Magnesium in PDB 8h5y: Crystal Structure of Radd- Adp Complex

All present enzymatic activity of Crystal Structure of Radd- Adp Complex:
3.6.4.12;

The structure of Crystal Structure of Radd- Adp Complex, PDB code: 8h5y was solved by X.X.Yan, L.F.Tian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.089, 78.77, 110.238, 90, 99.57, 90
R / Rfree (%)	22.3 / 26.9

The structure of Crystal Structure of Radd- Adp Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Radd- Adp Complex (pdb code 8h5y). 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 Radd- Adp Complex, PDB code: 8h5y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Radd- Adp 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 Radd- Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:29.5 occ:1.00 N B:SER38 2.6 24.7 1.0 O1B B:ADP602 2.6 28.7 1.0 OG B:SER38 2.8 26.3 1.0 N B:LYS37 2.8 27.0 1.0 CB B:SER38 3.1 23.0 1.0 C B:GLY36 3.2 26.5 1.0 CA B:GLY36 3.2 29.6 1.0 O1A B:ADP602 3.4 35.4 1.0 CA B:SER38 3.4 21.7 1.0 PB B:ADP602 3.5 25.1 1.0 C B:LYS37 3.6 28.6 1.0 CG B:LYS37 3.6 30.5 1.0 O2B B:ADP602 3.6 23.8 1.0 CA B:LYS37 3.7 25.6 1.0 O3A B:ADP602 3.9 35.4 1.0 CD B:LYS68 4.0 26.9 1.0 O B:GLY36 4.0 29.3 1.0 CB B:LYS37 4.2 18.4 1.0 N B:GLY36 4.2 35.9 1.0 PA B:ADP602 4.3 30.6 1.0 CB B:LYS68 4.4 32.5 1.0 C B:SER38 4.5 24.4 1.0 NZ B:LYS68 4.6 33.3 1.0 N B:LEU39 4.6 22.4 1.0 CE B:LYS68 4.7 32.6 1.0 NZ B:LYS37 4.7 43.3 1.0 O B:LYS37 4.7 23.6 1.0 CG B:LYS68 4.8 27.0 1.0 O3B B:ADP602 4.9 34.1 1.0 CD B:LYS37 4.9 39.0 1.0 O B:HOH712 4.9 22.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Radd- Adp 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 Radd- Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:17.3 occ:1.00 OG A:SER38 2.7 27.1 1.0 N A:SER38 2.7 22.4 1.0 O1B A:ADP602 2.7 19.9 1.0 N A:LYS37 2.8 21.5 1.0 C A:GLY36 3.0 23.4 1.0 CA A:GLY36 3.1 17.1 1.0 CB A:SER38 3.2 22.0 1.0 O2B A:ADP602 3.3 26.6 1.0 PB A:ADP602 3.4 20.6 1.0 O1A A:ADP602 3.5 22.6 1.0 CG A:LYS37 3.5 22.9 1.0 CA A:SER38 3.6 18.4 1.0 C A:LYS37 3.6 22.8 1.0 CA A:LYS37 3.6 16.6 1.0 O3A A:ADP602 3.7 29.4 1.0 O A:GLY36 3.8 23.4 1.0 N A:GLY36 4.0 22.7 1.0 CD A:LYS68 4.1 24.4 1.0 CB A:LYS37 4.2 13.5 1.0 PA A:ADP602 4.2 22.9 1.0 NZ A:LYS37 4.5 26.9 1.0 NZ A:LYS68 4.6 23.2 1.0 C A:SER38 4.6 19.7 1.0 CB A:LYS68 4.6 21.0 1.0 N A:LEU39 4.6 17.3 1.0 O A:LYS37 4.7 20.4 1.0 CD A:LYS37 4.8 24.3 1.0 CE A:LYS68 4.9 23.2 1.0 O3B A:ADP602 4.9 23.6 1.0

L.F.Tian, X.Kuang, K.Ding, H.Gao, Q.Tang, X.X.Yan, W.Xu. Biochemical and Structural Analyses Shed Light on the Mechanisms of Radd Dna Binding and Its Atpase From Escherichia Coli. Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
PubMed: 36614183
DOI: 10.3390/IJMS24010741