Zinc in PDB 3pfe: Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution

The structure of Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution, PDB code: 3pfe was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.77 / 1.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.388, 178.600, 50.803, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.3

The structure of Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution (pdb code 3pfe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution, PDB code: 3pfe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:13.4 occ:1.00 OD1 A:ASP129 2.0 13.7 1.0 NE2 A:HIS96 2.1 12.1 1.0 O A:HOH926 2.1 15.1 1.0 OD1 A:ASP190 2.1 14.1 1.0 OD2 A:ASP190 2.3 15.1 1.0 CG A:ASP190 2.5 13.9 1.0 CE1 A:HIS96 3.1 12.9 1.0 CG A:ASP129 3.1 16.2 1.0 CD2 A:HIS96 3.1 11.7 1.0 ZN A:ZN502 3.3 15.7 1.0 OD2 A:ASP129 3.5 13.3 1.0 OE1 A:GLU162 3.6 14.7 1.0 OE2 A:GLU163 3.8 16.1 1.0 O2 A:GOL518 3.9 27.0 1.0 CB A:ASP130 4.0 12.7 1.0 CB A:ASP190 4.0 11.6 1.0 C1 A:GOL518 4.1 24.1 1.0 O1 A:GOL518 4.1 27.0 1.0 CD A:GLU162 4.2 15.4 1.0 ND1 A:HIS96 4.2 13.4 1.0 CG A:HIS96 4.2 13.4 1.0 O A:HOH768 4.3 34.3 1.0 O A:HOH537 4.3 14.8 1.0 CB A:ASP129 4.4 13.8 1.0 O A:ASP190 4.4 14.9 1.0 CG A:ASP130 4.4 13.9 1.0 CD A:GLU163 4.5 15.3 1.0 OE2 A:GLU162 4.5 18.8 1.0 CA A:ASP129 4.6 13.5 1.0 C2 A:GOL518 4.7 30.1 1.0 OD2 A:ASP130 4.7 12.7 1.0 C A:ASP129 4.7 13.6 1.0 OD1 A:ASP130 4.8 11.9 1.0 OE1 A:GLU163 4.8 14.8 1.0 CA A:ASP190 4.8 13.5 1.0 CA A:ASP130 4.9 12.3 1.0 N A:ASP130 5.0 12.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:15.7 occ:1.00 OE2 A:GLU163 2.0 16.1 1.0 OD2 A:ASP129 2.0 13.3 1.0 NE2 A:HIS442 2.0 12.8 1.0 O A:HOH926 2.1 15.1 1.0 OE1 A:GLU163 2.6 14.8 1.0 CD A:GLU163 2.7 15.3 1.0 CG A:ASP129 2.9 16.2 1.0 CD2 A:HIS442 2.9 14.4 1.0 OD1 A:ASP129 3.1 13.7 1.0 CE1 A:HIS442 3.1 16.5 1.0 ZN A:ZN501 3.3 13.4 1.0 O1 A:GOL518 3.3 27.0 1.0 O A:HOH560 4.0 15.3 1.0 C1 A:GOL518 4.1 24.1 1.0 O A:HOH727 4.1 31.5 1.0 CG A:GLU163 4.1 14.8 1.0 CG A:HIS442 4.1 14.3 1.0 OE1 A:GLU162 4.2 14.7 1.0 ND1 A:HIS442 4.2 17.0 1.0 CB A:ASP129 4.3 13.8 1.0 NE2 A:HIS96 4.3 12.1 1.0 CG A:GLN100 4.4 14.0 1.0 CE1 A:HIS96 4.4 12.9 1.0 O A:HOH768 4.6 34.3 1.0 NE2 A:GLN100 4.6 17.4 1.0 O A:HOH529 4.9 14.7 1.0 CD A:GLN100 5.0 19.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:16.9 occ:1.00 ND1 A:HIS52 2.0 11.6 1.0 CL A:CL507 2.2 20.7 1.0 CL A:CL508 2.2 19.7 1.0 CE1 A:HIS52 2.9 16.7 1.0 CG A:HIS52 3.1 16.0 1.0 CB A:HIS52 3.5 14.9 1.0 CA A:HIS52 4.0 13.3 1.0 NE2 A:HIS52 4.1 16.0 1.0 CD2 A:HIS52 4.2 16.8 1.0 O A:HOH621 4.5 21.8 1.0 O A:HOH975 4.7 14.7 0.5 N A:HIS52 5.0 14.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A M20A Metallo Peptidase (Dape, LPG0809) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 at 1.50 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:19.4 occ:0.60 OE1 A:GLU410 2.0 19.8 1.0 N1 A:IMD513 2.1 26.6 1.0 CL A:CL505 2.2 27.3 1.0 O A:HOH1002 2.3 20.1 1.0 CD A:GLU410 2.7 18.6 1.0 OE2 A:GLU410 2.8 17.7 1.0 C2 A:IMD513 3.0 32.0 1.0 C5 A:IMD513 3.2 35.8 1.0 CE A:MSE408 4.0 18.1 0.5 CA A:GLY192 4.0 15.2 1.0 CG A:GLU410 4.1 17.7 1.0 O A:HOH941 4.1 35.0 1.0 N3 A:IMD513 4.2 30.4 1.0 C4 A:IMD513 4.3 27.1 1.0 N A:GLY411 4.3 15.1 1.0 CA A:GLU410 4.5 15.4 1.0 N A:GLY192 4.5 14.7 1.0 O A:HOH747 4.5 43.7 1.0 CB A:GLU410 4.6 17.7 1.0 C A:GLY192 4.9 16.1 1.0 O A:LEU435 5.0 15.0 1.0 C A:GLU410 5.0 15.0 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.