Magnesium in PDB 6hde: Structure of Escherichia Coli Dutpase Q93H Mutant

All present enzymatic activity of Structure of Escherichia Coli Dutpase Q93H Mutant:
3.6.1.23;

The structure of Structure of Escherichia Coli Dutpase Q93H Mutant, PDB code: 6hde was solved by A.Benedek, B.G.Vertessy, I.Leveles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.81 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.200, 66.500, 95.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.1

The binding sites of Magnesium atom in the Structure of Escherichia Coli Dutpase Q93H Mutant (pdb code 6hde). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Escherichia Coli Dutpase Q93H Mutant, PDB code: 6hde:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Escherichia Coli Dutpase Q93H Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Escherichia Coli Dutpase Q93H Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:24.0 occ:1.00 O A:HOH308 2.0 23.5 1.0 O A:HOH311 2.0 24.9 1.0 O1G A:DUP201 2.0 27.5 1.0 O A:HOH339 2.1 24.5 1.0 O2B A:DUP201 2.1 23.9 1.0 O2A A:DUP201 2.1 21.8 1.0 PB A:DUP201 3.2 24.1 1.0 PG A:DUP201 3.3 31.1 1.0 PA A:DUP201 3.4 22.2 1.0 O A:HOH303 3.4 18.0 1.0 O3B A:DUP201 3.6 26.2 1.0 N3A A:DUP201 3.7 23.6 1.0 O2G A:DUP201 3.9 34.3 1.0 NE A:ARG71 4.0 21.6 1.0 OD1 A:ASP32 4.1 29.2 1.0 OE1 A:GLN119 4.2 19.4 1.0 OD2 A:ASP32 4.2 30.3 1.0 NH2 A:ARG71 4.4 24.9 1.0 O A:HOH309 4.4 32.1 1.0 O1A A:DUP201 4.4 18.3 1.0 O5' A:DUP201 4.5 25.4 1.0 O3G A:DUP201 4.5 32.2 1.0 C5' A:DUP201 4.6 23.7 1.0 O1B A:DUP201 4.6 23.1 1.0 CG A:ASP32 4.6 25.9 1.0 CZ A:ARG71 4.6 25.3 1.0 CG A:ARG71 4.9 20.2 1.0 CD A:ARG71 4.9 24.0 1.0 CD A:GLN119 5.0 21.9 1.0

Magnesium binding site 2 out of 3 in the Structure of Escherichia Coli Dutpase Q93H Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Escherichia Coli Dutpase Q93H Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:24.9 occ:1.00 O2B A:DUP202 2.0 23.4 1.0 O1G A:DUP202 2.0 25.9 1.0 O2A A:DUP202 2.0 22.9 1.0 O A:HOH334 2.1 23.1 1.0 O B:HOH314 2.1 26.8 1.0 O B:HOH302 2.2 25.0 1.0 PB A:DUP202 3.1 27.9 1.0 O A:HOH301 3.2 30.2 1.0 PG A:DUP202 3.2 27.6 1.0 PA A:DUP202 3.3 27.1 1.0 O3B A:DUP202 3.5 27.9 1.0 N3A A:DUP202 3.6 28.6 1.0 O2G A:DUP202 3.8 25.3 1.0 NE B:ARG71 4.1 21.8 1.0 NH2 A:ARG141 4.1 38.7 1.0 OD1 B:ASP32 4.2 30.4 1.0 NH2 B:ARG71 4.2 24.4 1.0 OE1 B:GLN119 4.3 23.1 1.0 O5' A:DUP202 4.4 20.9 1.0 O1A A:DUP202 4.4 34.5 1.0 O3G A:DUP202 4.4 25.8 1.0 OG A:SER149 4.4 28.9 1.0 OD2 B:ASP32 4.4 30.9 1.0 C5' A:DUP202 4.5 18.3 1.0 O1B A:DUP202 4.5 28.4 1.0 CZ B:ARG71 4.6 23.7 1.0 O C:HOH302 4.7 31.0 1.0 CG B:ASP32 4.8 28.4 1.0 O C:HOH303 4.9 18.4 1.0 CD B:GLN119 5.0 21.5 1.0

Magnesium binding site 3 out of 3 in the Structure of Escherichia Coli Dutpase Q93H Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Escherichia Coli Dutpase Q93H Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:21.4 occ:1.00 O2B B:DUP201 1.9 21.0 1.0 O2A B:DUP201 2.0 23.1 1.0 O1G B:DUP201 2.1 22.4 1.0 O C:HOH318 2.1 21.6 1.0 O B:HOH341 2.1 22.3 1.0 O C:HOH305 2.2 22.9 1.0 PB B:DUP201 3.1 21.6 1.0 PG B:DUP201 3.2 25.6 1.0 PA B:DUP201 3.3 21.9 1.0 O3B B:DUP201 3.4 25.9 1.0 N3A B:DUP201 3.6 21.6 1.0 O2G B:DUP201 3.8 23.8 1.0 NH2 B:ARG141 4.0 23.4 1.0 NE C:ARG71 4.1 21.6 1.0 O C:HOH316 4.2 26.2 1.0 O A:HOH314 4.2 23.5 1.0 OD1 C:ASP32 4.3 28.5 1.0 OE1 C:GLN119 4.3 22.9 1.0 NH2 C:ARG71 4.4 18.3 1.0 O5' B:DUP201 4.4 22.2 1.0 O1A B:DUP201 4.4 23.6 1.0 O3G B:DUP201 4.4 23.9 1.0 O1B B:DUP201 4.4 20.3 1.0 OG B:SER149 4.5 27.1 1.0 OD2 C:ASP32 4.5 31.5 1.0 C5' B:DUP201 4.5 21.4 1.0 CZ C:ARG71 4.7 22.7 1.0 CG C:ASP32 4.8 28.3 1.0 CB C:ALA24 4.9 25.9 1.0 O A:HOH302 4.9 18.6 1.0 CD C:GLN119 4.9 24.3 1.0 CG C:ARG71 5.0 20.2 1.0

A.Benedek, F.Temesvary-Kis, T.Khatanbaatar, I.Leveles, E.V.Suranyi, J.E.Szabo, L.Wunderlich, B.G.Vertessy. The Role of A Key Amino Acid Position in Species-Specific Proteinaceous Dutpase Inhibition. Biomolecules V. 9 2019.
ISSN: ESSN 2218-273X
PubMed: 31174420
DOI: 10.3390/BIOM9060221