Atomistry » Magnesium » PDB 6z9a-6zid » 6zhu
Atomistry »
  Magnesium »
    PDB 6z9a-6zid »
      6zhu »

Magnesium in PDB 6zhu: Yeast UBA1 in Complex with UBC3 and Atp

Enzymatic activity of Yeast UBA1 in Complex with UBC3 and Atp

All present enzymatic activity of Yeast UBA1 in Complex with UBC3 and Atp:
2.3.2.23; 6.2.1.45;

Protein crystallography data

The structure of Yeast UBA1 in Complex with UBC3 and Atp, PDB code: 6zhu was solved by M.Misra, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.81 / 3.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.636, 152.408, 252.567, 90, 90.45, 90
R / Rfree (%) 21.7 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast UBA1 in Complex with UBC3 and Atp (pdb code 6zhu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Yeast UBA1 in Complex with UBC3 and Atp, PDB code: 6zhu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6zhu

Go back to Magnesium Binding Sites List in 6zhu
Magnesium binding site 1 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:72.3
occ:1.00
O A:HOH1203 2.0 72.8 1.0
OD2 A:ASP544 2.3 53.0 1.0
O A:HOH1201 2.4 75.1 1.0
O2G A:ATP1101 2.5 55.5 1.0
O2A A:ATP1101 2.8 54.9 1.0
HB2 A:ASP544 2.9 61.4 1.0
O1B A:ATP1101 2.9 55.5 1.0
CG A:ASP544 3.2 52.3 1.0
CB A:ASP544 3.5 51.2 1.0
HD12 A:ILE863 3.7 58.9 1.0
HB3 A:ASP544 3.7 61.4 1.0
PG A:ATP1101 3.8 49.4 1.0
PB A:ATP1101 3.9 49.7 1.0
O3B A:ATP1101 4.0 47.2 1.0
H5'2 A:ATP1101 4.1 64.1 1.0
PA A:ATP1101 4.2 46.0 1.0
O1G A:ATP1101 4.2 49.3 1.0
OD1 A:ASP544 4.3 53.1 1.0
O3A A:ATP1101 4.4 44.2 1.0
HB A:ILE863 4.5 58.4 1.0
O A:ASP544 4.5 52.5 1.0
CD1 A:ILE863 4.6 49.1 1.0
CA A:ASP544 4.8 51.2 1.0
HG13 A:ILE863 4.9 59.0 1.0
HD11 A:ILE863 5.0 58.9 1.0
O3G A:ATP1101 5.0 46.0 1.0

Magnesium binding site 2 out of 4 in 6zhu

Go back to Magnesium Binding Sites List in 6zhu
Magnesium binding site 2 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1102

b:67.6
occ:1.00
O E:HOH1202 1.7 69.4 1.0
O E:HOH1201 1.8 68.3 1.0
OD2 E:ASP544 2.2 59.7 1.0
O2G E:ATP1101 2.3 61.3 1.0
O1B E:ATP1101 2.3 61.0 1.0
O1A E:ATP1101 2.5 50.9 1.0
HB2 E:ASP544 2.8 65.9 1.0
CG E:ASP544 3.1 58.0 1.0
CB E:ASP544 3.3 54.9 1.0
HB3 E:ASP544 3.4 65.9 1.0
PG E:ATP1101 3.5 54.7 1.0
PB E:ATP1101 3.5 52.6 1.0
O3B E:ATP1101 3.7 51.9 1.0
PA E:ATP1101 3.8 47.3 1.0
HD12 E:ILE863 3.9 65.4 1.0
H5'1 E:ATP1101 3.9 66.7 1.0
O3A E:ATP1101 4.0 47.2 1.0
O1G E:ATP1101 4.2 56.4 1.0
OD1 E:ASP544 4.3 57.9 1.0
HB E:ILE863 4.4 66.1 1.0
O E:ASP544 4.6 54.5 1.0
HH21 E:ARG481 4.6 70.7 1.0
O3G E:ATP1101 4.7 50.5 1.0
CA E:ASP544 4.7 52.5 1.0
O2B E:ATP1101 4.8 56.6 1.0
O5' E:ATP1101 4.8 54.2 1.0
O2A E:ATP1101 4.8 43.5 1.0
CD1 E:ILE863 4.8 54.5 1.0
C5' E:ATP1101 4.8 55.6 1.0
H3' E:ATP1101 5.0 61.1 1.0

