Calcium in PDB 9lnp: The Hung Bound to Dna Product Embedding Uridine Ribonucleotide

All present enzymatic activity of The Hung Bound to Dna Product Embedding Uridine Ribonucleotide:
3.2.2.27;

The structure of The Hung Bound to Dna Product Embedding Uridine Ribonucleotide, PDB code: 9lnp was solved by Y.Liu, C.Zhou, X.Zhan, C.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.79 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.93, 65.29, 99.53, 90, 90, 90
R / Rfree (%)	16.8 / 20.8

The binding sites of Calcium atom in the The Hung Bound to Dna Product Embedding Uridine Ribonucleotide (pdb code 9lnp). 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 The Hung Bound to Dna Product Embedding Uridine Ribonucleotide, PDB code: 9lnp:

Calcium binding site 1 out of 1 in the The Hung Bound to Dna Product Embedding Uridine Ribonucleotide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Hung Bound to Dna Product Embedding Uridine Ribonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:35.9 occ:1.00 H E:PHE158 2.5 23.6 1.0 HA E:PRO146 2.6 24.5 1.0 H E:TYR147 2.6 24.2 1.0 HD22 E:ASN204 2.7 26.5 1.0 O A:HOH114 2.9 28.9 1.0 HA E:CYS157 2.9 24.5 1.0 O E:HOH649 3.2 26.0 1.0 N E:PHE158 3.3 19.7 1.0 N E:TYR147 3.4 20.2 1.0 ND2 E:ASN204 3.4 22.1 1.0 O E:HOH537 3.5 21.3 1.0 CA E:PRO146 3.5 20.4 1.0 HD2 E:TYR147 3.6 23.0 1.0 HD21 E:ASN204 3.6 26.5 1.0 CD2 E:TYR147 3.7 19.1 1.0 HB3 E:PRO146 3.7 25.2 1.0 CA E:CYS157 3.8 20.4 1.0 HA E:ALA153 3.9 21.7 1.0 HA E:PHE158 3.9 25.2 1.0 O E:LEU156 3.9 24.7 1.0 C E:PRO146 4.0 19.6 1.0 HB2 E:ALA153 4.0 23.4 1.0 C E:CYS157 4.0 22.2 1.0 CE2 E:TYR147 4.1 21.3 1.0 CG E:TYR147 4.2 19.1 1.0 CA E:PHE158 4.2 21.0 1.0 CB E:PRO146 4.2 21.0 1.0 HE2 E:TYR147 4.2 25.6 1.0 HB1 E:ALA153 4.2 23.4 1.0 H E:SER159 4.3 23.9 1.0 O E:ASP145 4.3 22.8 1.0 HB2 E:TYR147 4.4 27.4 1.0 CB E:ALA153 4.5 19.5 1.0 HB2 E:CYS157 4.5 27.4 1.0 C E:LEU156 4.5 19.7 1.0 CA E:TYR147 4.6 18.3 1.0 N E:PRO146 4.6 20.4 1.0 N E:CYS157 4.6 19.6 1.0 CB E:TYR147 4.6 22.8 1.0 CG E:ASN204 4.6 24.3 1.0 O E:HOH668 4.7 21.2 1.0 CA E:ALA153 4.7 18.1 1.0 CB E:CYS157 4.7 22.8 1.0 N E:SER159 4.7 19.9 1.0 CZ E:TYR147 4.8 21.1 1.0 C E:ASP145 4.8 20.6 1.0 C E:PHE158 4.8 19.7 1.0 HB2 E:PRO146 4.8 25.2 1.0 H E:HIS154 4.9 27.3 1.0 O E:SER159 4.9 21.5 1.0 CD1 E:TYR147 4.9 19.4 1.0 OD1 E:ASN204 4.9 22.0 1.0 HA E:TYR147 4.9 21.9 1.0 HG3 E:PRO146 5.0 27.0 1.0 H E:GLY155 5.0 23.5 1.0 HB3 E:CYS157 5.0 27.4 1.0

C.Fan, X.Zhan, F.Guo, Q.Li, K.Lu, X.Shan, Y.Zhou, M.Ren, M.M.Greenberg, Y.Liu, C.Zhou. Uridine Embedded Within Dna Is Repaired By Uracil Dna Glycosylase Via A Mechanism Distinct From That of Ribonuclease H2. J.Am.Chem.Soc. V. 147 11574 2025.
ISSN: ESSN 1520-5126
PubMed: 40130361
DOI: 10.1021/JACS.5C01436