Atomistry » Magnesium » PDB 4iaj-4iik » 4ii2
Atomistry »
  Magnesium »
    PDB 4iaj-4iik »
      4ii2 »

Magnesium in PDB 4ii2: Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg

Enzymatic activity of Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg

All present enzymatic activity of Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg, PDB code: 4ii2 was solved by S.K.Olsen, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.600, 111.200, 181.300, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg (pdb code 4ii2). 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 Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg, PDB code: 4ii2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4ii2

Go back to Magnesium Binding Sites List in 4ii2
Magnesium binding site 1 out of 2 in the Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg


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 Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:52.7
occ:1.00
OD2 A:ASP537 2.3 44.6 1.0
O3G A:ATP1103 2.4 40.7 1.0
O A:HOH1210 2.4 45.2 1.0
O A:HOH1208 2.4 42.4 1.0
O2B A:ATP1103 2.4 40.2 1.0
O2A A:ATP1103 2.6 38.3 1.0
CG A:ASP537 3.2 41.7 1.0
CB A:ASP537 3.5 40.0 1.0
PB A:ATP1103 3.5 37.8 1.0
PG A:ATP1103 3.5 39.2 1.0
O3B A:ATP1103 3.7 40.4 1.0
PA A:ATP1103 3.8 34.5 1.0
O3A A:ATP1103 4.0 39.4 1.0
O A:HOH1205 4.2 42.0 1.0
O1G A:ATP1103 4.3 39.1 1.0
OD1 A:ASP537 4.3 44.1 1.0
O A:HOH1211 4.4 43.4 1.0
C5' A:ATP1103 4.4 37.3 1.0
O A:HOH1318 4.4 62.3 1.0
O A:HOH1207 4.5 38.0 1.0
O A:HOH1206 4.5 43.0 1.0
O5' A:ATP1103 4.6 38.4 1.0
O2G A:ATP1103 4.7 44.2 1.0
O B:HOH201 4.7 35.3 1.0
O1B A:ATP1103 4.9 45.7 1.0
CA A:ASP537 5.0 38.0 1.0

Magnesium binding site 2 out of 2 in 4ii2

Go back to Magnesium Binding Sites List in 4ii2
Magnesium binding site 2 out of 2 in the Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg


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 Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:47.0
occ:1.00
O A:HOH1211 2.3 43.4 1.0
O A:HOH1201 2.3 37.0 1.0
O A:HOH1209 2.4 42.6 1.0
OD2 A:ASP465 2.5 54.9 1.0
O1B A:ATP1103 2.5 45.7 1.0
O A:HOH1204 2.6 45.3 1.0
CG A:ASP465 3.3 51.8 1.0
PB A:ATP1103 3.4 37.8 1.0
OD1 A:ASP465 3.4 51.2 1.0
O2B A:ATP1103 3.5 40.2 1.0
OE2 A:GLU468 3.8 52.8 1.0
O1G A:ATP1103 3.9 39.1 1.0
O3B A:ATP1103 4.1 40.4 1.0
CD A:GLU468 4.2 50.7 1.0
NZ A:LYS487 4.2 39.4 1.0
OD1 A:ASN471 4.3 35.7 1.0
ND2 A:ASN471 4.4 33.0 1.0
OE1 A:GLU468 4.5 55.8 1.0
O A:SER466 4.5 38.9 1.0
CB A:ASP465 4.6 47.8 1.0
CE A:LYS487 4.6 37.6 1.0
O3A A:ATP1103 4.7 39.4 1.0
PG A:ATP1103 4.7 39.2 1.0
O A:HOH1206 4.8 43.0 1.0
CG A:ASN471 4.8 35.6 1.0
CG A:GLU468 4.9 47.0 1.0

Reference:

S.K.Olsen, C.D.Lima. Structure of A Ubiquitin E1-E2 Complex: Insights to E1-E2 Thioester Transfer. Mol.Cell V. 49 884 2013.
ISSN: ISSN 1097-2765
PubMed: 23416107
DOI: 10.1016/J.MOLCEL.2013.01.013
Page generated: Mon Dec 14 18:53:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy