Manganese in PDB 1ho5: 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate

All present enzymatic activity of 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate:
3.1.3.5; 3.6.1.45;

The structure of 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate, PDB code: 1ho5 was solved by T.Knoefel, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.900, 75.700, 221.700, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 27.9

The binding sites of Manganese atom in the 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate (pdb code 1ho5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate, PDB code: 1ho5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1601 b:26.0 occ:1.00 OE1 A:GLN254 1.9 20.4 1.0 OD2 A:ASP84 2.0 24.0 1.0 OD2 A:ASP41 2.1 21.6 1.0 NE2 A:HIS43 2.2 29.8 1.0 O A:HOH1775 2.2 26.7 1.0 O A:HOH1823 2.3 32.0 1.0 CD A:GLN254 3.1 24.4 1.0 CG A:ASP84 3.1 20.7 1.0 CE1 A:HIS43 3.1 26.4 1.0 CD2 A:HIS43 3.2 23.2 1.0 CG A:ASP41 3.2 19.9 1.0 CB A:ASP84 3.6 18.6 1.0 MN A:MN1602 3.6 23.5 1.0 CG A:GLN254 3.7 23.6 1.0 CB A:ASP41 3.7 18.6 1.0 O2 A:PO41603 3.9 31.9 1.0 O A:HOH1638 4.1 27.4 1.0 OD1 A:ASP84 4.1 18.4 1.0 O A:HIS252 4.2 21.9 1.0 NE2 A:GLN254 4.2 20.6 1.0 ND1 A:HIS43 4.3 25.8 1.0 O4 A:PO41603 4.3 23.4 1.0 OD1 A:ASP41 4.3 20.9 1.0 CG A:HIS43 4.3 23.8 1.0 CE1 A:HIS217 4.4 16.5 1.0 CD2 A:HIS117 4.4 21.7 1.0 CA A:ASP41 4.5 18.1 1.0 NE2 A:HIS217 4.6 19.9 1.0 CA A:HIS252 4.6 20.1 1.0 P A:PO41603 4.7 37.5 1.0 C A:HIS252 4.8 21.3 1.0 NE2 A:HIS117 4.9 23.4 1.0 O A:HOH1741 4.9 35.8 1.0

Manganese binding site 2 out of 4 in the 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1602 b:23.5 occ:1.00 OD1 A:ASN116 2.0 27.0 1.0 NE2 A:HIS217 2.2 19.9 1.0 O4 A:PO41603 2.3 23.4 1.0 ND1 A:HIS252 2.3 25.1 1.0 OD2 A:ASP84 2.5 24.0 1.0 O A:HOH1823 2.6 32.0 1.0 CG A:ASN116 3.0 25.4 1.0 OD1 A:ASP84 3.0 18.4 1.0 CG A:ASP84 3.0 20.7 1.0 CE1 A:HIS252 3.1 21.4 1.0 CE1 A:HIS217 3.1 16.5 1.0 CD2 A:HIS217 3.2 16.5 1.0 ND2 A:ASN116 3.4 24.5 1.0 CG A:HIS252 3.4 23.3 1.0 P A:PO41603 3.5 37.5 1.0 MN A:MN1601 3.6 26.0 1.0 O2 A:PO41603 3.7 31.9 1.0 CA A:HIS252 3.8 20.1 1.0 CB A:HIS252 3.9 20.6 1.0 CD2 A:HIS117 3.9 21.7 1.0 O A:HOH1775 4.0 26.7 1.0 OD2 A:ASP41 4.1 21.6 1.0 ND1 A:HIS217 4.2 19.5 1.0 O3 A:PO41603 4.3 35.4 1.0 NE2 A:HIS252 4.3 23.2 1.0 O A:HIS252 4.3 21.9 1.0 CG A:HIS217 4.3 19.1 1.0 CB A:ASN116 4.4 23.7 1.0 CB A:ASP84 4.4 18.6 1.0 CD2 A:HIS252 4.5 20.8 1.0 N A:ASN116 4.5 22.5 1.0 C A:HIS252 4.5 21.3 1.0 NE2 A:HIS117 4.6 23.4 1.0 O1 A:PO41603 4.6 39.3 1.0 N A:HIS117 4.8 25.6 1.0 N A:HIS252 4.8 16.3 1.0 CA A:ASN116 5.0 26.8 1.0

