Zinc in PDB 8x4o: Crystal Structure of the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii

All present enzymatic activity of Crystal Structure of the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii:
2.1.1.182;

The structure of Crystal Structure of the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii, PDB code: 8x4o was solved by S.Saha, S.P.Kanaujia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.85 / 3.00
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	125.539, 125.539, 37.14, 90, 90, 120
R / Rfree (%)	21.9 / 30.4

The binding sites of Zinc atom in the Crystal Structure of the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii (pdb code 8x4o). 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 the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii, PDB code: 8x4o:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii


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 the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:70.3 occ:1.00 ND1 A:HIS231 2.1 84.4 1.0 O A:HOH403 2.3 44.6 1.0 CG A:HIS231 2.9 81.6 1.0 CB A:HIS231 3.0 76.1 1.0 CE1 A:HIS231 3.2 85.3 1.0 CA A:HIS231 3.9 72.2 1.0 CD2 A:HIS231 4.1 81.8 1.0 NE2 A:HIS231 4.2 85.5 1.0 C A:HIS231 4.6 65.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii


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 the Y135A Mutant of DIMT1 in Complex with 5'- Methylthioadenosine From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:70.2 occ:1.00 NE2 A:HIS286 2.1 87.0 1.0 O A:HOH405 2.1 40.9 1.0 ND1 B:HIS231 2.1 84.2 1.0 O B:HOH406 2.3 45.9 1.0 CG B:HIS231 2.9 80.8 1.0 CB B:HIS231 3.0 76.2 1.0 CD2 A:HIS286 3.0 86.6 1.0 CE1 A:HIS286 3.1 85.6 1.0 CE1 B:HIS231 3.2 84.7 1.0 CA B:HIS231 3.9 72.3 1.0 OH A:TYR282 4.0 75.6 1.0 CD2 B:HIS231 4.1 80.6 1.0 ND1 A:HIS286 4.2 82.9 1.0 CG A:HIS286 4.2 85.5 1.0 CE1 A:TYR282 4.2 71.8 1.0 NE2 B:HIS231 4.2 84.0 1.0 CZ A:TYR282 4.5 73.2 1.0 C B:HIS231 4.6 65.0 1.0 ND2 A:ASN260 4.6 78.0 1.0

S.Saha, S.P.Kanaujia. Structural and Functional Characterization of Archaeal DIMT1 Unveils Distinct Protein Dynamics Essential For Efficient Catalysis. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 39146930
DOI: 10.1016/J.STR.2024.07.013