Sodium in PDB 3kgd: Crystal Structure of E. Coli Rna 3' Cyclase

All present enzymatic activity of Crystal Structure of E. Coli Rna 3' Cyclase:
6.5.1.4;

The structure of Crystal Structure of E. Coli Rna 3' Cyclase, PDB code: 3kgd was solved by S.Shuman, N.Tanaka, P.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.14 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.728, 81.932, 105.176, 90.00, 103.44, 90.00
R / Rfree (%)	16.8 / 20.7

The binding sites of Sodium atom in the Crystal Structure of E. Coli Rna 3' Cyclase (pdb code 3kgd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of E. Coli Rna 3' Cyclase, PDB code: 3kgd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of E. Coli Rna 3' Cyclase


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 E. Coli Rna 3' Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:43.6 occ:1.00 O4 A:SO4344 3.0 26.9 0.5 O A:HOH471 3.0 23.4 1.0 O A:HOH462 3.2 30.9 1.0 CA A:GLY17 3.4 19.0 1.0 O3 A:SO4344 3.8 31.1 0.5 OE2 A:GLU14 3.8 24.6 1.0 N A:GLY17 3.8 17.3 1.0 O A:HOH429 3.8 38.8 1.0 S A:SO4344 3.9 33.3 0.5 O A:HOH677 3.9 39.9 1.0 O4 A:SO4343 4.0 60.6 1.0 O2 A:SO4343 4.0 54.3 1.0 O A:HOH367 4.1 23.4 1.0 NE2 A:HIS52 4.1 24.4 1.0 C A:GLY16 4.3 19.3 1.0 O2 A:SO4344 4.4 31.6 0.5 O A:HOH710 4.4 53.3 1.0 CD A:GLU14 4.5 25.9 1.0 O A:GLY16 4.6 19.5 1.0 S A:SO4343 4.6 53.1 1.0 OE1 A:GLU14 4.7 29.4 1.0 C A:GLY17 4.7 17.1 1.0 CD2 A:HIS52 4.7 28.0 1.0 O A:HOH832 4.9 47.8 1.0 CA A:GLU14 4.9 24.6 1.0 N A:GLN18 5.0 14.3 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of E. Coli Rna 3' Cyclase


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 E. Coli Rna 3' Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na342 b:32.6 occ:1.00 O B:HOH473 2.6 15.4 0.3 O4 B:SO4343 2.7 70.0 1.0 O B:HOH985 3.1 26.9 1.0 O B:HOH473 3.2 20.1 0.7 O2 B:SO4343 3.2 67.3 1.0 S B:SO4343 3.5 63.9 1.0 CA B:ARG40 3.6 18.0 1.0 CA B:GLY13 3.7 18.1 0.6 CG B:ARG40 3.8 17.0 1.0 CA B:GLY13 3.8 18.3 0.4 NE B:ARG43 3.9 22.8 1.0 N B:GLY13 4.0 19.3 0.4 CB B:ARG40 4.0 19.6 1.0 N B:GLU14 4.2 19.5 0.4 N B:ARG40 4.2 17.9 1.0 N B:GLU14 4.2 17.2 0.6 CG B:ARG43 4.3 22.7 1.0 NH1 B:ARG43 4.3 29.0 1.0 C B:GLY13 4.4 15.6 0.6 O1 B:SO4343 4.4 68.7 1.0 C B:GLY13 4.5 17.0 0.4 N B:GLY13 4.5 18.7 0.6 O B:GLY10 4.5 18.0 0.4 CZ B:ARG43 4.5 24.2 1.0 O3 B:SO4343 4.6 83.8 1.0 C B:ARG40 4.6 18.2 1.0 O B:ALA11 4.7 16.0 0.4 O B:GLY10 4.7 16.8 0.6 CD B:ARG43 4.8 24.6 1.0 C B:ALA11 4.8 16.3 0.4 O B:HOH475 4.8 22.0 1.0 O B:HOH468 4.9 31.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of E. Coli Rna 3' Cyclase