Manganese binding site 3 out of 4 in the 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2601 b:39.0 occ:1.00 OE1 B:GLN254 2.1 36.6 1.0 OD1 B:ASP41 2.1 33.2 1.0 NE2 B:HIS43 2.1 34.4 1.0 O B:HOH2704 2.3 33.5 1.0 OD2 B:ASP84 2.4 35.4 1.0 CE1 B:HIS43 2.9 33.2 1.0 CD B:GLN254 3.1 33.8 1.0 CG B:ASP41 3.2 30.7 1.0 CG B:ASP84 3.3 34.7 1.0 CD2 B:HIS43 3.3 33.8 1.0 CB B:ASP84 3.6 34.4 1.0 MN B:MN2602 3.6 41.0 1.0 CG B:GLN254 3.6 33.1 1.0 CB B:ASP41 3.8 29.6 1.0 O2 B:PO42603 3.9 61.5 1.0 ND1 B:HIS43 4.1 33.7 1.0 O4 B:PO42603 4.1 62.1 1.0 O B:HOH2672 4.2 36.3 1.0 O B:HIS252 4.2 33.2 1.0 OD2 B:ASP41 4.2 34.5 1.0 CE1 B:HIS217 4.2 37.6 1.0 CD2 B:HIS117 4.3 38.3 1.0 NE2 B:GLN254 4.3 34.6 1.0 CG B:HIS43 4.3 32.8 1.0 NE2 B:HIS217 4.4 37.8 1.0 OD1 B:ASP84 4.4 34.4 1.0 CA B:ASP41 4.6 29.2 1.0 P B:PO42603 4.6 62.0 1.0 CA B:HIS252 4.7 37.5 1.0 NE2 B:HIS117 4.8 40.0 1.0 C B:HIS252 4.8 36.5 1.0

Manganese binding site 4 out of 4 in the 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 5'-Nucleotidase (E. Coli) in Complex with Adenosine and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2602 b:41.0 occ:1.00 ND1 B:HIS252 2.1 37.2 1.0 OD2 B:ASP84 2.2 35.4 1.0 OD1 B:ASN116 2.2 39.3 1.0 O4 B:PO42603 2.2 62.1 1.0 NE2 B:HIS217 2.2 37.8 1.0 O B:HOH2704 2.6 33.5 1.0 CE1 B:HIS252 2.7 32.9 1.0 CG B:ASP84 3.1 34.7 1.0 CE1 B:HIS217 3.2 37.6 1.0 CD2 B:HIS217 3.2 38.7 1.0 CG B:ASN116 3.2 40.9 1.0 CG B:HIS252 3.3 36.5 1.0 P B:PO42603 3.5 62.0 1.0 OD1 B:ASP84 3.5 34.4 1.0 MN B:MN2601 3.6 39.0 1.0 ND2 B:ASN116 3.6 37.9 1.0 O2 B:PO42603 3.7 61.5 1.0 CD2 B:HIS117 3.8 38.3 1.0 CA B:HIS252 3.8 37.5 1.0 NE2 B:HIS252 3.9 35.3 1.0 CB B:HIS252 4.0 36.5 1.0 O B:HIS252 4.0 33.2 1.0 OD1 B:ASP41 4.1 33.2 1.0 O3 B:PO42603 4.2 62.1 1.0 ND1 B:HIS217 4.3 35.7 1.0 CD2 B:HIS252 4.3 33.7 1.0 CG B:HIS217 4.3 38.1 1.0 NE2 B:HIS117 4.3 40.0 1.0 C B:HIS252 4.4 36.5 1.0 CB B:ASP84 4.4 34.4 1.0 CB B:ASN116 4.5 39.9 1.0 O1 B:PO42603 4.6 60.5 1.0 N B:ASN116 4.6 39.3 1.0 N B:HIS252 4.9 34.7 1.0 CG B:HIS117 5.0 40.9 1.0

T.Knofel, N.Strater. Mechanism of Hydrolysis of Phosphate Esters By the Dimetal Center of 5'-Nucleotidase Based on Crystal Structures. J.Mol.Biol. V. 309 239 2001.
ISSN: ISSN 0022-2836
PubMed: 11491293
DOI: 10.1006/JMBI.2001.4656