Magnesium in PDB 1kdn: Structure of Nucleoside Diphosphate Kinase

All present enzymatic activity of Structure of Nucleoside Diphosphate Kinase:
2.7.4.6;

The structure of Structure of Nucleoside Diphosphate Kinase, PDB code: 1kdn was solved by J.Cherfils, Y.W.Xu, S.Morera, J.Janin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.354, 71.354, 153.494, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 17.9

The structure of Structure of Nucleoside Diphosphate Kinase also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Aluminium	(Al)	3 atoms

The binding sites of Magnesium atom in the Structure of Nucleoside Diphosphate Kinase (pdb code 1kdn). 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 Nucleoside Diphosphate Kinase, PDB code: 1kdn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Nucleoside Diphosphate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg156 b:14.1 occ:1.00 F3 A:AF3157 1.9 19.1 1.0 O A:HOH690 2.0 9.1 1.0 O1A A:ADP158 2.1 14.1 1.0 O A:HOH698 2.2 12.4 1.0 O A:HOH671 2.2 20.4 1.0 O1B A:ADP158 2.2 14.0 1.0 PB A:ADP158 3.3 11.2 1.0 PA A:ADP158 3.4 13.4 1.0 AL A:AF3157 3.5 22.4 1.0 O3A A:ADP158 3.6 13.4 1.0 O3B A:ADP158 3.8 9.4 1.0 F2 A:AF3157 4.0 24.0 1.0 O A:HOH683 4.3 11.0 1.0 OD2 A:ASP125 4.3 18.6 1.0 CE1 A:HIS122 4.3 5.8 1.0 NE2 A:HIS59 4.3 12.4 1.0 O5' A:ADP158 4.4 10.4 1.0 O A:HOH802 4.4 37.9 1.0 ND1 A:HIS122 4.4 7.3 1.0 NH2 A:ARG92 4.5 18.4 1.0 C5' A:ADP158 4.5 11.3 1.0 O2A A:ADP158 4.5 13.4 1.0 O A:HOH612 4.6 17.4 1.0 O2B A:ADP158 4.6 9.6 1.0 O A:HOH721 4.7 19.8 1.0 O A:GLY123 4.8 9.7 1.0 CG A:ASP125 4.8 17.3 1.0 OE2 A:GLU58 4.8 27.5 1.0

Magnesium binding site 2 out of 3 in the Structure of Nucleoside Diphosphate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg156 b:21.7 occ:1.00 O B:HOH847 1.8 25.2 1.0 F3 B:AF3157 1.9 32.3 1.0 O B:HOH604 2.2 29.9 1.0 O B:HOH669 2.2 16.7 1.0 O1A B:ADP158 2.4 19.4 1.0 O1B B:ADP158 2.4 22.8 1.0 AL B:AF3157 3.5 27.6 1.0 PB B:ADP158 3.6 18.3 1.0 PA B:ADP158 3.7 19.6 1.0 O3A B:ADP158 4.0 18.5 1.0 O3B B:ADP158 4.0 19.2 1.0 O B:HOH639 4.1 15.0 1.0 NE2 B:HIS59 4.1 19.9 1.0 OD2 B:ASP125 4.3 25.2 1.0 F2 B:AF3157 4.3 26.1 1.0 C5' B:ADP158 4.3 14.8 1.0 O B:HOH603 4.5 16.0 1.0 CE1 B:HIS122 4.5 7.0 1.0 O5' B:ADP158 4.5 19.4 1.0 NH1 B:ARG92 4.6 34.8 1.0 ND1 B:HIS122 4.6 7.5 1.0 OE1 B:GLU58 4.6 21.6 1.0 CG B:ASP125 4.7 20.4 1.0 O B:HOH827 4.7 26.6 1.0 CE1 B:HIS59 4.7 19.9 1.0 O B:GLY123 4.7 11.9 1.0 O2A B:ADP158 4.8 19.9 1.0 O2B B:ADP158 4.9 17.0 1.0 F1 B:AF3157 4.9 29.1 1.0 OE2 B:GLU58 4.9 26.6 1.0 CD B:GLU58 5.0 25.1 1.0 CB B:ASP125 5.0 15.7 1.0

Magnesium binding site 3 out of 3 in the Structure of Nucleoside Diphosphate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg156 b:22.6 occ:1.00 O C:HOH766 2.0 26.4 1.0 F3 C:AF3157 2.0 23.3 1.0 O1A C:ADP158 2.1 14.3 1.0 O C:HOH722 2.2 25.3 1.0 O C:HOH667 2.2 13.4 1.0 O1B C:ADP158 2.4 12.6 1.0 PA C:ADP158 3.4 16.7 1.0 PB C:ADP158 3.4 11.0 1.0 AL C:AF3157 3.6 23.5 1.0 O3A C:ADP158 3.7 15.2 1.0 O3B C:ADP158 3.9 13.8 1.0 OD2 C:ASP125 4.2 24.2 1.0 O5' C:ADP158 4.2 16.4 1.0 O C:HOH630 4.3 12.4 1.0 F1 C:AF3157 4.3 22.3 1.0 C5' C:ADP158 4.3 15.8 1.0 NE2 C:HIS59 4.4 20.3 1.0 CE1 C:HIS122 4.4 4.6 1.0 O C:HOH622 4.4 13.1 1.0 O2A C:ADP158 4.6 19.4 1.0 ND1 C:HIS122 4.6 6.2 1.0 O2B C:ADP158 4.7 12.5 1.0 CG C:ASP125 4.8 18.2 1.0 O C:GLY123 4.9 11.8 1.0 OE2 C:GLU58 4.9 32.5 1.0 NH2 C:ARG92 4.9 26.3 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