Zinc in PDB 4tyq: Crystal Structure of An Adenylate Kinase Mutant--AKM2

All present enzymatic activity of Crystal Structure of An Adenylate Kinase Mutant--AKM2:
2.7.4.3;

The structure of Crystal Structure of An Adenylate Kinase Mutant--AKM2, PDB code: 4tyq was solved by S.Moon, E.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.003, 48.790, 54.832, 90.98, 97.34, 95.83
R / Rfree (%)	17.5 / 21.9

The structure of Crystal Structure of An Adenylate Kinase Mutant--AKM2 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Zinc atom in the Crystal Structure of An Adenylate Kinase Mutant--AKM2 (pdb code 4tyq). 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 An Adenylate Kinase Mutant--AKM2, PDB code: 4tyq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of An Adenylate Kinase Mutant--AKM2


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 An Adenylate Kinase Mutant--AKM2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:23.4 occ:1.00 OD2 A:ASP153 2.1 12.1 1.0 SG A:CYS150 2.3 11.7 1.0 SG A:CYS130 2.3 12.2 1.0 SG A:CYS133 2.4 15.7 1.0 CG A:ASP153 2.6 13.7 1.0 OD1 A:ASP153 2.7 16.1 1.0 CB A:CYS130 3.1 13.8 1.0 CB A:CYS150 3.2 13.4 1.0 CB A:CYS133 3.4 17.0 1.0 N A:CYS133 3.7 14.7 1.0 CB A:ASP153 4.1 13.1 1.0 CA A:CYS133 4.1 14.9 1.0 CB A:VAL132 4.3 15.5 1.0 O A:HOH441 4.3 37.5 1.0 CB A:LYS152 4.4 15.8 1.0 N A:ASP153 4.4 14.3 1.0 CA A:CYS130 4.6 13.0 1.0 CA A:CYS150 4.7 12.4 1.0 C A:VAL132 4.7 17.6 1.0 CD A:LYS152 4.8 22.6 1.0 C A:CYS133 4.8 15.0 1.0 OG1 A:THR135 4.8 17.2 1.0 CB A:THR135 4.8 15.3 1.0 CG1 A:VAL132 4.8 16.5 1.0 CA A:ASP153 4.8 13.6 1.0 CA A:VAL132 4.8 16.4 1.0 N A:VAL132 4.9 17.7 1.0 N A:GLY134 4.9 16.1 1.0 CE A:LYS152 4.9 27.2 1.0 CG A:LYS152 5.0 20.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of An Adenylate Kinase Mutant--AKM2


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 An Adenylate Kinase Mutant--AKM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:22.4 occ:1.00 OD2 B:ASP153 2.1 12.6 1.0 SG B:CYS133 2.3 14.2 1.0 SG B:CYS130 2.3 11.8 1.0 SG B:CYS150 2.4 12.1 1.0 CG B:ASP153 2.6 14.2 1.0 OD1 B:ASP153 2.7 13.7 1.0 CB B:CYS130 3.1 14.1 1.0 CB B:CYS150 3.2 12.8 1.0 CB B:CYS133 3.4 13.8 1.0 N B:CYS133 3.8 13.4 1.0 CB B:ASP153 4.1 12.6 1.0 CA B:CYS133 4.1 14.9 1.0 CB B:VAL132 4.3 13.7 1.0 CB B:LYS152 4.4 16.7 1.0 N B:ASP153 4.4 12.4 1.0 CA B:CYS130 4.5 11.6 1.0 C B:VAL132 4.6 14.5 1.0 CA B:CYS150 4.6 11.2 1.0 CD B:LYS152 4.7 22.6 1.0 CA B:VAL132 4.8 14.4 1.0 N B:VAL132 4.8 14.0 1.0 CB B:THR135 4.8 13.0 1.0 CA B:ASP153 4.8 13.0 1.0 OG1 B:THR135 4.8 14.0 1.0 C B:CYS133 4.8 15.0 1.0 CE B:LYS152 4.8 26.8 1.0 CG1 B:VAL132 4.8 15.2 1.0 N B:GLY134 4.9 14.9 1.0

S.Moon, E.Bae. Crystal Structures of Thermally Stable Adenylate Kinase Mutants Designed By Local Structural Entropy Optimization and Structure-Guided Mutagenesis J Korean Soc Appl Biol Chem V. 57 661 2014.
ISSN: ISSN 1738-2203
DOI: 10.1007/S13765-014-4228-4