Zinc in PDB 8x47: Crystal Structure of DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) From Pyrococcus Horikoshii

All present enzymatic activity of Crystal Structure of DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) From Pyrococcus Horikoshii:
2.1.1.182;

The structure of Crystal Structure of DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) From Pyrococcus Horikoshii, PDB code: 8x47 was solved by S.Saha, A.Dutta, S.P.Kanaujia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.45 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.99, 100.17, 77.9, 90, 90, 90
R / Rfree (%)	18.4 / 27.6

The binding sites of Zinc atom in the Crystal Structure of DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) From Pyrococcus Horikoshii (pdb code 8x47). 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 DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) From Pyrococcus Horikoshii, PDB code: 8x47:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) 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 DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:66.8 occ:1.00 OE1 A:GLU58 2.0 67.1 1.0 CD A:GLU58 2.6 65.6 1.0 OE2 A:GLU58 2.6 67.4 1.0 CG A:GLU58 4.0 65.6 1.0 CB A:GLU54 4.5 63.7 1.0 CG A:GLU54 4.6 74.2 1.0 C A:GLU54 4.9 49.8 1.0 O A:GLU54 4.9 48.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) 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 DIMT1 in Complex with S-Adenosyl-L-Homocysteine (Sah) From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:47.1 occ:1.00 O A:HOH410 1.9 40.5 1.0 ND1 A:HIS263 2.2 45.2 1.0 O A:HOH433 2.3 19.3 1.0 O A:HOH435 2.7 38.1 1.0 CE1 A:HIS263 3.0 42.6 1.0 CG A:HIS263 3.3 44.9 1.0 CB A:HIS263 3.7 43.9 1.0 CA A:HIS263 3.7 45.7 1.0 OE2 A:GLU275 4.1 45.2 1.0 NE2 A:HIS263 4.2 43.4 1.0 CD2 A:HIS263 4.3 43.5 1.0 N A:HIS263 4.3 46.2 1.0 O A:HOH416 4.4 41.3 1.0 CD A:GLU275 4.8 46.7 1.0 C A:HIS263 4.9 45.0 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