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

Enzymatic activity of 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;

Protein crystallography data

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

Manganese Binding Sites:

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 1ho5

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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 1ho5

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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 1ho5

Go back to Manganese Binding Sites List in 1ho5
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 1ho5

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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

Reference:

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
Page generated: Tue Dec 15 03:48:57 2020

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