Zinc in PDB 4mkf: Crystal Structure of A Stable Adenylate Kinase Variant AKV3

All present enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKV3:
2.7.4.3;

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3, PDB code: 4mkf was solved by S.Moon, D.Jung, E.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.99 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.447, 75.008, 77.195, 90.00, 100.89, 90.00
R / Rfree (%)	15.7 / 20.3

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	7 atoms

The binding sites of Zinc atom in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3 (pdb code 4mkf). 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 A Stable Adenylate Kinase Variant AKV3, PDB code: 4mkf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


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 A Stable Adenylate Kinase Variant AKV3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.6 occ:1.00 OD2 A:ASP153 2.1 28.6 1.0 SG A:CYS130 2.3 22.6 1.0 SG A:CYS150 2.4 19.8 1.0 SG A:CYS133 2.5 27.9 1.0 CG A:ASP153 2.8 28.6 1.0 OD1 A:ASP153 2.8 31.6 1.0 CB A:CYS130 3.1 19.7 1.0 CB A:CYS150 3.2 20.2 1.0 CB A:CYS133 3.3 28.2 1.0 N A:CYS133 3.7 28.4 1.0 CA A:CYS133 4.0 26.6 1.0 CB A:ASP153 4.3 28.8 1.0 O A:HOH410 4.4 36.5 1.0 CB A:LYS152 4.4 26.8 1.0 CG2 A:THR135 4.4 29.0 1.0 CB A:VAL132 4.5 29.4 1.0 CA A:CYS130 4.5 20.4 1.0 CA A:CYS150 4.6 20.3 1.0 C A:VAL132 4.6 28.7 1.0 N A:ASP153 4.7 27.2 1.0 C A:CYS133 4.8 26.4 1.0 CD A:LYS152 4.8 32.7 1.0 N A:GLY134 4.8 23.5 1.0 N A:VAL132 4.9 26.5 1.0 CA A:VAL132 4.9 28.3 1.0 CG1 A:VAL132 4.9 30.8 1.0 C A:CYS130 5.0 21.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


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 A Stable Adenylate Kinase Variant AKV3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:23.2 occ:1.00 SG B:CYS133 2.1 24.6 1.0 OD2 B:ASP153 2.1 24.1 1.0 SG B:CYS150 2.3 16.7 1.0 SG B:CYS130 2.3 17.6 1.0 CG B:ASP153 2.8 25.4 1.0 CB B:CYS130 3.0 17.7 1.0 OD1 B:ASP153 3.0 25.8 1.0 CB B:CYS150 3.1 18.7 1.0 CB B:CYS133 3.2 24.1 1.0 N B:CYS133 3.7 19.4 1.0 CA B:CYS133 4.0 20.6 1.0 O B:HOH453 4.3 27.7 1.0 CB B:ASP153 4.3 26.7 1.0 CB B:LYS152 4.3 26.3 1.0 OG1 B:THR135 4.4 25.0 1.0 CB B:THR135 4.4 22.6 1.0 CA B:CYS130 4.5 14.9 1.0 CB B:VAL132 4.5 23.3 1.0 N B:ASP153 4.5 25.5 1.0 CA B:CYS150 4.6 18.5 1.0 C B:VAL132 4.7 22.2 1.0 C B:CYS133 4.7 21.6 1.0 N B:GLY134 4.8 18.1 1.0 N B:THR135 4.9 19.7 1.0 CG1 B:VAL132 4.9 24.5 1.0 N B:VAL132 4.9 21.3 1.0 CA B:VAL132 4.9 22.4 1.0 CD B:LYS152 5.0 28.6 1.0 CA B:ASP153 5.0 26.1 1.0

S.Moon, D.Jung, G.N.Phillips, E.Bae. An Integrated Approach For Thermal Stabilization of A Mesophilic Adenylate Kinase Proteins 2014.
ISSN: ESSN 1097-0134
PubMed: 24615904
DOI: 10.1002/PROT.24549