Magnesium in PDB 2bef: Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3

All present enzymatic activity of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3:
2.7.4.6;

The structure of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3, PDB code: 2bef was solved by Y.W.Xu, J.Cherfils, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.560, 71.560, 153.750, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / n/a

The structure of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 (pdb code 2bef). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3, PDB code: 2bef:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


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 Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg156 b:10.7 occ:1.00 O A:HOH693 1.9 17.5 1.0 O A:HOH626 1.9 8.9 1.0 O A:HOH619 2.0 17.8 1.0 F3 A:BEF157 2.1 33.1 1.0 O1A A:ADP158 2.1 13.4 1.0 O1B A:ADP158 2.2 15.4 1.0 BE A:BEF157 3.2 29.8 1.0 PB A:ADP158 3.3 9.9 1.0 PA A:ADP158 3.4 13.8 1.0 O3A A:ADP158 3.6 16.8 1.0 O3B A:ADP158 3.7 12.7 1.0 F1 A:BEF157 3.9 33.5 1.0 C5' A:ADP158 4.2 13.5 1.0 O5' A:ADP158 4.2 12.6 1.0 NE2 A:HIS59 4.2 12.2 1.0 CE1 A:HIS122 4.3 5.6 1.0 O A:HOH677 4.4 22.9 1.0 ND1 A:HIS122 4.4 12.3 1.0 OD2 A:ASP125 4.4 19.9 1.0 O A:HOH737 4.4 15.5 1.0 O2B A:ADP158 4.5 8.6 1.0 O2A A:ADP158 4.6 15.8 1.0 F2 A:BEF157 4.6 29.3 1.0 O A:HOH757 4.6 34.3 1.0 OE2 A:GLU58 4.7 27.1 1.0 CE1 A:HIS59 4.8 8.0 1.0 NH2 A:ARG92 4.8 23.5 1.0 CE1 A:TYR56 4.9 12.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


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 Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg156 b:15.2 occ:1.00 O B:HOH706 2.0 17.9 1.0 O B:HOH779 2.0 20.8 1.0 O B:HOH620 2.2 11.6 1.0 F1 B:BEF157 2.2 34.5 1.0 O1B B:ADP158 2.4 20.8 1.0 O1A B:ADP158 2.5 17.6 1.0 BE B:BEF157 3.6 26.4 1.0 PB B:ADP158 3.7 17.6 1.0 PA B:ADP158 3.9 16.4 1.0 O B:HOH802 4.0 45.1 1.0 O B:HOH699 4.0 19.7 1.0 O3A B:ADP158 4.1 19.1 1.0 O3B B:ADP158 4.1 18.4 1.0 NH2 B:ARG92 4.3 32.6 1.0 F2 B:BEF157 4.3 29.3 1.0 NE2 B:HIS59 4.4 18.0 1.0 O B:HOH638 4.4 7.1 1.0 CE1 B:HIS122 4.4 6.5 1.0 OD2 B:ASP125 4.4 19.8 1.0 C5' B:ADP158 4.6 10.0 1.0 ND1 B:HIS122 4.6 12.9 1.0 CG B:ASP125 4.6 18.9 1.0 OE1 B:GLU58 4.6 33.5 1.0 O B:GLY123 4.7 10.8 1.0 CB B:ASP125 4.7 17.2 1.0 F3 B:BEF157 4.7 27.2 1.0 O5' B:ADP158 4.8 16.2 1.0 O B:HOH738 4.8 31.4 1.0 O2B B:ADP158 4.9 18.0 1.0 CZ B:ARG92 4.9 29.9 1.0 O2A B:ADP158 4.9 20.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg156 b:19.4 occ:1.00 O C:HOH777 1.9 21.7 1.0 O C:HOH643 2.0 20.7 1.0 O1A C:ADP158 2.1 19.3 1.0 O C:HOH778 2.1 32.7 1.0 O1B C:ADP158 2.3 17.0 1.0 F1 C:BEF157 2.3 32.3 1.0 PA C:ADP158 3.3 17.8 1.0 PB C:ADP158 3.4 17.0 1.0 BE C:BEF157 3.6 26.1 1.0 O3A C:ADP158 3.6 19.9 1.0 O3B C:ADP158 3.9 17.3 1.0 NE2 C:HIS59 4.2 26.2 1.0 F2 C:BEF157 4.2 28.7 1.0 C5' C:ADP158 4.3 16.4 1.0 O5' C:ADP158 4.3 20.3 1.0 NH1 C:ARG92 4.3 23.9 1.0 OD2 C:ASP125 4.4 29.8 1.0 O2A C:ADP158 4.4 22.7 1.0 CE1 C:HIS122 4.4 2.0 1.0 O C:HOH612 4.5 11.4 1.0 O C:HOH610 4.6 14.3 1.0 O2B C:ADP158 4.6 16.4 1.0 ND1 C:HIS122 4.7 7.0 1.0 F3 C:BEF157 4.9 25.8 1.0 O C:GLY123 4.9 13.1 1.0 CG C:ASP125 4.9 21.9 1.0 OE2 C:GLU58 5.0 32.4 1.0 CE1 C:HIS59 5.0 24.2 1.0

Y.W.Xu, S.Morera, J.Janin, J.Cherfils. ALF3 Mimics the Transition State of Protein Phosphorylation in the Crystal Structure of Nucleoside Diphosphate Kinase and Mgadp. Proc.Natl.Acad.Sci.Usa V. 94 3579 1997.
ISSN: ISSN 0027-8424
PubMed: 9108019
DOI: 10.1073/PNAS.94.8.3579