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Nickel in PDB 1umh: Structural Basis of Sugar-Recognizing Ubiquitin Ligase

Enzymatic activity of Structural Basis of Sugar-Recognizing Ubiquitin Ligase

All present enzymatic activity of Structural Basis of Sugar-Recognizing Ubiquitin Ligase:
6.3.2.19;

Protein crystallography data

The structure of Structural Basis of Sugar-Recognizing Ubiquitin Ligase, PDB code: 1umh was solved by T.Mizushima, T.Hirao, Y.Yoshida, S.J.Lee, T.Chiba, K.Iwai, Y.Yamaguchi, K.Kato, T.Tsukihara, K.Tanaka, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.23 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.440, 62.440, 117.300, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 19.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Structural Basis of Sugar-Recognizing Ubiquitin Ligase (pdb code 1umh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Structural Basis of Sugar-Recognizing Ubiquitin Ligase, PDB code: 1umh:

Nickel binding site 1 out of 1 in 1umh

Go back to Nickel Binding Sites List in 1umh
Nickel binding site 1 out of 1 in the Structural Basis of Sugar-Recognizing Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structural Basis of Sugar-Recognizing Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:31.8
occ:1.00
N A:SER115 1.8 33.2 1.0
N A:GLY114 2.1 37.1 1.0
OG A:SER115 2.2 31.9 1.0
CA A:GLY114 2.4 34.8 1.0
C A:GLY114 2.4 35.3 1.0
CA A:SER115 2.9 30.1 1.0
CB A:SER115 3.0 31.1 1.0
CB A:TYR118 3.5 22.0 1.0
O A:SER115 3.6 24.1 1.0
O A:GLY114 3.6 35.3 1.0
C A:SER115 3.7 27.6 1.0
CG A:TYR118 4.0 23.9 1.0
CD2 A:TYR118 4.1 28.6 1.0
CA A:TYR118 4.9 21.6 1.0
CD1 A:TYR118 4.9 26.6 1.0
N A:TYR118 5.0 21.8 1.0

Reference:

T.Mizushima, T.Hirao, Y.Yoshida, S.J.Lee, T.Chiba, K.Iwai, Y.Yamaguchi, K.Kato, T.Tsukihara, K.Tanaka. Structural Basis of Sugar-Recognizing Ubiquitin Ligase Nat.Struct.Mol.Biol. V. 11 365 2004.
ISSN: ISSN 1545-9993
PubMed: 14990996
DOI: 10.1038/NSMB732
Page generated: Fri Sep 25 08:02:55 2020
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