Magnesium in PDB 3pnl: Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex

The structure of Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex, PDB code: 3pnl was solved by R.Shi, L.Mcdonald, A.Matte, M.Cygler, I.Ekiel, Montreal-Kingston Bacterialstructural Genomics Initiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.92 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.572, 74.572, 268.779, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex (pdb code 3pnl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex, PDB code: 3pnl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1212 b:35.2 occ:1.00 OD1 B:ASP37 1.9 37.6 1.0 O1A B:ADP1211 2.0 32.8 1.0 O1B B:ADP1211 2.1 36.5 1.0 OD2 B:ASP35 2.1 32.7 1.0 OD2 B:ASP30 2.1 35.7 1.0 O B:HOH254 2.1 32.6 1.0 CG B:ASP37 3.1 38.8 1.0 CG B:ASP30 3.2 37.2 1.0 CG B:ASP35 3.2 36.2 1.0 PB B:ADP1211 3.2 35.6 1.0 PA B:ADP1211 3.3 33.8 1.0 OD1 B:ASP30 3.5 38.7 1.0 O3B B:ADP1211 3.6 37.6 1.0 O3A B:ADP1211 3.6 35.2 1.0 MG B:MG1213 3.6 41.3 1.0 OD1 B:ASP35 3.6 36.7 1.0 OD2 B:ASP37 3.7 41.4 1.0 N B:HIS38 4.0 37.8 1.0 N B:ASP37 4.0 38.8 1.0 N B:ASP35 4.2 37.6 1.0 CB B:ASP37 4.2 38.1 1.0 O2A B:ADP1211 4.3 31.8 1.0 CA B:ASP37 4.4 38.8 1.0 O5' B:ADP1211 4.4 31.9 1.0 C B:ASP37 4.4 38.7 1.0 CB B:ASP35 4.4 37.2 1.0 NE B:ARG178 4.5 34.8 1.0 CB B:ASP30 4.5 37.1 1.0 O2B B:ADP1211 4.5 37.5 1.0 N B:ALA36 4.6 38.1 1.0 CA B:HIS38 4.6 37.7 1.0 CA B:ASP35 4.6 37.6 1.0 C B:ASP35 4.6 38.4 1.0 C5' B:ADP1211 4.6 35.8 1.0 CB B:HIS38 4.7 35.7 1.0 CD B:ARG178 5.0 32.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E.Coli Dha Kinase Dhak-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1213 b:41.3 occ:1.00 OD1 B:ASP35 2.2 36.7 1.0 O A:PHE78 2.3 32.4 1.0 O B:HOH231 2.3 39.4 1.0 O1B B:ADP1211 2.5 36.5 1.0 OD2 B:ASP37 2.5 41.4 1.0 CG B:ASP37 3.1 38.8 1.0 CG B:ASP35 3.1 36.2 1.0 OD1 B:ASP37 3.3 37.6 1.0 OD2 B:ASP35 3.3 32.7 1.0 C A:PHE78 3.4 33.1 1.0 PB B:ADP1211 3.6 35.6 1.0 MG B:MG1212 3.6 35.2 1.0 O2B B:ADP1211 3.7 37.5 1.0 NH1 B:ARG178 3.8 29.5 1.0 CA A:THR79 3.9 34.3 1.0 N A:THR79 4.1 34.6 1.0 OG1 A:THR79 4.2 36.0 1.0 CB B:ASP37 4.2 38.1 1.0 NE B:ARG178 4.4 34.8 1.0 CZ B:ARG178 4.4 30.7 1.0 CB B:ASP35 4.5 37.2 1.0 C3 A:GOL1228 4.5 30.9 1.0 O3A B:ADP1211 4.5 35.2 1.0 CB A:THR79 4.5 34.5 1.0 CB A:PHE78 4.5 31.6 1.0 CA A:PHE78 4.6 32.6 1.0 O3B B:ADP1211 4.7 37.6 1.0 O3 A:GOL1228 4.7 31.9 1.0 O1A B:ADP1211 4.9 32.8 1.0 CG2 A:THR79 4.9 32.0 1.0 O B:HOH254 4.9 32.6 1.0 OD1 B:ASN41 4.9 44.8 1.0 N A:SER80 4.9 35.8 1.0 O B:HOH243 4.9 39.0 1.0 CD2 A:HIS218 4.9 26.5 1.0 C A:THR79 5.0 35.4 1.0

R.Shi, L.Mcdonald, Q.Cui, A.Matte, M.Cygler, I.Ekiel. Structural and Mechanistic Insight Into Covalent Substrate Binding By Escherichia Coli Dihydroxyacetone Kinase. Proc.Natl.Acad.Sci.Usa V. 108 1302 2011.
ISSN: ISSN 0027-8424
PubMed: 21209328
DOI: 10.1073/PNAS.1012596108