Zinc in PDB 6a6j: Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna

The structure of Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna, PDB code: 6a6j was solved by M.M.Zhang, B.X.Wu, Y.Huang, J.B.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.21 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.201, 60.866, 56.513, 90.00, 118.97, 90.00
R / Rfree (%)	22.5 / 27.2

The binding sites of Zinc atom in the Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna (pdb code 6a6j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna, PDB code: 6a6j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:35.1 occ:0.97 OE1 A:GLU97 2.0 33.4 1.0 N3 B:C2 2.1 26.9 1.0 OE1 A:GLU101 2.2 55.4 1.0 O B:HOH103 2.2 33.6 1.0 CD A:GLU97 2.8 47.9 1.0 C2 B:C2 2.9 33.1 1.0 OE2 A:GLU97 2.9 41.7 1.0 O2 B:C2 3.0 36.5 1.0 C4 B:C2 3.0 30.3 1.0 N4 B:C2 3.2 37.4 1.0 CD A:GLU101 3.2 47.0 1.0 O A:HOH305 3.4 29.7 1.0 OE2 A:GLU101 3.6 65.1 1.0 O A:HOH316 3.8 38.0 1.0 CG A:GLU97 4.2 46.9 1.0 N1 B:C2 4.2 33.1 1.0 N A:GLU97 4.3 38.5 1.0 C5 B:C2 4.3 18.8 1.0 CG A:GLU101 4.5 42.5 1.0 CA A:GLY96 4.6 33.7 1.0 CB A:GLU97 4.7 34.6 1.0 CB A:GLU101 4.7 32.8 1.0 C6 B:C2 4.8 35.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Zebra Fish Y-Box PROTEIN1 (Yb-1) Cold-Shock Domain in Complex with 6MER M5C Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:37.1 occ:1.00 OE1 C:GLU97 2.1 40.7 1.0 O C:HOH313 2.2 32.3 1.0 OE1 C:GLU101 2.2 46.9 1.0 OE2 C:GLU101 2.2 38.0 1.0 N3 D:C2 2.3 21.7 1.0 CD C:GLU101 2.5 37.1 1.0 CD C:GLU97 2.8 41.0 1.0 OE2 C:GLU97 3.0 53.3 1.0 C2 D:C2 3.1 25.1 1.0 O2 D:C2 3.1 27.7 1.0 C4 D:C2 3.3 28.6 1.0 N4 D:C2 3.4 37.8 1.0 O C:HOH312 3.7 35.6 1.0 CG C:GLU101 4.0 32.9 1.0 O C:HOH304 4.1 27.5 1.0 CG C:GLU97 4.2 27.9 1.0 N C:GLU97 4.3 38.7 1.0 N1 D:C2 4.5 33.9 1.0 O D:HOH106 4.5 28.4 1.0 C5 D:C2 4.6 33.0 1.0 CB C:GLU97 4.7 30.1 1.0 CB C:GLU101 4.8 30.8 1.0 CA C:GLY96 4.8 29.6 1.0

Y.Yang, L.Wang, X.Han, W.L.Yang, M.Zhang, H.L.Ma, B.F.Sun, A.Li, J.Xia, J.Chen, J.Heng, B.Wu, Y.S.Chen, J.W.Xu, X.Yang, H.Yao, J.Sun, C.Lyu, H.L.Wang, Y.Huang, Y.P.Sun, Y.L.Zhao, A.Meng, J.Ma, F.Liu, Y.G.Yang. Rna 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition By Preventing Maternal Mrna Decay. Mol.Cell V. 75 1188 2019.
ISSN: ISSN 1097-2765
PubMed: 31399345
DOI: 10.1016/J.MOLCEL.2019.06.033