Calcium in PDB 5yz4: Structure of the Pin Domain Endonuclease UTP24

Protein crystallography data

The structure of Structure of the Pin Domain Endonuclease UTP24, PDB code: 5yz4 was solved by Y.Du, W.An, K.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.59 / 2.14
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.740, 73.328, 74.262, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 28.7

Other elements in 5yz4:

The structure of Structure of the Pin Domain Endonuclease UTP24 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Pin Domain Endonuclease UTP24 (pdb code 5yz4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of the Pin Domain Endonuclease UTP24, PDB code: 5yz4:

Calcium binding site 1 out of 1 in 5yz4

Go back to Calcium Binding Sites List in 5yz4
Calcium binding site 1 out of 1 in the Structure of the Pin Domain Endonuclease UTP24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Pin Domain Endonuclease UTP24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:8.9
occ:0.50
OE1 A:GLU128 2.1 24.3 1.0
NE2 A:HIS66 2.2 18.8 1.0
CD A:GLU128 3.0 20.6 1.0
CD2 A:HIS66 3.0 17.6 1.0
CE1 A:HIS66 3.2 21.8 1.0
OE2 A:GLU128 3.2 20.2 1.0
CD1 A:ILE97 4.2 18.0 1.0
CG A:HIS66 4.2 20.9 1.0
ND1 A:HIS66 4.3 20.4 1.0
CG A:GLU128 4.4 20.9 1.0
CB A:GLU128 4.7 22.5 1.0
CG2 A:ILE97 4.9 20.8 1.0

Reference:

W.An, Y.Du, K.Ye. Structural and Functional Analysis of UTP24, An Endonuclease For Processing 18S Ribosomal Rna. Plos One V. 13 95723 2018.
ISSN: ESSN 1932-6203
PubMed: 29641590
DOI: 10.1371/JOURNAL.PONE.0195723
Page generated: Sat Dec 12 05:55:16 2020

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