Calcium in PDB 7pvn: Crystal Structure of Human UBA6 in Complex with Atp

All present enzymatic activity of Crystal Structure of Human UBA6 in Complex with Atp:
6.2.1.45;

The structure of Crystal Structure of Human UBA6 in Complex with Atp, PDB code: 7pvn was solved by N.Truongvan, S.Li, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.71
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.949, 113.748, 183.537, 90, 96.49, 90
R / Rfree (%)	23.3 / 26.2

The structure of Crystal Structure of Human UBA6 in Complex with Atp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom
Arsenic	(As)	16 atoms

The binding sites of Calcium atom in the Crystal Structure of Human UBA6 in Complex with Atp (pdb code 7pvn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human UBA6 in Complex with Atp, PDB code: 7pvn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Human UBA6 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human UBA6 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1107 b:89.5 occ:1.00 OE1 A:GLU426 3.4 68.4 1.0 OE2 A:GLU426 3.5 67.8 1.0 OD1 A:ASP423 3.5 44.9 1.0 O A:HOH1325 3.8 33.3 1.0 CD A:GLU426 3.9 65.9 1.0 HB3 A:ALA422 3.9 46.0 1.0 CG A:ASP423 4.2 42.4 1.0 OD2 A:ASP423 4.3 45.8 1.0 HD21 A:ASN318 4.4 89.5 1.0 HD22 A:ASN318 4.6 89.5 1.0 O A:HOH1223 4.6 29.9 1.0 HB1 A:ALA422 4.6 46.0 1.0 CB A:ALA422 4.7 37.9 1.0 ND2 A:ASN318 4.8 74.1 1.0 HE3 A:LYS922 4.9 57.6 1.0 HA A:ASP423 5.0 42.3 1.0 H A:ASP423 5.0 44.8 1.0 HZ1 A:LYS922 5.0 67.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human UBA6 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human UBA6 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1108 b:49.5 occ:1.00 O A:HOH1243 2.3 58.4 1.0 OD2 A:ASP499 3.2 54.0 1.0 OD1 A:ASP499 3.2 53.4 1.0 OE1 A:GLU502 3.3 72.8 1.0 HD21 A:ASN505 3.3 42.0 1.0 CD A:GLU502 3.3 70.1 1.0 CG A:ASP499 3.3 49.8 1.0 HG3 A:GLU502 3.4 76.3 1.0 HZ3 A:LYS521 3.4 54.0 1.0 HZ1 A:LYS521 3.6 54.0 1.0 O1B A:ATP1101 3.6 37.8 1.0 OE2 A:GLU502 3.6 72.4 1.0 O A:LEU500 3.8 37.3 1.0 CG A:GLU502 3.9 63.1 1.0 NZ A:LYS521 3.9 44.5 1.0 HOB2 A:ATP1101 4.0 36.0 1.0 ND2 A:ASN505 4.2 34.6 1.0 HE3 A:LYS521 4.2 50.4 1.0 HB3 A:ASP499 4.3 51.9 1.0 CB A:ASP499 4.5 42.8 1.0 HG2 A:GLU502 4.6 76.3 1.0 HB2 A:GLU502 4.6 71.0 1.0 O2B A:ATP1101 4.6 29.5 1.0 CE A:LYS521 4.6 41.5 1.0 HZ2 A:LYS521 4.7 54.0 1.0 OD1 A:ASN505 4.7 39.9 1.0 PB A:ATP1101 4.7 71.2 1.0 HD22 A:ASN505 4.7 42.0 1.0 H A:LEU500 4.8 34.3 1.0 CG A:ASN505 4.9 34.5 1.0 CB A:GLU502 4.9 58.7 1.0 HB2 A:ASP499 4.9 51.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human UBA6 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human UBA6 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1107 b:65.0 occ:1.00 O B:HOH1224 2.9 42.6 1.0 OD2 B:ASP499 3.0 93.5 1.0 OD1 B:ASP499 3.1 95.1 1.0 HD21 B:ASN505 3.2 90.2 1.0 CG B:ASP499 3.2 92.9 1.0 OE1 B:GLU502 3.3 117.6 1.0 HZ2 B:LYS521 3.4 101.1 1.0 HZ3 B:LYS521 3.4 101.1 1.0 O1B B:ATP1101 3.5 77.2 1.0 CD B:GLU502 3.6 115.9 1.0 HOB2 B:ATP1101 3.7 93.5 1.0 HG3 B:GLU502 3.7 135.4 1.0 NZ B:LYS521 3.8 83.8 1.0 OE2 B:GLU502 3.9 116.8 1.0 HB3 B:ASP499 4.0 104.9 1.0 ND2 B:ASN505 4.0 74.7 1.0 O B:LEU500 4.0 69.0 1.0 CB B:ASP499 4.2 87.0 1.0 CG B:GLU502 4.2 112.4 1.0 HE3 B:LYS521 4.3 101.8 1.0 O2B B:ATP1101 4.3 77.5 1.0 PB B:ATP1101 4.5 79.2 1.0 HZ1 B:LYS521 4.5 101.1 1.0 HD22 B:ASN505 4.5 90.2 1.0 HB2 B:ASP499 4.6 104.9 1.0 CE B:LYS521 4.7 84.3 1.0 OD1 B:ASN505 4.7 75.5 1.0 H B:LEU500 4.8 96.8 1.0 CG B:ASN505 4.8 74.6 1.0 HG2 B:GLU502 4.8 135.4 1.0 O1G B:ATP1101 4.9 82.6 1.0

N.Truongvan, S.Li, M.Misra, M.Kuhn, H.Schindelin. Structures of UBA6 Explain Its Dual Specificity For Ubiquitin and FAT10. Nat Commun V. 13 4789 2022.
ISSN: ESSN 2041-1723
PubMed: 35970836
DOI: 10.1038/S41467-022-32040-6