Magnesium in PDB 6z9i: Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products

All present enzymatic activity of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products:
4.1.2.4;

The structure of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products, PDB code: 6z9i was solved by J.Paakkonen, N.Hakulinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.27 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.900, 53.300, 81.200, 90.00, 110.20, 90.00
R / Rfree (%)	16.1 / 20.9

The binding sites of Magnesium atom in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products (pdb code 6z9i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products, PDB code: 6z9i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:35.9 occ:1.00 O A:HOH682 2.0 28.2 1.0 O A:HOH750 2.3 32.7 1.0 O A:HOH418 2.5 19.9 1.0 O A:HOH604 4.4 30.0 1.0 O A:HOH582 4.5 22.9 1.0 OD2 A:ASP120 4.6 17.1 1.0 O A:HOH467 4.7 26.4 1.0

Magnesium binding site 2 out of 2 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant Complex with Reaction Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:28.5 occ:1.00 OD2 A:ASP81 2.1 16.4 1.0 O A:HOH611 2.1 17.5 1.0 O A:HOH421 2.3 24.3 1.0 O A:HOH570 2.4 24.4 1.0 CG A:ASP81 3.1 18.2 1.0 OD1 A:ASP81 3.4 21.1 1.0 O A:HOH596 3.6 22.1 1.0 O A:HOH510 4.1 20.8 1.0 CB A:ASP81 4.4 15.4 1.0 C A:ASP81 4.5 11.9 1.0 N A:ASP82 4.6 11.7 1.0 N A:ASP81 4.6 13.9 1.0 O A:ASP81 4.7 11.3 1.0 CA A:ASP81 4.7 14.1 1.0 O A:HOH676 4.9 23.5 1.0

S.Voutilainen, M.Heinonen, M.Andberg, E.Jokinen, H.Maaheimo, J.Paakkonen, N.Hakulinen, J.Rouvinen, H.Lahdesmaki, S.Kaski, J.Rousu, M.Penttila, A.Koivula. Substrate Specificity of 2-Deoxy-D-Ribose 5-Phosphate Aldolase (Dera) Assessed By Different Protein Engineering and Machine Learning Methods. Appl.Microbiol.Biotechnol. V. 104 10515 2020.
ISSN: ESSN 1432-0614
PubMed: 33147349
DOI: 10.1007/S00253-020-10960-X