Zinc in PDB 3it5: Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa

The structure of Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa, PDB code: 3it5 was solved by J.Spencer, L.M.Murphy, R.Conners, R.B.Sessions, S.J.Gamblin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.818, 34.079, 105.837, 90.00, 102.04, 90.00
R / Rfree (%)	18.6 / 26.2

The binding sites of Zinc atom in the Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa (pdb code 3it5). 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 the Lasa Virulence Factor From Pseudomonas Aeruginosa, PDB code: 3it5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa


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 the Lasa Virulence Factor From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn183 b:14.5 occ:1.00 OD1 A:ASP36 2.1 6.1 1.0 O A:HOH222 2.1 10.5 1.0 ND1 A:HIS122 2.2 5.8 1.0 NE2 A:HIS23 2.2 5.2 1.0 O A:HOH369 2.7 22.9 1.0 CG A:ASP36 2.8 6.0 1.0 OD2 A:ASP36 2.8 6.9 1.0 CE1 A:HIS23 3.1 5.6 1.0 CG A:HIS122 3.2 4.8 1.0 CE1 A:HIS122 3.2 6.0 1.0 CD2 A:HIS23 3.2 5.4 1.0 CB A:HIS122 3.4 4.2 1.0 OH A:TYR151 4.0 8.5 1.0 CA A:HIS122 4.0 4.1 1.0 CB A:ASP36 4.2 6.2 1.0 ND1 A:HIS23 4.3 5.4 1.0 NE2 A:HIS122 4.3 5.2 1.0 CD2 A:HIS122 4.3 5.5 1.0 NE2 A:HIS120 4.3 3.6 1.0 CG A:HIS23 4.4 6.3 1.0 O A:HOH228 4.4 2.0 1.0 CE2 A:TYR151 4.6 8.8 1.0 CD2 A:HIS120 4.7 4.1 1.0 CZ A:TYR151 4.7 9.0 1.0 N A:ASP36 4.7 6.5 1.0 CA A:ASP36 4.8 6.2 1.0 CB A:SER34 5.0 7.2 1.0 C A:PHE35 5.0 6.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa


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 the Lasa Virulence Factor From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn183 b:12.7 occ:1.00 OD1 B:ASP36 2.0 6.1 1.0 ND1 B:HIS122 2.1 5.8 1.0 NE2 B:HIS23 2.2 5.2 1.0 O B:HOH370 2.5 20.6 1.0 CG B:ASP36 2.7 6.0 1.0 OD2 B:ASP36 2.7 5.9 1.0 CE1 B:HIS122 3.0 5.9 1.0 CE1 B:HIS23 3.0 5.6 1.0 CG B:HIS122 3.2 4.9 1.0 CD2 B:HIS23 3.2 5.5 1.0 CB B:HIS122 3.6 4.3 1.0 OH B:TYR151 4.0 7.5 1.0 CA B:HIS122 4.0 4.3 1.0 NE2 B:HIS122 4.1 6.1 1.0 CB B:ASP36 4.1 6.2 1.0 ND1 B:HIS23 4.2 5.2 1.0 CD2 B:HIS122 4.2 5.8 1.0 CG B:HIS23 4.3 6.2 1.0 N B:ASP36 4.6 6.6 1.0 CE2 B:TYR151 4.6 8.7 1.0 CA B:ASP36 4.7 6.2 1.0 CZ B:TYR151 4.7 8.4 1.0 NE2 B:HIS120 4.7 3.8 1.0 C B:PHE35 4.8 6.8 1.0 O B:HOH439 4.8 2.0 1.0 CB B:SER34 4.9 7.2 1.0 O B:PHE35 4.9 7.2 1.0 CD2 B:HIS120 5.0 3.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa


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 the Lasa Virulence Factor From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn183 b:12.6 occ:1.00 OD1 E:ASP36 2.0 5.9 1.0 ND1 E:HIS122 2.1 5.7 1.0 O E:HOH395 2.2 7.6 1.0 NE2 E:HIS23 2.2 5.1 1.0 O E:HOH393 2.3 8.3 1.0 CG E:ASP36 2.7 6.0 1.0 OD2 E:ASP36 2.7 5.8 1.0 CE1 E:HIS122 2.9 6.0 1.0 CE1 E:HIS23 3.0 5.5 1.0 CG E:HIS122 3.2 4.8 1.0 CD2 E:HIS23 3.3 5.5 1.0 CB E:HIS122 3.7 4.4 1.0 NE2 E:HIS122 4.1 5.8 1.0 CB E:ASP36 4.1 6.1 1.0 ND1 E:HIS23 4.2 5.3 1.0 CD2 E:HIS122 4.2 5.7 1.0 CA E:HIS122 4.2 4.3 1.0 CG E:HIS23 4.3 6.2 1.0 NE2 E:HIS120 4.4 3.9 1.0 CE2 E:TYR151 4.4 8.9 1.0 OH E:TYR151 4.5 7.9 1.0 N E:ASP36 4.6 6.5 1.0 CA E:ASP36 4.7 6.2 1.0 CD2 E:HIS120 4.8 3.9 1.0 CB E:SER34 4.9 7.2 1.0 C E:PHE35 4.9 6.8 1.0 CZ E:TYR151 4.9 8.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa


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 the Lasa Virulence Factor From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn183 b:11.8 occ:1.00 OD1 G:ASP36 2.0 6.1 1.0 NE2 G:HIS23 2.1 5.2 1.0 ND1 G:HIS122 2.1 5.9 1.0 O G:HOH454 2.5 3.4 1.0 O G:HOH368 2.7 24.5 1.0 CG G:ASP36 2.7 6.1 1.0 CE1 G:HIS122 2.7 6.0 1.0 OD2 G:ASP36 2.7 6.9 1.0 CE1 G:HIS23 3.0 5.6 1.0 CD2 G:HIS23 3.1 5.5 1.0 CG G:HIS122 3.3 4.8 1.0 NE2 G:HIS122 3.9 5.7 1.0 CB G:HIS122 4.0 4.5 1.0 ND1 G:HIS23 4.1 5.5 1.0 CB G:ASP36 4.2 6.2 1.0 CG G:HIS23 4.2 6.3 1.0 CD2 G:HIS122 4.3 5.5 1.0 CA G:HIS122 4.4 4.3 1.0 CE2 G:TYR151 4.5 8.8 1.0 OH G:TYR151 4.5 8.3 1.0 NE2 G:HIS120 4.6 3.6 1.0 N G:ASP36 4.6 6.5 1.0 CA G:ASP36 4.7 6.2 1.0 CB G:SER34 4.8 7.2 1.0 C G:PHE35 4.8 6.8 1.0 O G:HOH687 4.9 15.2 1.0 CD2 G:HIS120 4.9 4.1 1.0

J.Spencer, L.M.Murphy, R.Conners, R.B.Sessions, S.J.Gamblin. Crystal Structure of the Lasa Virulence Factor From Pseudomonas Aeruginosa: Substrate Specificity and Mechanism of M23 Metallopeptidases. J.Mol.Biol. V. 396 908 2010.
ISSN: ISSN 0022-2836
PubMed: 20026068
DOI: 10.1016/J.JMB.2009.12.021