Zinc in PDB 3dl0: Crystal Structure of Adenylate Kinase Variant AKLSE3

All present enzymatic activity of Crystal Structure of Adenylate Kinase Variant AKLSE3:
2.7.4.3;

The structure of Crystal Structure of Adenylate Kinase Variant AKLSE3, PDB code: 3dl0 was solved by R.M.Bannen, C.M.Bianchetti, C.A.Bingman, J.G.Mccoy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.84 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.003, 76.688, 77.993, 90.00, 95.30, 90.00
R / Rfree (%)	20 / 23.9

The structure of Crystal Structure of Adenylate Kinase Variant AKLSE3 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Adenylate Kinase Variant AKLSE3 (pdb code 3dl0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Adenylate Kinase Variant AKLSE3, PDB code: 3dl0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Adenylate Kinase Variant AKLSE3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Adenylate Kinase Variant AKLSE3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn219 b:15.3 occ:1.00 OD1 A:ASP153 2.1 20.4 1.0 SG A:CYS130 2.3 14.1 1.0 SG A:CYS133 2.3 17.1 1.0 SG A:CYS150 2.4 13.5 1.0 CG A:ASP153 2.9 18.1 1.0 CB A:CYS150 3.1 13.8 1.0 CB A:CYS130 3.1 14.6 1.0 OD2 A:ASP153 3.1 18.7 1.0 CB A:CYS133 3.5 14.2 1.0 N A:CYS133 3.8 16.0 1.0 N A:ASP153 4.1 16.5 1.0 CA A:CYS133 4.2 15.4 1.0 CB A:ASP153 4.3 15.7 1.0 N A:GLY155 4.5 16.8 1.0 CB A:LYS152 4.5 16.3 1.0 CB A:VAL132 4.6 18.3 1.0 CA A:CYS130 4.6 13.5 1.0 CA A:CYS150 4.6 13.2 1.0 CA A:ASP153 4.6 16.5 1.0 OG1 A:THR135 4.7 15.5 1.0 CA A:GLY155 4.8 16.0 1.0 CB A:THR135 4.8 15.3 1.0 C A:VAL132 4.8 17.5 1.0 C A:CYS133 4.9 15.1 1.0 N A:GLY134 4.9 14.2 1.0 C A:ASP153 5.0 15.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Adenylate Kinase Variant AKLSE3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Adenylate Kinase Variant AKLSE3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn219 b:14.2 occ:1.00 OD1 B:ASP153 2.0 16.3 1.0 SG B:CYS130 2.3 13.5 1.0 SG B:CYS150 2.3 11.4 1.0 SG B:CYS133 2.3 15.0 1.0 CG B:ASP153 2.8 17.4 1.0 OD2 B:ASP153 3.1 17.9 1.0 CB B:CYS130 3.1 14.7 1.0 CB B:CYS150 3.1 13.1 1.0 CB B:CYS133 3.4 14.0 1.0 N B:CYS133 3.8 16.2 1.0 CA B:CYS133 4.1 15.1 1.0 N B:ASP153 4.1 15.9 1.0 CB B:ASP153 4.2 16.5 1.0 N B:GLY155 4.5 17.5 1.0 CA B:CYS130 4.5 13.4 1.0 CB B:LYS152 4.6 15.1 1.0 CA B:ASP153 4.6 16.6 1.0 CA B:CYS150 4.6 12.4 1.0 CB B:VAL132 4.6 17.1 1.0 CA B:GLY155 4.7 17.0 1.0 C B:CYS133 4.8 14.2 1.0 OG1 B:THR135 4.8 13.5 1.0 C B:VAL132 4.8 17.5 1.0 CB B:THR135 4.9 12.9 1.0 N B:GLY134 4.9 13.8 1.0 C B:ASP153 4.9 16.8 1.0 N B:GLY154 4.9 16.7 1.0

S.Moon, R.M.Bannen, T.J.Rutkoski, G.N.Phillips, E.Bae. Effectiveness and Limitations of Local Structural Entropy Optimization in the Thermal Stabilization of Mesophilic and Thermophilic Adenylate Kinases. Proteins V. 82 2631 2014.
ISSN: ISSN 0887-3585
PubMed: 24931334
DOI: 10.1002/PROT.24627