Magnesium in PDB 6dc6: Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin

Enzymatic activity of Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin

All present enzymatic activity of Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin:
6.2.1.45;

Protein crystallography data

The structure of Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin, PDB code: 6dc6 was solved by Z.Lv, L.Yuan, K.M.Williams, J.H.Atkison, S.K.Olsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.70 / 3.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.999, 70.438, 188.851, 90.00, 95.19, 90.00
R / Rfree (%) 21.3 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin (pdb code 6dc6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin, PDB code: 6dc6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6dc6

Go back to Magnesium Binding Sites List in 6dc6
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin


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 Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:36.9
occ:1.00
 OD2 A:ASP576 2.2 99.6 1.0
O6 A:POP1103 2.2 86.8 1.0
CG A:ASP576 2.8 85.9 1.0
O2 A:POP1103 2.9 79.6 1.0
CB A:ASP576 2.9 72.8 1.0
P2 A:POP1103 3.5 76.7 1.0
P1 A:POP1103 3.7 57.2 1.0
O A:POP1103 3.7 73.8 1.0
CD1 A:ILE891 3.8 98.3 1.0
OD1 A:ASP576 3.9 89.3 1.0
O3 A:POP1103 4.1 49.6 1.0
O4 A:POP1103 4.3 44.2 1.0
CA A:ASP576 4.5 57.3 1.0
O5 A:POP1103 4.5 3.8 1.0
CG1 A:ILE891 4.6 0.5 1.0
O B:GLY76 4.6 96.4 1.0
O A:ASP576 4.8 49.1 1.0

Magnesium binding site 2 out of 4 in 6dc6

Go back to Magnesium Binding Sites List in 6dc6
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin


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 Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:23.8
occ:1.00
 OD2 A:ASP506 2.0 65.5 1.0
O5 A:POP1103 2.6 3.8 1.0
OE2 A:GLU509 2.8 84.0 1.0
O3 A:POP1103 3.0 49.6 1.0
CG A:ASP506 3.0 61.5 1.0
CD A:GLU509 3.3 88.3 1.0
OD1 A:ASP506 3.4 51.5 1.0
OE1 A:GLU509 3.7 1.0 1.0
NZ A:LYS528 3.9 46.4 1.0
P2 A:POP1103 3.9 76.7 1.0
OD1 A:ASN512 4.1 52.6 1.0
O6 A:POP1103 4.2 86.8 1.0
CG A:GLU509 4.3 75.0 1.0
CB A:ASP506 4.3 58.2 1.0
P1 A:POP1103 4.3 57.2 1.0
ND2 A:ASN512 4.4 75.6 1.0
O A:POP1103 4.5 73.8 1.0
O A:THR507 4.5 56.8 1.0
CE A:LYS528 4.6 48.0 1.0
CG A:ASN512 4.7 47.3 1.0

Magnesium binding site 3 out of 4 in 6dc6

Go back to Magnesium Binding Sites List in 6dc6
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:34.0
occ:1.00
 OD2 C:ASP576 2.3 0.8 1.0
O1 C:POP1103 2.4 63.3 1.0
CG C:ASP576 2.8 84.9 1.0
CB C:ASP576 2.9 64.0 1.0
O6 C:POP1103 3.2 43.8 1.0
O4 C:POP1103 3.6 90.1 1.0
P1 C:POP1103 3.6 45.4 1.0
O2 C:POP1103 3.8 33.6 1.0
P2 C:POP1103 3.9 77.8 1.0
OD1 C:ASP576 3.9 94.5 1.0
O C:POP1103 4.3 51.3 1.0
CA C:ASP576 4.4 63.9 1.0
O C:ASP576 4.6 62.6 1.0
CG2 C:ILE891 4.7 44.8 1.0
O3 C:POP1103 4.8 26.3 1.0
C C:ASP576 4.9 63.2 1.0

Magnesium binding site 4 out of 4 in 6dc6

Go back to Magnesium Binding Sites List in 6dc6
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Ubiquitin Activating Enzyme E1 (UBA1) in Complex with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:30.6
occ:1.00
 OD2 C:ASP506 2.2 67.8 1.0
O4 C:POP1103 2.6 90.1 1.0
O C:POP1103 2.8 51.3 1.0
P2 C:POP1103 3.0 77.8 1.0
OE2 C:GLU509 3.1 67.1 1.0
NZ C:LYS528 3.2 68.7 1.0
CG C:ASP506 3.3 70.3 1.0
O5 C:POP1103 3.3 99.9 1.0
CD C:GLU509 3.5 69.7 1.0
P1 C:POP1103 3.7 45.4 1.0
OD1 C:ASN512 3.8 68.6 1.0
OD1 C:ASP506 3.9 79.6 1.0
O3 C:POP1103 3.9 26.3 1.0
O1 C:POP1103 3.9 63.3 1.0
OE1 C:GLU509 3.9 79.8 1.0
ND2 C:ASN512 3.9 81.9 1.0
CE C:LYS528 4.2 69.9 1.0
CG C:ASN512 4.3 68.4 1.0
CG C:GLU509 4.3 73.5 1.0
O6 C:POP1103 4.5 43.8 1.0
CB C:ASP506 4.6 69.2 1.0
O C:THR507 4.6 91.5 1.0

Reference:

Z.Lv, K.M.Williams, L.Yuan, J.H.Atkison, S.K.Olsen. Crystal Structure of A Human Ubiquitin E1-Ubiquitin Complex Reveals Conserved Functional Elements Essential For Activity. J. Biol. Chem. V. 293 18337 2018.
ISSN: ESSN 1083-351X
PubMed: 30279270
DOI: 10.1074/JBC.RA118.003975
Page generated: Mon Dec 14 22:34:37 2020

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