Zinc in PDB 7lm3: Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe

The structure of Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe, PDB code: 7lm3 was solved by R.Shrestha, C.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.04 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.531, 121.338, 57.145, 90, 129.58, 90
R / Rfree (%)	20.1 / 25.3

The binding sites of Zinc atom in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe (pdb code 7lm3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe, PDB code: 7lm3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe


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 THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:81.8 occ:1.00 NE2 A:HIS406 2.0 65.7 1.0 NE2 A:HIS404 2.0 81.3 1.0 NE2 A:HIS356 2.1 74.3 1.0 SG A:CYS397 2.3 67.6 1.0 CD2 A:HIS404 2.6 82.4 1.0 CE1 A:HIS406 2.9 70.1 1.0 CD2 A:HIS356 3.0 65.2 1.0 CE1 A:HIS356 3.0 73.6 1.0 CD2 A:HIS406 3.1 70.3 1.0 CE1 A:HIS404 3.2 83.2 1.0 CB A:CYS397 3.5 73.0 1.0 CG A:HIS404 3.8 78.2 1.0 ND1 A:HIS406 4.1 71.7 1.0 ND1 A:HIS404 4.1 86.7 1.0 ND1 A:HIS356 4.1 67.8 1.0 CG A:HIS356 4.1 60.6 1.0 O A:CYS397 4.2 83.8 1.0 CG A:HIS406 4.2 73.1 1.0 OG A:SER352 4.4 71.2 1.0 CA A:CYS397 4.7 74.1 1.0 C A:CYS397 4.7 81.0 1.0 CD1 A:ILE394 4.7 59.8 1.0 O A:HIS404 4.8 79.9 1.0 O A:LYS399 4.8 87.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe


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 THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:66.2 occ:1.00 OD2 A:ASP354 1.9 57.3 1.0 NE2 A:HIS343 2.2 56.5 1.0 NE2 A:HIS341 2.3 62.4 1.0 CG A:ASP354 2.6 58.8 1.0 OD1 A:ASP354 2.6 59.1 1.0 CD2 A:HIS343 3.0 63.3 1.0 CD2 A:HIS341 3.2 63.1 1.0 CE1 A:HIS343 3.3 64.3 1.0 CE1 A:HIS341 3.3 58.9 1.0 OE1 A:GLU286 3.4 90.5 1.0 CB A:ASP354 4.0 58.7 1.0 CG A:HIS343 4.2 66.0 1.0 CB A:SER351 4.3 61.3 1.0 ND1 A:HIS343 4.3 68.6 1.0 CD A:GLU286 4.3 93.4 1.0 OG A:SER351 4.4 64.5 1.0 CG A:HIS341 4.4 63.4 1.0 ND1 A:HIS341 4.4 67.8 1.0 OE2 A:GLU286 4.6 96.5 1.0 N A:SER351 4.6 62.8 1.0 O A:PHE349 4.8 63.3 1.0 O A:ASP315 4.9 86.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:76.4 occ:1.00 NE2 B:HIS406 2.0 64.6 1.0 NE2 B:HIS356 2.0 69.7 1.0 NE2 B:HIS404 2.1 79.9 1.0 SG B:CYS397 2.3 75.1 1.0 CD2 B:HIS404 2.6 80.4 1.0 CE1 B:HIS406 2.9 68.9 1.0 CE1 B:HIS356 3.0 70.9 1.0 CD2 B:HIS356 3.0 61.0 1.0 CD2 B:HIS406 3.1 68.7 1.0 CE1 B:HIS404 3.2 82.7 1.0 CB B:CYS397 3.4 75.7 1.0 CG B:HIS404 3.9 76.6 1.0 ND1 B:HIS406 4.1 70.5 1.0 ND1 B:HIS356 4.1 63.0 1.0 ND1 B:HIS404 4.1 84.5 1.0 CG B:HIS356 4.1 56.2 1.0 CG B:HIS406 4.2 67.9 1.0 O B:CYS397 4.3 82.0 1.0 OG B:SER352 4.6 77.4 1.0 CD1 B:ILE394 4.6 59.5 1.0 CA B:CYS397 4.7 77.1 1.0 C B:CYS397 4.7 80.6 1.0 CG B:LYS399 4.8 90.2 1.0 O B:HIS404 4.9 77.9 1.0 O B:LYS399 5.0 87.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:58.0 occ:1.00 OD2 B:ASP354 1.9 56.5 1.0 NE2 B:HIS343 2.2 58.2 1.0 NE2 B:HIS341 2.3 61.0 1.0 CG B:ASP354 2.7 58.0 1.0 OD1 B:ASP354 2.8 56.1 1.0 CD2 B:HIS343 3.0 61.8 1.0 CD2 B:HIS341 3.2 65.0 1.0 CE1 B:HIS341 3.4 60.9 1.0 CE1 B:HIS343 3.4 62.9 1.0 OE2 B:GLU286 3.8 89.3 1.0 CB B:ASP354 4.1 60.1 1.0 CG B:HIS343 4.2 68.1 1.0 OE1 B:GLU286 4.2 87.0 1.0 CB B:SER351 4.2 61.8 1.0 OG B:SER351 4.2 65.1 1.0 CG B:HIS341 4.4 59.0 1.0 CD B:GLU286 4.4 87.5 1.0 ND1 B:HIS343 4.4 68.3 1.0 ND1 B:HIS341 4.4 64.3 1.0 N B:SER351 4.7 66.1 1.0 O B:PHE349 4.7 65.2 1.0

R.Shrestha, C.Das. Crystal Structure of the THR316ALA Mutant of A Yeast Jamm Deubiquitinase: Implication of Active-Site Loop Dynamics in Catalysis. Acta Crystallogr.,Sect.F V. 77 163 2021.
ISSN: ESSN 2053-230X
PubMed: 34100774
DOI: 10.1107/S2053230X21005124