Zinc in PDB 4u09: Structure of Leptospira Interrogans Lrr Protein LIC12759

The structure of Structure of Leptospira Interrogans Lrr Protein LIC12759, PDB code: 4u09 was solved by W.Shepard, F.A.Saul, A.Haouz, M.Picardeau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.79 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.166, 104.796, 116.597, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

The structure of Structure of Leptospira Interrogans Lrr Protein LIC12759 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Structure of Leptospira Interrogans Lrr Protein LIC12759 (pdb code 4u09). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Leptospira Interrogans Lrr Protein LIC12759, PDB code: 4u09:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of Leptospira Interrogans Lrr Protein LIC12759


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Leptospira Interrogans Lrr Protein LIC12759 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:42.4 occ:1.00 OE1 A:GLU392 2.0 32.9 1.0 NE2 B:HIS303 2.0 28.6 1.0 OE2 A:GLU369 2.0 34.5 1.0 CL B:CL508 2.5 59.8 1.0 CD A:GLU392 2.7 45.8 1.0 OE2 A:GLU392 2.8 33.4 1.0 CD2 B:HIS303 2.9 28.3 1.0 CE1 B:HIS303 3.0 28.1 1.0 CD A:GLU369 3.1 39.0 1.0 CG A:GLU369 3.5 29.3 1.0 O A:HOH692 3.8 35.0 1.0 OH B:TYR280 3.9 29.2 1.0 CG B:HIS303 4.1 27.3 1.0 CB A:GLU369 4.1 27.2 1.0 O A:HOH661 4.1 36.4 1.0 ND1 B:HIS303 4.1 28.7 1.0 OE1 A:GLU369 4.2 31.3 1.0 CG A:GLU392 4.2 34.4 1.0 CE1 B:TYR280 4.2 28.7 1.0 CZ B:TYR280 4.4 30.8 1.0 OG A:SER348 4.6 34.3 1.0 CB A:GLU392 4.8 30.6 1.0

Zinc binding site 2 out of 6 in the Structure of Leptospira Interrogans Lrr Protein LIC12759


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Leptospira Interrogans Lrr Protein LIC12759 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:42.6 occ:1.00 NE2 A:HIS303 2.1 32.9 1.0 CL B:CL505 2.2 31.7 1.0 OD2 B:ASP394 2.3 40.9 1.0 CL B:CL507 2.4 35.8 1.0 CG B:ASP394 2.9 41.0 1.0 OD1 B:ASP394 2.9 39.6 1.0 CD2 A:HIS303 2.9 33.0 1.0 CE1 A:HIS303 3.1 32.4 1.0 CA B:GLY371 3.7 30.7 1.0 CG A:HIS303 4.1 31.7 1.0 ND1 A:HIS303 4.2 32.7 1.0 O B:HOH737 4.3 41.0 1.0 OH A:TYR280 4.3 36.8 1.0 N B:GLY371 4.3 31.8 1.0 O B:HOH706 4.4 35.8 1.0 C B:GLY371 4.4 35.2 1.0 CB B:ASP394 4.4 34.2 1.0 CE1 A:TYR280 4.5 33.9 1.0 O A:HOH690 4.6 37.4 1.0 CB B:GLU392 4.6 32.2 1.0 CB B:SER348 4.7 33.2 1.0 O B:GLY419 4.7 40.5 1.0 ND2 B:ASN372 4.9 37.3 1.0 CZ A:TYR280 4.9 37.7 1.0 N B:ASN372 4.9 32.5 1.0 O B:GLY371 4.9 33.7 1.0 O B:ASP394 4.9 38.1 1.0

Zinc binding site 3 out of 6 in the Structure of Leptospira Interrogans Lrr Protein LIC12759


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Leptospira Interrogans Lrr Protein LIC12759 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:43.2 occ:1.00 O B:HOH681 1.9 27.4 1.0 OE2 A:GLU257 2.0 37.3 1.0 OE2 B:GLU369 2.1 32.7 1.0 CL B:CL506 2.3 34.2 1.0 CD A:GLU257 2.7 38.4 1.0 OE1 A:GLU257 2.8 31.4 1.0 CD B:GLU369 2.9 42.5 1.0 CG B:GLU369 3.2 33.8 1.0 OE2 B:GLU392 4.0 35.6 1.0 OE1 B:GLU369 4.0 46.2 1.0 CD B:ARG390 4.1 31.0 1.0 NE B:ARG390 4.1 35.1 1.0 CG A:GLU257 4.2 28.4 1.0 CG B:GLU392 4.2 36.9 1.0 CB B:ARG367 4.3 29.7 1.0 NE1 B:TRP344 4.4 29.2 1.0 CD B:ARG367 4.4 36.5 1.0 CG B:ARG367 4.5 34.6 1.0 CZ B:ARG390 4.6 40.4 1.0 CD B:GLU392 4.7 41.9 1.0 CZ2 B:TRP344 4.7 30.6 1.0 CG B:ARG390 4.7 31.7 1.0 CB B:GLU369 4.7 30.6 1.0 CE2 B:TRP344 4.8 31.2 1.0 CD1 A:TYR280 4.8 33.7 1.0 CE1 A:TYR280 4.8 33.9 1.0 NH1 B:ARG367 4.9 34.0 1.0 O A:HOH715 4.9 34.9 1.0 CG A:TYR280 4.9 31.3 1.0 CZ A:TYR280 4.9 37.7 1.0 NH1 B:ARG390 5.0 32.8 1.0 CB B:ARG390 5.0 33.9 1.0

