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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7pvn:

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

Calcium (Ca) 3 atoms
Chlorine (Cl) 1 atom
Arsenic (As) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human UBA6 in Complex with Atp, PDB code: 7pvn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7pvn

Go back to Magnesium Binding Sites List in 7pvn
Magnesium binding site 1 out of 2 in the Crystal Structure of Human UBA6 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1106

b:11.6
occ:1.00
O A:HOH1248 2.1 10.5 1.0
O A:HOH1263 2.2 11.5 1.0
O3A A:ATP1101 2.2 29.6 1.0
OD2 A:ASP569 2.3 45.4 1.0
HB3 A:ASP569 2.6 47.6 1.0
O1A A:ATP1101 2.8 37.0 1.0
O3B A:ATP1101 2.8 27.3 1.0
H5'1 A:ATP1101 2.9 40.3 1.0
CG A:ASP569 3.0 43.7 1.0
PB A:ATP1101 3.0 71.2 1.0
HB2 A:ASP569 3.0 47.6 1.0
CB A:ASP569 3.0 39.2 1.0
PA A:ATP1101 3.0 36.7 1.0
O1B A:ATP1101 3.4 37.8 1.0
H3' A:ATP1101 3.8 41.5 1.0
C5' A:ATP1101 3.8 33.1 1.0
O5' A:ATP1101 3.9 34.1 1.0
PG A:ATP1101 4.1 62.3 1.0
OD1 A:ASP569 4.1 46.4 1.0
O3G A:ATP1101 4.3 35.8 1.0
O2A A:ATP1101 4.3 30.0 1.0
H5'2 A:ATP1101 4.4 40.3 1.0
O2B A:ATP1101 4.4 29.5 1.0
H2' A:ATP1101 4.5 32.9 1.0
CA A:ASP569 4.5 34.0 1.0
O1G A:ATP1101 4.6 38.0 1.0
C3' A:ATP1101 4.6 34.1 1.0
C4' A:ATP1101 4.8 32.7 1.0
HA A:ASP569 4.8 41.3 1.0

Magnesium binding site 2 out of 2 in 7pvn

Go back to Magnesium Binding Sites List in 7pvn
Magnesium binding site 2 out of 2 in the Crystal Structure of Human UBA6 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg1106

b:38.1
occ:1.00
O B:HOH1247 2.1 39.9 1.0
O B:HOH1230 2.3 49.6 1.0
OD2 B:ASP569 2.6 84.5 1.0
O3B B:ATP1101 2.7 81.7 1.0
O3A B:ATP1101 2.7 75.5 1.0
PB B:ATP1101 2.9 79.2 1.0
O1B B:ATP1101 3.0 77.2 1.0
HB3 B:ASP569 3.2 96.6 1.0
CG B:ASP569 3.3 83.9 1.0
HB2 B:ASP569 3.3 96.6 1.0
CB B:ASP569 3.5 80.0 1.0
O3G B:ATP1101 3.5 82.4 1.0
O1A B:ATP1101 3.7 73.8 1.0
PG B:ATP1101 3.7 83.7 1.0
H5'1 B:ATP1101 3.8 78.4 1.0
PA B:ATP1101 3.8 73.1 1.0
O B:HOH1212 3.9 46.9 1.0
H3' B:ATP1101 4.1 70.1 1.0
OD1 B:ASP569 4.3 83.9 1.0
O2G B:ATP1101 4.4 83.9 1.0
HOG3 B:ATP1101 4.4 99.5 1.0
O2B B:ATP1101 4.5 77.5 1.0
H2' B:ATP1101 4.5 70.2 1.0
C5' B:ATP1101 4.7 64.8 1.0
O B:HOH1224 4.7 42.6 1.0
O5' B:ATP1101 4.8 68.9 1.0
HD13 B:ILE891 4.8 96.8 1.0
O2A B:ATP1101 4.9 70.8 1.0
O1G B:ATP1101 5.0 82.6 1.0

Reference:

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
Page generated: Thu Apr 6 19:17:32 2023

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