Manganese in PDB 3jyf: The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578

The structure of The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578, PDB code: 3jyf was solved by Y.Fan, L.Volkart, G.Cobb, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.43
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.041, 106.041, 182.967, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.1

The binding sites of Manganese atom in the The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 (pdb code 3jyf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578, PDB code: 3jyf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:25.4 occ:0.70 OD2 A:ASP16 2.2 24.8 1.0 NE2 A:HIS244 2.3 22.5 1.0 OD2 A:ASP61 2.3 25.1 1.0 NE2 A:HIS18 2.4 25.2 1.0 O A:HOH517 2.5 24.6 1.0 MN A:MN342 3.1 32.0 0.7 CE1 A:HIS18 3.1 25.2 1.0 CE1 A:HIS244 3.2 22.2 1.0 CG A:ASP16 3.3 22.9 1.0 CD2 A:HIS244 3.3 21.1 1.0 CG A:ASP61 3.3 23.1 1.0 CD2 A:HIS18 3.5 23.1 1.0 CB A:ASP61 3.6 21.9 1.0 O1S A:EPE341 3.8 38.7 0.7 CB A:ASP16 3.9 21.3 1.0 CE1 A:HIS210 4.3 22.6 1.0 OD1 A:ASP16 4.3 24.5 1.0 ND1 A:HIS244 4.3 22.8 1.0 ND1 A:HIS18 4.3 23.2 1.0 O2S A:EPE341 4.4 39.0 0.7 NE2 A:HIS210 4.4 23.9 1.0 O A:HIS242 4.4 21.3 1.0 CD2 A:HIS102 4.4 20.6 1.0 CG A:HIS244 4.4 22.2 1.0 OD1 A:ASP61 4.5 23.8 1.0 CG A:HIS18 4.6 24.8 1.0 S A:EPE341 4.6 39.8 0.7 CA A:ASP16 4.6 21.8 1.0 CA A:HIS242 4.6 19.6 1.0 O3S A:EPE341 4.9 39.8 0.7 C A:HIS242 4.9 20.2 1.0 NE2 A:HIS102 4.9 19.7 1.0

Manganese binding site 2 out of 4 in the The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn342 b:32.0 occ:0.70 NE2 A:HIS210 2.4 23.9 1.0 OD1 A:ASN101 2.4 22.9 1.0 O1S A:EPE341 2.4 38.7 0.7 OD2 A:ASP61 2.4 25.1 1.0 ND1 A:HIS242 2.5 17.1 1.0 MN A:MN340 3.1 25.4 0.7 CE1 A:HIS210 3.2 22.6 1.0 CE1 A:HIS242 3.3 18.1 1.0 CG A:ASP61 3.3 23.1 1.0 CG A:ASN101 3.3 20.6 1.0 CD2 A:HIS210 3.4 22.2 1.0 CG A:HIS242 3.5 19.1 1.0 ND2 A:ASN101 3.5 20.9 1.0 OD1 A:ASP61 3.7 23.8 1.0 O A:HOH517 3.7 24.6 1.0 S A:EPE341 3.7 39.8 0.7 CA A:HIS242 3.7 19.6 1.0 OD2 A:ASP16 3.9 24.8 1.0 CB A:HIS242 3.9 19.1 1.0 O A:HIS242 4.1 21.3 1.0 O2S A:EPE341 4.1 39.0 0.7 CD2 A:HIS102 4.1 20.6 1.0 ND1 A:HIS210 4.4 21.7 1.0 C A:HIS242 4.4 20.2 1.0 CB A:ASP61 4.4 21.9 1.0 NE2 A:HIS242 4.4 17.6 1.0 CG A:HIS210 4.5 20.7 1.0 CD2 A:HIS242 4.6 19.2 1.0 N A:ASN101 4.6 19.1 1.0 O3S A:EPE341 4.7 39.8 0.7 CB A:ASN101 4.7 19.4 1.0 C10 A:EPE341 4.7 39.0 0.7 NE2 A:HIS102 4.7 19.7 1.0 N A:HIS242 4.8 19.6 1.0 NE2 A:HIS244 4.9 22.5 1.0

