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Praseodymium in PDB 5xit: Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II

Enzymatic activity of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II

All present enzymatic activity of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II, PDB code: 5xit was solved by T.S.Takahashi, Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.99 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.372, 50.019, 64.407, 73.49, 69.69, 73.82
R / Rfree (%) 22 / 23.9

Praseodymium Binding Sites:

The binding sites of Praseodymium atom in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II (pdb code 5xit). This binding sites where shown within 5.0 Angstroms radius around Praseodymium atom.
In total 3 binding sites of Praseodymium where determined in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II, PDB code: 5xit:
Jump to Praseodymium binding site number: 1; 2; 3;

Praseodymium binding site 1 out of 3 in 5xit

Go back to Praseodymium Binding Sites List in 5xit
Praseodymium binding site 1 out of 3 in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 1 of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Pr201

b:89.0
occ:1.00
O E:HOH306 2.7 68.5 1.0
O H:HOH104 2.9 68.3 1.0
O E:HOH308 3.1 68.0 1.0
O H:HOH103 3.6 63.6 1.0
OE2 E:GLU135 4.5 77.5 1.0
OE1 E:GLU135 4.7 74.2 1.0

Praseodymium binding site 2 out of 3 in 5xit

Go back to Praseodymium Binding Sites List in 5xit
Praseodymium binding site 2 out of 3 in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 2 of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Pr202

b:0.0
occ:1.00
OE1 E:GLU137 4.5 88.5 1.0
OE2 E:GLU137 5.0 94.2 1.0

Praseodymium binding site 3 out of 3 in 5xit

Go back to Praseodymium Binding Sites List in 5xit
Praseodymium binding site 3 out of 3 in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 3 of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Pr203

b:0.7
occ:1.00
OE1 E:GLU154 4.9 0.2 1.0
OE2 E:GLU154 5.0 0.5 1.0

Reference:

T.S.Takahashi, Y.Hirade, A.Toma, Y.Sato, A.Yamagata, S.Goto-Ito, A.Tomita, S.Nakada, S.Fukai. Structural Insights Into Two Distinct Binding Modules For LYS63-Linked Polyubiquitin Chains in RNF168. Nat Commun V. 9 170 2018.
ISSN: ESSN 2041-1723
PubMed: 29330428
DOI: 10.1038/S41467-017-02345-Y
Page generated: Wed Dec 16 02:03:10 2020

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