Zinc in PDB 4qbh: Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5

All present enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5:
2.7.4.3;

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5, PDB code: 4qbh 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 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.089, 75.360, 81.982, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.3

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5 (pdb code 4qbh). 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 AKLSE5, PDB code: 4qbh:
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 AKLSE5


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 AKLSE5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:26.2 occ:1.00 SG A:CYS130 2.3 22.7 1.0 SG A:CYS153 2.3 26.3 1.0 SG A:CYS133 2.3 24.6 1.0 SG A:CYS150 2.4 23.8 1.0 CB A:CYS130 3.1 23.4 1.0 CB A:CYS150 3.1 23.1 1.0 CB A:CYS133 3.3 29.7 1.0 CB A:CYS153 3.5 30.6 1.0 N A:CYS153 3.7 27.6 1.0 N A:CYS133 3.7 29.7 1.0 CA A:CYS133 4.0 28.9 1.0 CA A:CYS153 4.1 29.8 1.0 N A:GLY155 4.4 22.9 1.0 CB A:ALA135 4.6 23.7 1.0 CA A:CYS130 4.6 21.7 1.0 CB A:LYS152 4.6 30.4 1.0 C A:CYS133 4.6 28.7 1.0 CA A:CYS150 4.6 22.6 1.0 C A:LYS152 4.7 29.9 1.0 N A:GLY134 4.7 25.3 1.0 CB A:ASN132 4.7 30.5 1.0 C A:CYS153 4.7 27.1 1.0 CA A:GLY155 4.8 24.1 1.0 N A:GLY154 4.8 24.8 1.0 C A:ASN132 4.8 30.8 1.0 N A:ALA135 4.9 22.8 1.0 N A:ASN132 5.0 28.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5


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 AKLSE5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:43.8 occ:1.00 SG B:CYS150 2.2 35.0 1.0 SG B:CYS133 2.3 32.4 1.0 SG B:CYS130 2.4 27.1 1.0 SG B:CYS153 2.4 39.0 1.0 CB B:CYS130 3.1 25.6 1.0 CB B:CYS150 3.2 32.7 1.0 CB B:CYS133 3.3 35.8 1.0 CB B:CYS153 3.5 47.0 1.0 N B:CYS153 3.7 46.9 1.0 N B:CYS133 3.8 37.2 1.0 CA B:CYS133 4.1 34.9 1.0 CA B:CYS153 4.1 48.2 1.0 CB B:ALA135 4.5 29.2 1.0 N B:GLY155 4.5 33.9 1.0 CA B:CYS130 4.5 23.8 1.0 C B:ASN132 4.5 40.6 1.0 CB B:LYS152 4.5 52.7 1.0 C B:LYS152 4.6 51.1 1.0 N B:GLY154 4.7 42.0 1.0 C B:CYS153 4.7 46.2 1.0 CA B:CYS150 4.7 32.8 1.0 C B:CYS133 4.7 31.6 1.0 N B:ALA135 4.8 26.9 1.0 N B:LYS152 4.8 47.9 1.0 N B:GLY134 4.8 28.3 1.0 CA B:LYS152 4.9 51.9 1.0 N B:ASN132 4.9 34.7 1.0 CA B:GLY155 4.9 32.4 1.0 C B:CYS130 5.0 27.8 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 2014.
ISSN: ESSN 1097-0134
DOI: 10.1002/PROT.24627