Magnesium binding site 3 out of 4 in 6zhu

Go back to Magnesium Binding Sites List in 6zhu
Magnesium binding site 3 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:69.0
occ:1.00
O C:HOH1201 1.8 69.4 1.0
O C:HOH1202 2.1 72.2 1.0
O2G C:ATP1101 2.2 59.5 1.0
O2B C:ATP1101 2.8 58.0 1.0
O2A C:ATP1101 2.9 51.7 1.0
OD2 C:ASP544 3.0 61.0 1.0
HB2 C:ASP544 3.1 71.5 1.0
PG C:ATP1101 3.3 48.9 1.0
HD12 C:ILE863 3.6 63.7 1.0
O1G C:ATP1101 3.7 44.5 1.0
O3B C:ATP1101 3.7 47.7 1.0
CG C:ASP544 3.7 60.9 1.0
PB C:ATP1101 3.8 50.6 1.0
CB C:ASP544 3.8 59.6 1.0
HB C:ILE863 4.0 61.6 1.0
HB3 C:ASP544 4.0 71.5 1.0
PA C:ATP1101 4.2 45.6 1.0
O3A C:ATP1101 4.4 46.3 1.0
CD1 C:ILE863 4.5 53.0 1.0
H5'1 C:ATP1101 4.5 62.8 1.0
H C:ILE863 4.6 58.0 1.0
O3G C:ATP1101 4.6 47.3 1.0
HG13 C:ILE863 4.7 61.2 1.0
HH21 C:ARG481 4.7 71.6 1.0
CB C:ILE863 4.8 51.3 1.0
HD11 C:ILE863 4.9 63.7 1.0
OD1 C:ASP544 4.9 61.1 1.0
O C:ASP544 4.9 60.2 1.0
CG1 C:ILE863 4.9 51.0 1.0

Magnesium binding site 4 out of 4 in 6zhu

Go back to Magnesium Binding Sites List in 6zhu
Magnesium binding site 4 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1102

b:62.5
occ:1.00
O G:HOH1201 1.8 73.6 1.0
OD2 G:ASP544 2.0 77.8 1.0
O2A G:ATP1101 2.4 66.3 1.0
O1G G:ATP1101 2.5 71.5 1.0
O2B G:ATP1101 2.6 67.5 1.0
HB2 G:ASP544 2.6 84.5 1.0
O G:HOH1202 2.8 80.7 1.0
CG G:ASP544 2.9 70.2 1.0
CB G:ASP544 3.1 70.4 1.0
HB3 G:ASP544 3.3 84.5 1.0
PB G:ATP1101 3.6 64.2 1.0
PG G:ATP1101 3.7 67.7 1.0
PA G:ATP1101 3.7 65.2 1.0
H5'2 G:ATP1101 3.8 81.6 1.0
O3B G:ATP1101 3.8 65.1 1.0
OD1 G:ASP544 4.0 70.9 1.0
O3A G:ATP1101 4.1 64.1 1.0
O3G G:ATP1101 4.2 67.5 1.0
O G:ASP544 4.5 70.5 1.0
CA G:ASP544 4.5 71.3 1.0
HD12 G:ILE863 4.6 79.8 1.0
C5' G:ATP1101 4.7 68.0 1.0
HB G:ILE863 4.7 78.7 1.0
O5' G:ATP1101 4.7 67.8 1.0
O1A G:ATP1101 4.8 69.7 1.0
HH21 G:ARG481 4.9 88.6 1.0
H3' G:ATP1101 4.9 78.3 1.0
HA G:ASP544 4.9 85.5 1.0
C G:ASP544 5.0 71.2 1.0

Reference:

M.Misra, A.Schaefer, M.Kuhn, L.Pluska, I.Tessmer, T.Sommer, H.Schindelin. Atp Induced Conformational Changes Facilitate E1-E2 Disulfide Bridging in the Ubiquitin System To Be Published.
Page generated: Wed Oct 2 02:19:09 2024

Last articles

Zn in 1CYY
Zn in 1CXX
Zn in 1CVR
Zn in 1CW0
Zn in 1CVE
Zn in 1CVH
Zn in 1CU1
Zn in 1CVD
Zn in 1CVB
Zn in 1CVC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy