Calcium in PDB 6o83: S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic

All present enzymatic activity of S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic:
6.2.1.45;

The structure of S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic, PDB code: 6o83 was solved by Z.S.Hann, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	113.49 / 3.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.575, 150.522, 172.776, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25.2

The binding sites of Calcium atom in the S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic (pdb code 6o83). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic, PDB code: 6o83:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:30.2 occ:1.00 OE2 A:GLU320 2.4 74.3 1.0 NE2 A:HIS305 2.4 80.5 1.0 OE1 A:GLU320 2.5 72.2 1.0 CD A:GLU320 2.7 76.3 1.0 CD2 A:HIS305 3.1 79.6 1.0 CE1 A:HIS305 3.3 80.4 1.0 CG A:GLU320 4.1 77.5 1.0 CG A:HIS305 4.2 80.3 1.0 ND1 A:HIS305 4.3 80.7 1.0 CE2 A:PHE301 4.8 63.1 1.0 CZ A:PHE301 4.8 62.3 1.0 CB A:GLU320 4.9 76.8 1.0

Calcium binding site 2 out of 2 in the S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of S. Pombe Ubiquitin E1~Ubiquitin-Amp Tetrahedral Intermediate Mimic within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1101 b:96.6 occ:1.00 NE2 C:HIS305 2.2 77.5 1.0 OE2 C:GLU320 2.3 73.1 1.0 OE1 C:GLU320 2.3 70.8 1.0 CD C:GLU320 2.6 71.8 1.0 CD2 C:HIS305 2.8 75.1 1.0 CE1 C:HIS305 3.4 76.2 1.0 CG C:HIS305 4.1 74.7 1.0 CG C:GLU320 4.1 71.6 1.0 ND1 C:HIS305 4.4 72.4 1.0 CE2 C:PHE301 4.8 59.1 1.0 CB C:GLU320 4.9 68.6 1.0 CZ C:PHE301 4.9 58.9 1.0

Z.S.Hann, C.Ji, S.K.Olsen, X.Lu, M.C.Lux, D.S.Tan, C.D.Lima. Structural Basis For Adenylation and Thioester Bond Formation in the Ubiquitin E1. Proc.Natl.Acad.Sci.Usa V. 116 15475 2019.
ISSN: ESSN 1091-6490
PubMed: 31235585
DOI: 10.1073/PNAS.1905488116