
Zinc binding site 2 out of 2 in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:15.4
occ:1.00
OD1 B:ASP286 1.9 14.2 1.0
O4 B:TLA502 1.9 14.2 1.0
NE2 B:HIS340 2.0 15.3 1.0
NE2 B:HIS336 2.1 14.0 1.0
O41 B:TLA502 2.6 14.2 1.0
C4 B:TLA502 2.6 14.5 1.0
CG B:ASP286 2.9 17.1 1.0
CD2 B:HIS340 2.9 15.7 1.0
CD2 B:HIS336 3.0 13.5 1.0
CE1 B:HIS340 3.1 19.3 1.0
CE1 B:HIS336 3.1 14.0 1.0
OD2 B:ASP286 3.2 18.0 1.0
O1 B:TLA502 3.9 18.2 1.0
NH1 A:ARG471 3.9 17.1 1.0
C3 B:TLA502 4.1 16.7 1.0
CG B:HIS340 4.1 16.0 1.0
ND1 B:HIS340 4.1 19.5 1.0
CG B:HIS336 4.2 12.7 1.0
ND1 B:HIS336 4.2 13.2 1.0
CB B:ASP286 4.3 14.4 1.0
C1 B:TLA502 4.3 19.0 1.0
CB B:ASP285 4.4 13.4 1.0
O3 B:TLA502 4.5 17.6 1.0
CD2 B:HIS427 4.6 15.0 1.0
NE2 B:HIS427 4.6 16.3 1.0
CA B:ASP286 4.6 13.0 1.0
N B:ASP286 4.6 13.9 1.0
O11 B:TLA502 4.8 18.9 1.0
C2 B:TLA502 4.8 17.0 1.0
CA B:PRO376 5.0 14.6 1.0
OD2 B:ASP285 5.0 19.1 1.0
C B:ASP285 5.0 14.5 1.0

Reference:

L.Grifoll-Romero, M.A.Sainz-Polo, D.Albesa-Jove, M.E.Guerin, X.Biarnes, A.Planas. Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis with Dual N-Acetylmuramic and N-Acetylglucosamine Specificities To Be Published.
Page generated: Wed Dec 16 11:56:10 2020

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