Magnesium in PDB 1b4s: Structure of Nucleoside Diphosphate Kinase H122G Mutant

All present enzymatic activity of Structure of Nucleoside Diphosphate Kinase H122G Mutant:
2.7.4.6;

The structure of Structure of Nucleoside Diphosphate Kinase H122G Mutant, PDB code: 1b4s was solved by P.Meyer, J.Janin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.000, 70.000, 151.770, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 30.5

The binding sites of Magnesium atom in the Structure of Nucleoside Diphosphate Kinase H122G Mutant (pdb code 1b4s). 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 H122G Mutant, PDB code: 1b4s:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Nucleoside Diphosphate Kinase H122G 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 Nucleoside Diphosphate Kinase H122G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg162 b:20.9 occ:1.00 O1 A:PO4161 2.2 24.4 1.0 O1A A:ADP160 2.5 28.5 1.0 O1B A:ADP160 2.6 27.9 1.0 P A:PO4161 3.6 20.1 1.0 PB A:ADP160 3.8 28.1 1.0 OE2 A:GLU58 3.9 38.7 1.0 PA A:ADP160 3.9 20.7 1.0 OD2 A:ASP125 3.9 33.0 1.0 O4 A:PO4161 4.0 20.0 1.0 NH1 A:ARG92 4.1 17.6 1.0 O3A A:ADP160 4.2 32.9 1.0 O2 A:PO4161 4.2 18.5 1.0 O A:GLY123 4.3 25.4 1.0 O3B A:ADP160 4.3 17.2 1.0 NE2 A:HIS59 4.4 18.5 1.0 CG A:ASP125 4.6 27.3 1.0 O3 A:PO4161 4.6 15.3 1.0 NH2 A:ARG92 4.7 14.2 1.0 CZ A:ARG92 4.7 17.9 1.0 CB A:ASP125 4.8 23.1 1.0 C5' A:ADP160 4.8 14.5 1.0 CD A:GLU58 4.8 41.8 1.0 O5' A:ADP160 4.9 20.9 1.0 O2A A:ADP160 4.9 28.8 1.0

Magnesium binding site 2 out of 3 in the Structure of Nucleoside Diphosphate Kinase H122G 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 Nucleoside Diphosphate Kinase H122G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg162 b:29.1 occ:1.00 O B:HOH205 1.8 23.1 1.0 O2 B:PO4161 2.0 41.7 1.0 O B:HOH204 2.1 50.2 1.0 O B:HOH203 2.1 16.9 1.0 O1B B:ADP160 2.2 14.0 1.0 O1A B:ADP160 2.3 25.4 1.0 P B:PO4161 3.4 36.1 1.0 PB B:ADP160 3.5 26.6 1.0 PA B:ADP160 3.6 22.2 1.0 O1 B:PO4161 3.8 28.3 1.0 O3A B:ADP160 3.9 29.6 1.0 O B:HOH173 3.9 25.1 1.0 OE2 B:GLU58 3.9 44.2 1.0 NH1 B:ARG92 4.0 16.9 1.0 OD2 B:ASP125 4.2 31.2 1.0 O B:HOH182 4.2 21.1 1.0 O4 B:PO4161 4.2 30.5 1.0 O B:HOH170 4.2 18.8 1.0 O3B B:ADP160 4.2 24.0 1.0 NE2 B:HIS59 4.3 25.3 1.0 O B:GLY123 4.4 21.5 1.0 O3 B:PO4161 4.4 31.1 1.0 C5' B:ADP160 4.5 23.2 1.0 O B:HOH184 4.6 21.6 1.0 O2A B:ADP160 4.6 14.9 1.0 O5' B:ADP160 4.6 22.5 1.0 CG B:ASP125 4.7 31.6 1.0 CZ B:ARG92 4.7 16.9 1.0 O2B B:ADP160 4.7 26.0 1.0 NH2 B:ARG92 4.8 12.9 1.0 CB B:ASP125 4.8 27.8 1.0 CD B:GLU58 4.9 39.6 1.0

Magnesium binding site 3 out of 3 in the Structure of Nucleoside Diphosphate Kinase H122G 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 Nucleoside Diphosphate Kinase H122G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg162 b:50.1 occ:1.00 O1A C:ADP160 2.1 32.7 1.0 O1 C:PO4161 2.4 34.4 1.0 O1B C:ADP160 2.6 21.8 1.0 PA C:ADP160 3.5 21.7 1.0 PB C:ADP160 3.8 28.4 1.0 P C:PO4161 3.8 40.7 1.0 OE2 C:GLU58 3.8 32.5 1.0 O3A C:ADP160 3.9 35.4 1.0 O C:HOH170 3.9 14.8 1.0 OD2 C:ASP125 3.9 34.8 1.0 NE2 C:HIS59 4.0 28.5 1.0 O4 C:PO4161 4.1 31.4 1.0 NH1 C:ARG92 4.4 22.4 1.0 O5' C:ADP160 4.4 26.5 1.0 O3B C:ADP160 4.5 25.8 1.0 C5' C:ADP160 4.5 27.8 1.0 O2 C:PO4161 4.5 45.8 1.0 O2A C:ADP160 4.5 35.2 1.0 CD C:GLU58 4.7 38.5 1.0 O C:GLY123 4.7 24.7 1.0 CE1 C:HIS59 4.7 25.2 1.0 CG C:ASP125 4.7 32.9 1.0 O3 C:PO4161 4.8 27.6 1.0 O2B C:ADP160 4.9 27.5 1.0 NH2 C:ARG92 4.9 8.2 1.0 CB C:ASP125 5.0 28.7 1.0

S.J.Admiraal, B.Schneider, P.Meyer, J.Janin, M.Veron, D.Deville-Bonne, D.Herschlag. Nucleophilic Activation By Positioning in Phosphoryl Transfer Catalyzed By Nucleoside Diphosphate Kinase. Biochemistry V. 38 4701 1999.
ISSN: ISSN 0006-2960
PubMed: 10200157
DOI: 10.1021/BI9827565