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 E. Coli Rna 3' Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na343 b:35.0 occ:1.00 O C:HOH442 3.1 32.7 1.0 O C:SER277 3.2 19.7 1.0 O C:LEU275 3.3 22.6 1.0 C C:SER277 3.4 18.2 1.0 O C:ALA276 3.5 26.1 1.0 C C:ALA276 3.5 24.9 1.0 N C:SER277 3.7 19.3 1.0 CA C:SER277 3.8 17.5 0.3 O C:HOH519 3.8 37.5 1.0 N C:THR278 3.9 15.7 1.0 CA C:SER277 3.9 17.0 0.7 CG2 C:THR278 4.1 19.0 1.0 CA C:ALA276 4.2 26.9 1.0 CA C:THR278 4.2 17.2 1.0 C C:LEU275 4.3 22.6 1.0 NH2 C:ARG186 4.3 18.2 1.0 O C:HOH1033 4.4 43.6 1.0 N C:ALA276 4.7 19.8 1.0 CB C:THR278 4.8 16.3 1.0 O C:HOH443 4.9 23.6 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of E. Coli Rna 3' Cyclase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of E. Coli Rna 3' Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na344 b:32.1 occ:1.00 O C:HOH367 2.7 18.5 0.6 O C:HOH1026 3.0 29.4 1.0 O4 C:SO4345 3.1 43.7 1.0 O1 C:SO4345 3.2 0.3 1.0 O C:HOH367 3.3 13.5 0.4 S C:SO4345 3.5 42.1 1.0 CA C:ARG40 3.5 14.8 1.0 O3 C:SO4345 3.6 43.0 1.0 CG C:ARG40 3.8 16.7 1.0 CA C:GLY13 3.9 24.5 1.0 NE C:ARG43 3.9 23.7 1.0 CB C:ARG40 4.0 15.4 1.0 CG C:ARG43 4.1 20.6 1.0 N C:ARG40 4.2 17.9 1.0 N C:GLY13 4.2 22.1 1.0 N C:GLU14 4.4 20.2 1.0 NH2 C:ARG43 4.4 25.6 1.0 C C:ARG40 4.5 15.0 1.0 C C:GLY13 4.5 28.1 1.0 O C:GLY10 4.5 24.2 0.5 CZ C:ARG43 4.5 26.3 1.0 O C:GLY10 4.6 17.3 0.5 CD C:ARG43 4.7 22.5 1.0 O C:ALA11 4.8 19.9 0.5 O C:HOH400 4.9 29.6 1.0 O2 C:SO4345 4.9 46.8 1.0 O C:HOH370 4.9 19.3 1.0 CD C:ARG40 5.0 19.1 1.0 N C:ALA41 5.0 17.3 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of E. Coli Rna 3' Cyclase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of E. Coli Rna 3' Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na343 b:32.2 occ:1.00 O D:HOH1378 2.6 16.2 0.3 O3 D:SO4344 2.8 72.2 1.0 O1 D:SO4344 2.9 52.3 1.0 O D:HOH1378 3.2 19.8 0.7 S D:SO4344 3.5 55.2 1.0 CA D:ARG40 3.6 16.2 1.0 CG D:ARG40 3.7 18.1 1.0 CA D:GLY13 3.8 23.5 1.0 NE D:ARG43 3.9 26.0 1.0 CB D:ARG40 4.1 18.1 1.0 N D:ARG40 4.2 18.6 1.0 N D:GLU14 4.3 22.9 1.0 O D:HOH766 4.3 38.3 1.0 CG D:ARG43 4.3 26.6 1.0 NH2 D:ARG43 4.4 35.4 1.0 N D:GLY13 4.4 24.6 1.0 O2 D:SO4344 4.4 53.9 1.0 C D:GLY13 4.4 26.4 1.0 O4 D:SO4344 4.5 74.9 1.0 CZ D:ARG43 4.5 26.3 1.0 C D:ARG40 4.6 19.6 1.0 O D:GLY10 4.6 16.7 0.4 O D:GLY10 4.7 17.2 0.6 O D:HOH358 4.7 22.9 1.0 CD D:ARG43 4.8 24.1 1.0 O D:HOH521 4.8 31.8 1.0 O D:ALA11 4.9 18.2 0.4 CD D:ARG40 4.9 18.4 1.0

N.Tanaka, P.Smith, S.Shuman. Structure of the Rna 3'-Phosphate Cyclase-Adenylate Intermediate Illuminates Nucleotide Specificity and Covalent Nucleotidyl Transfer. Structure V. 18 449 2010.
ISSN: ISSN 0969-2126
PubMed: 20399182
DOI: 10.1016/J.STR.2010.01.016