Zinc binding site 4 out of 6 in the Structure of Leptospira Interrogans Lrr Protein LIC12759


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Leptospira Interrogans Lrr Protein LIC12759 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:60.6 occ:1.00 O A:HOH666 2.1 55.3 1.0 ND1 A:HIS188 2.2 35.9 1.0 OE1 B:GLU343 2.3 61.2 1.0 O B:HOH693 2.3 38.7 1.0 O B:HOH713 2.9 60.2 1.0 CD B:GLU343 3.2 58.1 1.0 CE1 A:HIS188 3.2 35.6 1.0 CG A:HIS188 3.2 34.0 1.0 OE2 B:GLU343 3.5 56.5 1.0 CB A:HIS188 3.5 30.6 1.0 CA A:HIS188 3.8 29.1 1.0 NE2 B:GLN366 4.2 46.1 1.0 OE1 B:GLN366 4.2 50.6 1.0 O B:HOH803 4.2 53.7 1.0 O A:SER211 4.3 33.5 1.0 C A:HIS188 4.3 33.0 1.0 NE2 A:HIS188 4.3 36.5 1.0 CD2 A:HIS188 4.4 36.4 1.0 CG B:GLU343 4.5 39.6 1.0 CB A:SER211 4.5 28.8 1.0 NE2 B:GLN320 4.5 65.7 1.0 O A:HOH775 4.5 54.1 1.0 CD B:GLN366 4.6 52.5 1.0 O A:HIS188 4.7 31.7 1.0 CD B:GLN320 4.7 67.4 1.0 CB B:GLU343 4.8 35.6 1.0 N A:ASN189 4.9 32.7 1.0

Zinc binding site 5 out of 6 in the Structure of Leptospira Interrogans Lrr Protein LIC12759


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Leptospira Interrogans Lrr Protein LIC12759 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:69.3 occ:1.00 OD2 B:ASP185 2.3 35.5 1.0 OG B:SER162 2.4 38.3 1.0 O B:HOH791 2.5 50.9 1.0 CG B:ASP185 3.2 29.6 1.0 CB B:ASP185 3.3 25.0 1.0 CB B:SER162 3.5 33.5 1.0 O B:HOH856 3.9 57.7 1.0 OD2 B:ASP141 4.1 33.2 1.0 O B:HOH698 4.2 40.1 1.0 OD1 B:ASP141 4.3 30.0 1.0 OD1 B:ASP185 4.4 27.9 1.0 CA B:SER162 4.4 29.4 1.0 O B:HOH718 4.5 37.3 1.0 CG B:ASP141 4.6 32.9 1.0 CA B:ASP185 4.8 24.5 1.0 OE2 B:GLU160 5.0 82.2 1.0

Zinc binding site 6 out of 6 in the Structure of Leptospira Interrogans Lrr Protein LIC12759


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Leptospira Interrogans Lrr Protein LIC12759 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:60.5 occ:1.00 O A:HOH662 2.0 42.0 1.0 OE2 B:GLU257 2.0 29.2 1.0 O B:HOH727 2.3 52.3 1.0 O A:HOH694 2.4 39.9 1.0 O A:HOH730 2.8 40.7 1.0 CD B:GLU257 2.9 33.0 1.0 OE1 B:GLU257 3.1 30.8 1.0 O1 A:PEG507 4.0 48.5 1.0 CZ3 A:TRP344 4.1 35.6 1.0 OE1 A:GLU321 4.1 34.6 1.0 O B:HOH747 4.2 48.4 1.0 CG B:GLU257 4.3 24.8 1.0 OE2 A:GLU321 4.3 36.6 1.0 CH2 A:TRP344 4.5 36.0 1.0 O B:HOH754 4.6 40.6 1.0 CD A:GLU321 4.7 44.4 1.0 CE2 A:TYR298 4.7 40.3 1.0 C1 A:PEG507 4.7 45.4 1.0 OH A:TYR298 4.7 51.7 1.0 OH B:TYR279 4.8 30.6 1.0 CE3 A:TRP344 4.8 33.4 1.0 CE2 B:TYR279 4.9 28.4 1.0 CG2 B:THR233 4.9 23.8 1.0

I.Miras, F.Saul, M.Nowakowski, P.Weber, A.Haouz, W.Shepard, M.Picardeau. Structural Characterization of A Novel Subfamily of Leucine-Rich Repeat Proteins From the Human Pathogen Leptospira Interrogans. Acta Crystallogr.,Sect.D V. 71 1351 2015.
ISSN: ESSN 1399-0047
PubMed: 26057675
DOI: 10.1107/S139900471500704X