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Yttrium in PDB 3n9d: Monoclinic Structure of P. Aeruginosa Ligd Phosphoesterase Domain

Protein crystallography data

The structure of Monoclinic Structure of P. Aeruginosa Ligd Phosphoesterase Domain, PDB code: 3n9d 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) 28.29 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.997, 56.585, 43.503, 90.00, 118.33, 90.00
R / Rfree (%) 21.2 / 26.3

Other elements in 3n9d:

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

Manganese (Mn) 1 atom

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Monoclinic Structure of P. Aeruginosa Ligd Phosphoesterase Domain (pdb code 3n9d). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 2 binding sites of Yttrium where determined in the Monoclinic Structure of P. Aeruginosa Ligd Phosphoesterase Domain, PDB code: 3n9d:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in 3n9d

Go back to Yttrium Binding Sites List in 3n9d
Yttrium binding site 1 out of 2 in the Monoclinic Structure of 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 Monoclinic Structure of P. Aeruginosa Ligd Phosphoesterase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y189

b:69.9
occ:0.50
OE1 A:GLU124 2.7 43.0 1.0
OE2 A:GLU124 2.8 46.0 1.0
OE2 A:GLU121 2.9 52.5 1.0
OE1 A:GLU121 2.9 56.0 1.0
CD A:GLU124 3.1 47.5 1.0
CD A:GLU121 3.3 50.4 1.0
CG A:GLU124 4.6 40.9 1.0
CG A:GLU121 4.8 45.2 1.0

Yttrium binding site 2 out of 2 in 3n9d

Go back to Yttrium Binding Sites List in 3n9d
Yttrium binding site 2 out of 2 in the Monoclinic Structure of 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 Monoclinic Structure of P. Aeruginosa Ligd Phosphoesterase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y190

b:31.9
occ:1.00
O4 A:SO42 2.6 26.0 1.0
OE1 A:GLU135 2.7 30.9 1.0
OE2 A:GLU135 2.7 32.6 1.0
O A:HOH254 2.8 32.1 1.0
CD A:GLU135 3.0 33.1 1.0
O1 A:SO42 3.6 26.7 1.0
S A:SO42 3.6 24.0 1.0
O A:HOH249 3.6 31.8 1.0
O3 A:SO42 4.3 27.2 1.0
CG A:GLU135 4.5 28.0 1.0
O2 A:SO42 4.8 21.9 1.0

Reference:

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
Page generated: Wed Dec 16 02:40:57 2020

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