Sodium in PDB 7p8p: Crystal Structure of Fhit Covalently Bound to A Nucleotide

All present enzymatic activity of Crystal Structure of Fhit Covalently Bound to A Nucleotide:
3.6.1.29;

The structure of Crystal Structure of Fhit Covalently Bound to A Nucleotide, PDB code: 7p8p was solved by D.Herzog, M.Missun, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.33 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.422, 61.736, 198.009, 90, 90, 90
R / Rfree (%)	19.3 / 24.6

The binding sites of Sodium atom in the Crystal Structure of Fhit Covalently Bound to A Nucleotide (pdb code 7p8p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Fhit Covalently Bound to A Nucleotide, PDB code: 7p8p:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Fhit Covalently Bound to A Nucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Fhit Covalently Bound to A Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:57.4 occ:1.00 OD1 A:ASN96 2.2 46.3 1.0 HG3 A:GLN90 2.5 56.8 1.0 HE21 A:GLN90 2.7 56.3 1.0 O11 A:6BI201 2.7 49.4 1.0 O A:VAL92 2.9 42.7 1.0 O A:HIS94 2.9 41.8 1.0 HG2 A:GLN90 3.1 56.8 1.0 CG A:GLN90 3.2 47.3 1.0 O3 A:6BI201 3.3 41.5 1.0 CG A:ASN96 3.4 46.4 1.0 P A:6BI201 3.4 53.8 1.0 NE2 A:GLN90 3.4 46.9 1.0 HB A:VAL92 3.6 61.5 1.0 O A:HOH311 3.6 38.6 1.0 H A:HIS94 3.7 53.3 1.0 CD A:GLN90 3.8 48.7 1.0 H A:VAL92 3.8 64.2 1.0 H A:ASN96 3.9 43.1 1.0 O2 A:6BI201 4.0 60.3 1.0 HD21 A:ASN96 4.0 53.0 1.0 C A:VAL92 4.0 47.9 1.0 HA A:GLN90 4.1 56.3 1.0 C A:HIS94 4.1 41.5 1.0 HE22 A:GLN90 4.1 56.3 1.0 ND2 A:ASN96 4.2 44.1 1.0 N A:ASN96 4.3 35.9 1.0 HB3 A:ASN96 4.3 52.5 1.0 O A:GLN83 4.4 42.4 1.0 HA A:VAL95 4.4 47.8 1.0 H A:THR91 4.4 67.8 1.0 N A:VAL92 4.4 53.4 1.0 CB A:ASN96 4.4 43.7 1.0 CB A:VAL92 4.4 51.2 1.0 CB A:GLN90 4.4 41.0 1.0 N A:HIS94 4.5 44.4 1.0 HZ A:PHE5 4.5 50.8 1.0 CA A:VAL92 4.5 53.3 1.0 HE2 A:HIS98 4.6 48.9 1.0 HB2 A:GLN83 4.6 51.9 1.0 C3 A:6BI201 4.6 51.0 1.0 CA A:GLN90 4.7 46.9 1.0 HE1 A:PHE5 4.8 54.5 1.0 HB2 A:GLN90 4.8 49.2 1.0 HG12 A:VAL92 4.8 56.3 1.0 C A:VAL95 4.8 40.9 1.0 O A:ASN96 4.9 35.7 1.0 HB3 A:HIS94 4.9 52.5 1.0 O4 A:6BI201 4.9 53.0 1.0 CA A:ASN96 4.9 31.4 1.0 CA A:HIS94 4.9 42.6 1.0 N A:THR91 4.9 56.5 1.0 CA A:VAL95 4.9 39.8 1.0 N A:VAL95 5.0 38.2 1.0 HD22 A:ASN96 5.0 53.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Fhit Covalently Bound to A Nucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Fhit Covalently Bound to A Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:52.6 occ:1.00 HG3 B:GLN90 2.2 56.4 1.0 HE21 B:GLN90 2.4 51.8 1.0 OD1 B:ASN96 2.6 42.8 1.0 O B:HIS94 2.9 39.4 1.0 NA B:NA204 2.9 52.8 1.0 NE2 B:GLN90 3.0 43.1 1.0 CG B:GLN90 3.1 46.9 1.0 H B:ASN96 3.4 55.5 1.0 O B:HOH308 3.4 35.1 1.0 CD B:GLN90 3.4 42.5 1.0 HG2 B:GLN90 