Yttrium in PDB 3n9b: Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain

The structure of Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain, PDB code: 3n9b was solved by S.Shuman, P.Nair, P.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.40 / 1.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.583, 45.550, 53.384, 102.32, 109.43, 104.59
R / Rfree (%)	14.7 / 19.9

The structure of Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Yttrium atom in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain (pdb code 3n9b). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 4 binding sites of Yttrium where determined in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain, PDB code: 3n9b:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Y1 b:25.9 occ:0.66 OD1 A:ASP179 2.4 17.0 1.0 O A:HOH226 2.5 38.1 1.0 O A:HOH304 2.7 28.4 1.0 O A:HOH198 2.7 38.6 1.0 CG A:ASP179 3.5 28.9 1.0 OD2 A:ASP179 3.9 17.7 1.0 CB A:ASP179 4.7 10.0 1.0 O A:HOH283 4.7 27.9 1.0 CG A:PRO178 5.0 18.3 1.0

Yttrium binding site 2 out of 4 in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Y189 b:36.8 occ:0.54 O A:HOH303 2.5 28.1 1.0 OE2 A:GLU124 2.6 64.6 1.0 OE1 A:GLU124 2.8 0.8 1.0 CD A:GLU124 3.0 61.4 1.0 O A:HOH264 3.7 42.1 1.0 CG A:GLU124 4.4 74.2 1.0

Yttrium binding site 3 out of 4 in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Y190 b:22.5 occ:0.95 O4 A:SO43 2.3 26.1 1.0 O A:HOH215 2.4 34.9 1.0 OE1 A:GLU135 2.5 17.0 1.0 O A:HOH242 2.5 22.5 1.0 OE2 A:GLU135 2.6 21.0 1.0 O A:HOH300 2.8 58.0 1.0 CD A:GLU135 2.9 42.5 1.0 S A:SO43 3.5 24.1 1.0 O2 A:SO43 3.7 37.7 1.0 O3 A:SO43 4.3 34.3 1.0 O A:HOH193 4.4 39.5 1.0 CG A:GLU135 4.4 20.9 1.0 O A:HOH366 4.4 35.8 1.0 O1 A:SO43 4.5 22.6 1.0 O A:GLU135 5.0 18.5 1.0

Yttrium binding site 4 out of 4 in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Y191 b:20.3 occ:0.98 O4 A:SO44 2.2 21.5 1.0 OE2 A:GLU184 2.3 23.9 1.0 OD2 A:ASP179 2.3 17.7 1.0 O A:HOH232 2.4 38.5 1.0 OE1 A:GLU184 2.5 27.6 1.0 O A:HOH333 2.6 57.2 1.0 CD A:GLU184 2.6 34.7 1.0 CG A:ASP179 3.4 28.9 1.0 S A:SO44 3.5 22.1 1.0 CB A:ASP179 3.8 10.0 1.0 O1 A:SO44 3.9 21.4 1.0 CG A:GLU184 4.1 58.5 1.0 O3 A:SO44 4.2 19.9 1.0 O A:HOH226 4.3 38.1 1.0 O A:HOH363 4.4 34.5 1.0 O2 A:SO44 4.4 28.4 1.0 OD1 A:ASP179 4.5 17.0 1.0 CB A:GLU184 4.9 44.4 1.0

P.A.Nair, P.Smith, S.Shuman. Structure of Bacterial Ligd 3'-Phosphoesterase Unveils A Dna Repair Superfamily Proc.Natl.Acad.Sci.Usa V. 107 12822 2010.
ISSN: ISSN 0027-8424
PubMed: 20616014
DOI: 10.1073/PNAS.1005830107