Manganese binding site 3 out of 4 in the The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn340 b:31.2 occ:0.70 OD2 B:ASP61 2.2 24.4 1.0 OD1 B:ASN101 2.2 31.4 1.0 NE2 B:HIS210 2.3 21.7 1.0 ND1 B:HIS242 2.4 21.6 1.0 O1S B:EPE342 2.7 31.6 0.5 MN B:MN341 2.9 33.9 0.7 CE1 B:HIS210 3.2 20.8 1.0 CE1 B:HIS242 3.2 20.4 1.0 CG B:ASN101 3.2 29.5 1.0 CG B:ASP61 3.3 25.7 1.0 CD2 B:HIS210 3.3 21.9 1.0 O B:HOH459 3.5 38.6 1.0 CG B:HIS242 3.5 21.2 1.0 ND2 B:ASN101 3.6 30.9 1.0 CA B:HIS242 3.8 22.4 1.0 OD1 B:ASP16 3.8 28.6 1.0 O B:HIS242 3.9 24.1 1.0 OD1 B:ASP61 3.9 26.3 1.0 CB B:HIS242 3.9 21.7 1.0 S B:EPE342 4.1 35.1 0.5 CD2 B:HIS102 4.2 32.1 1.0 C B:HIS242 4.3 23.0 1.0 ND1 B:HIS210 4.4 22.0 1.0 NE2 B:HIS242 4.4 21.5 1.0 CB B:ASP61 4.4 26.5 1.0 CG B:HIS210 4.5 21.0 1.0 CD2 B:HIS242 4.6 22.3 1.0 O2S B:EPE342 4.6 33.9 0.5 CB B:ASN101 4.6 27.6 1.0 N B:ASN101 4.7 26.3 1.0 O3S B:EPE342 4.7 34.7 0.5 NE2 B:HIS102 4.7 32.9 1.0 N B:HIS242 4.9 22.0 1.0 CG B:ASP16 4.9 27.9 1.0

Manganese binding site 4 out of 4 in the The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of A 2,3-Cyclic Nucleotide 2- Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn341 b:33.9 occ:0.70 OD1 B:ASP16 2.1 28.6 1.0 OD2 B:ASP61 2.5 24.4 1.0 NE2 B:HIS18 2.5 33.0 1.0 NE2 B:HIS244 2.5 30.2 1.0 O B:HOH459 2.6 38.6 1.0 MN B:MN340 2.9 31.2 0.7 CE1 B:HIS18 3.2 33.0 1.0 CG B:ASP16 3.3 27.9 1.0 CG B:ASP61 3.4 25.7 1.0 CD2 B:HIS244 3.4 30.3 1.0 CE1 B:HIS244 3.4 31.2 1.0 CB B:ASP61 3.6 26.5 1.0 CD2 B:HIS18 3.6 32.3 1.0 CB B:ASP16 4.0 27.1 1.0 O B:HIS242 4.1 24.1 1.0 O1S B:EPE342 4.2 31.6 0.5 CE1 B:HIS210 4.2 20.8 1.0 NE2 B:HIS210 4.2 21.7 1.0 OD2 B:ASP16 4.2 26.5 1.0 CD2 B:HIS102 4.3 32.1 1.0 ND1 B:HIS18 4.4 32.9 1.0 ND1 B:HIS244 4.5 32.5 1.0 OD1 B:ASP61 4.5 26.3 1.0 CG B:HIS244 4.5 30.3 1.0 CG B:HIS18 4.6 33.4 1.0 CA B:HIS242 4.6 22.4 1.0 CA B:ASP16 4.7 27.4 1.0 C B:HIS242 4.8 23.0 1.0 NE2 B:HIS102 4.8 32.9 1.0 O3S B:EPE342 4.9 34.7 0.5 OD1 B:ASN101 4.9 31.4 1.0 ND1 B:HIS242 5.0 21.6 1.0

Y.Fan, L.Volkart, G.Cobb, A.Joachimiak. The Crystal Structure of A 2,3-Cyclic Nucleotide 2-Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 To Be Published.