3.5 56.4 1.0 CG B:ASN96 3.6 45.1 1.0 HE22 B:GLN90 3.6 51.8 1.0 O B:GLN83 3.6 38.8 1.0 HA B:VAL95 3.7 49.0 1.0 O11 B:6BI201 3.7 51.5 1.0 O B:VAL92 3.7 44.5 1.0 N B:ASN96 3.9 46.2 1.0 H B:HIS94 3.9 46.3 1.0 C B:HIS94 3.9 38.4 1.0 HA B:GLN90 4.1 52.9 1.0 CB B:GLN90 4.2 41.7 1.0 HB2 B:GLN90 4.3 50.1 1.0 HD21 B:ASN96 4.3 51.2 1.0 O3 B:6BI201 4.3 46.8 1.0 ND2 B:ASN96 4.3 42.6 1.0 CA B:VAL95 4.3 40.8 1.0 C B:VAL95 4.4 42.1 1.0 HB3 B:ASN96 4.4 52.8 1.0 CB B:ASN96 4.5 43.9 1.0 HB2 B:GLN83 4.5 52.4 1.0 P B:6BI201 4.5 49.3 1.0 O B:ASN96 4.5 45.0 1.0 OE1 B:GLN90 4.5 53.9 1.0 N B:VAL95 4.6 40.2 1.0 CA B:ASN96 4.6 44.4 1.0 C B:GLN83 4.7 36.2 1.0 H B:GLN83 4.7 48.7 1.0 N B:HIS94 4.7 38.8 1.0 CA B:GLN90 4.7 44.0 1.0 HB B:VAL92 4.9 64.0 1.0 HE2 B:HIS98 4.9 54.3 1.0 H B:THR91 4.9 57.4 1.0 HA B:ASP84 4.9 49.7 1.0 C B:VAL92 4.9 46.1 1.0 H B:GLY85 5.0 44.4 1.0 CA B:HIS94 5.0 38.7 1.0 O2 B:6BI201 5.0 49.5 1.0 H B:VAL92 5.0 61.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Fhit Covalently Bound to A Nucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Fhit Covalently Bound to A Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:52.8 occ:1.00 O3 B:6BI201 2.3 46.8 1.0 HB B:VAL92 2.6 64.0 1.0 H B:VAL92 2.7 61.8 1.0 OD1 B:ASN96 2.8 42.8 1.0 NA B:NA203 2.9 52.6 1.0 P B:6BI201 3.0 49.3 1.0 C3 B:6BI201 3.0 45.6 1.0 O B:VAL92 3.1 44.5 1.0 O2 B:6BI201 3.1 49.5 1.0 O11 B:6BI201 3.3 51.5 1.0 N B:VAL92 3.3 51.4 1.0 HG3 B:GLN90 3.4 56.4 1.0 HZ B:PHE5 3.4 59.7 1.0 H B:THR91 3.4 57.4 1.0 CB B:VAL92 3.5 53.3 1.0 HG1 B:THR91 3.7 70.2 1.0 HG2 B:GLN90 3.7 56.4 1.0 CA B:VAL92 3.7 52.1 1.0 C B:VAL92 3.8 46.1 1.0 CG B:ASN96 3.9 45.1 1.0 HE21 B:GLN90 4.0 51.8 1.0 HG23 B:VAL92 4.0 53.2 1.0 CG B:GLN90 4.0 46.9 1.0 OG1 B:THR91 4.0 58.4 1.0 O B:HIS94 4.1 39.4 1.0 HA B:GLN90 4.1 52.9 1.0 N B:THR91 4.1 47.8 1.0 CZ B:PHE5 4.1 50.0 1.0 CG2 B:VAL92 4.2 44.3 1.0 HD21 B:ASN96 4.3 51.2 1.0 HE1 B:PHE5 4.3 60.0 1.0 C B:THR91 4.4 49.8 1.0 H B:HIS94 4.4 46.3 1.0 HG12 B:VAL92 4.4 53.2 1.0 C2 B:6BI201 4.5 42.7 1.0 HG21 B:VAL92 4.5 53.2 1.0 O4 B:6BI201 4.5 39.6 1.0 CG1 B:VAL92 4.5 44.2 1.0 ND2 B:ASN96 4.6 42.6 1.0 CE1 B:PHE5 4.6 50.3 1.0 CA B:THR91 4.7 48.6 1.0 HA B:VAL92 4.7 62.6 1.0 NE2 B:GLN90 4.7 43.1 1.0 HG11 B:VAL92 4.7 53.2 1.0 HE2 B:HIS98 4.8 54.3 1.0 CA B:GLN90 4.8 44.0 1.0 HB3 B:ASN96 4.9 52.8 1.0 C B:GLN90 4.9 42.1 1.0 O12 B:6BI201 4.9 47.7 1.0 CD B:GLN90 4.9 42.5 1.0 HB3 B:HIS94 5.0 47.4 1.0 CB B:THR91 5.0 43.5 1.0

D.Herzog, J.Jansen, M.Missun, K.Diederichs, F.Stengel, A.Marx. Chemical Proteomics of the Tumor Suppressor Fhit Covalently Bound to the Cofactor Ap 3 A Elucidates Its Inhibitory Action on Translation. J.Am.Chem.Soc. V. 144 8613 2022.
ISSN: ESSN 1520-5126
PubMed: 35522782
DOI: 10.1021/JACS.2C00815