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

Protein crystallography data

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

Other elements in 3n9b:

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

Yttrium (Y) 4 atoms
Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain, PDB code: 3n9b:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3n9b

Go back to Manganese Binding Sites List in 3n9b
Manganese binding site 1 out of 2 in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn188

b:19.8
occ:1.00
NE2 A:HIS48 2.2 18.8 1.0
OD2 A:ASP50 2.2 16.0 1.0
O1 A:SO42 2.2 27.0 1.0
ND1 A:HIS42 2.3 12.8 1.0
O A:HOH244 2.5 22.7 1.0
O A:HOH267 2.5 25.8 1.0
CG A:ASP50 3.0 24.8 1.0
CE1 A:HIS48 3.1 12.9 1.0
CE1 A:HIS42 3.2 19.7 1.0
OD1 A:ASP50 3.2 19.5 1.0
CD2 A:HIS48 3.2 19.3 1.0
CG A:HIS42 3.3 18.9 1.0
S A:SO42 3.4 45.3 1.0
O3 A:SO42 3.6 34.7 1.0
CB A:HIS42 3.7 13.3 1.0
O A:HOH255 3.9 23.7 1.0
O A:HOH332 3.9 32.9 1.0
ND1 A:HIS48 4.2 18.9 1.0
O4 A:SO42 4.2 28.3 1.0
O A:HOH364 4.3 34.9 1.0
CG A:HIS48 4.3 16.4 1.0
NE2 A:HIS42 4.3 18.3 1.0
O A:HOH239 4.4 22.1 1.0
CD2 A:HIS42 4.4 8.9 1.0
O2 A:SO42 4.5 36.8 1.0
CB A:ASP50 4.5 10.4 1.0

Manganese binding site 2 out of 2 in 3n9b

Go back to Manganese Binding Sites List in 3n9b
Manganese binding site 2 out of 2 in the Crystal Structure of the P. Aeruginosa Ligd Phosphoesterase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
B:Mn188

b:20.1
occ:1.00
NE2 B:HIS48 2.2 13.1 1.0
OD2 B:ASP50 2.2 17.3 1.0
ND1 B:HIS42 2.2 12.1 1.0
O3 B:SO41 2.3 36.5 1.0
O B:HOH225 2.3 25.2 1.0
O B:HOH208 2.7 21.9 1.0
CE1 B:HIS42 3.0 18.2 1.0
CG B:ASP50 3.1 25.0 1.0
CE1 B:HIS48 3.1 21.6 1.0
CD2 B:HIS48 3.2 15.3 1.0
CG B:HIS42 3.2 18.5 1.0
OD1 B:ASP50 3.2 16.5 1.0
S B:SO41 3.5 55.1 1.0
O2 B:SO41 3.6 34.2 1.0
CB B:HIS42 3.6 10.8 1.0
O B:HOH259 3.9 27.8 1.0
O B:HOH266 4.0 29.1 1.0
NE2 B:HIS42 4.2 16.1 1.0
ND1 B:HIS48 4.2 24.3 1.0
O B:HOH211 4.3 22.7 1.0
CD2 B:HIS42 4.3 17.0 1.0
CG B:HIS48 4.3 24.6 1.0
O4 B:SO41 4.4 39.6 1.0
O B:HOH251 4.4 43.8 1.0
O1 B:SO41 4.5 49.1 1.0
CB B:ASP50 4.5 12.2 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: Tue Dec 15 04:13:01 2020

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