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Magnesium in PDB 1y8r: Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex

Protein crystallography data

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex, PDB code: 1y8r was solved by L.M.Lois, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.197, 215.151, 100.870, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27.6

Other elements in 1y8r:

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex (pdb code 1y8r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex, PDB code: 1y8r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1y8r

Go back to Magnesium Binding Sites List in 1y8r
Magnesium binding site 1 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg641

b:16.1
occ:1.00
OD2 B:ASP117 2.1 37.3 1.0
O3B B:ATP802 2.2 33.3 1.0
O B:HOH803 2.2 11.5 1.0
O2A B:ATP802 2.3 26.6 1.0
O2B B:ATP802 2.4 33.8 1.0
O B:HOH804 2.5 25.4 1.0
PB B:ATP802 2.5 34.0 1.0
O3A B:ATP802 2.8 30.7 1.0
PA B:ATP802 3.1 28.1 1.0
CG B:ASP117 3.1 36.5 1.0
PG B:ATP802 3.3 33.5 1.0
O3G B:ATP802 3.3 34.6 1.0
CB B:ASP117 3.7 33.6 1.0
C5' B:ATP802 3.7 27.4 1.0
O1G B:ATP802 3.8 35.7 1.0
O5' B:ATP802 3.9 27.9 1.0
O1B B:ATP802 4.0 34.0 1.0
OD1 B:ASP117 4.2 37.4 1.0
O1A B:ATP802 4.3 26.1 1.0
O B:HOH852 4.5 29.5 1.0
O2G B:ATP802 4.6 30.3 1.0
C3' B:ATP802 4.6 28.6 1.0
C4' B:ATP802 4.7 28.9 1.0

Magnesium binding site 2 out of 2 in 1y8r

Go back to Magnesium Binding Sites List in 1y8r
Magnesium binding site 2 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg641

b:31.1
occ:1.00
O2B E:ATP801 2.0 25.4 1.0
O E:HOH852 2.2 20.2 1.0
O2G E:ATP801 2.6 29.8 1.0
OD1 E:ASP117 2.7 37.0 1.0
O E:HOH853 2.8 33.1 1.0
O3B E:ATP801 2.9 29.6 1.0
PB E:ATP801 2.9 25.1 1.0
PG E:ATP801 3.2 32.2 1.0
O1G E:ATP801 3.7 29.3 1.0
O2A E:ATP801 3.8 22.7 1.0
O1B E:ATP801 3.9 26.8 1.0
CG E:ASP117 3.9 36.0 1.0
O E:HOH817 4.0 22.9 1.0
O3A E:ATP801 4.1 28.0 1.0
NZ E:LYS346 4.4 54.7 1.0
O3G E:ATP801 4.6 28.9 1.0
PA E:ATP801 4.6 27.4 1.0
OD2 E:ASP117 4.6 33.9 1.0
O E:HOH827 4.8 32.3 1.0
CB E:ASP117 4.8 34.5 1.0

Reference:

L.M.Lois, C.D.Lima. Structures of the Sumo E1 Provide Mechanistic Insights Into Sumo Activation and E2 Recruitment to E1 Embo J. V. 24 439 2005.
ISSN: ISSN 0261-4189
PubMed: 15660128
DOI: 10.1038/SJ.EMBOJ.7600552
Page generated: Tue Aug 13 18:32:44 2024

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