Sodium in PDB 6j05: Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression

The structure of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression, PDB code: 6j05 was solved by C.Prabaharan, P.Kandavelu, C.Packianathan, P.B.Rosen, S.Thiyagarajan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.53 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.922, 42.727, 49.132, 90.00, 117.62, 90.00
R / Rfree (%)	16.5 / 23.1

The structure of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Sodium atom in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression (pdb code 6j05). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression, PDB code: 6j05:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:25.0 occ:1.00 OE1 A:GLU33 2.6 15.0 1.0 O A:LEU29 2.7 15.5 1.0 N A:ALA79 3.1 15.3 1.0 CA A:ARG78 3.4 17.1 1.0 CA A:GLY36 3.5 17.3 1.0 CD A:GLU33 3.5 17.0 1.0 C A:LEU29 3.6 15.3 1.0 CG A:GLU33 3.7 18.1 1.0 C A:ARG78 3.8 16.4 1.0 N A:GLU33 3.8 18.7 1.0 CB A:ARG78 3.8 18.7 1.0 N A:GLY36 3.8 18.5 1.0 C A:GLN32 3.9 17.7 1.0 O A:GLN32 3.9 17.4 1.0 CA A:GLU33 3.9 18.2 1.0 CA A:LEU29 3.9 14.7 1.0 CB A:LEU29 4.0 14.7 1.0 CG A:ARG78 4.0 20.3 1.0 CB A:ALA79 4.2 16.8 1.0 CD2 A:LEU29 4.2 15.5 1.0 CA A:ALA79 4.2 16.3 1.0 O A:TYR77 4.3 14.2 1.0 CB A:GLU33 4.5 18.1 1.0 OE2 A:GLU33 4.6 17.1 1.0 N A:ARG78 4.6 15.7 1.0 CB A:GLN32 4.6 16.0 1.0 O A:ALA79 4.7 16.3 1.0 N A:VAL30 4.7 15.4 1.0 CA A:GLN32 4.7 17.2 1.0 CG A:LEU29 4.7 15.3 1.0 C A:GLY36 4.8 16.0 1.0 NE A:ARG78 4.8 20.8 1.0 C A:TYR77 4.9 16.7 1.0 C A:ALA79 4.9 15.8 1.0 O A:ARG78 4.9 15.8 1.0 N A:GLN32 5.0 16.4 1.0 C A:THR35 5.0 19.2 1.0

Sodium binding site 2 out of 3 in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:28.2 occ:1.00 O B:LEU29 2.7 17.2 1.0 OE2 B:GLU33 2.8 20.0 1.0 N B:ALA79 3.2 18.6 1.0 CA B:GLY36 3.4 24.0 1.0 CA B:ARG78 3.4 20.2 1.0 C B:LEU29 3.5 16.5 1.0 N B:GLU33 3.6 18.5 1.0 CG B:GLU33 3.6 19.5 1.0 C B:GLN32 3.6 19.5 1.0 CD B:GLU33 3.7 20.1 1.0 N B:GLY36 3.7 24.4 1.0 O B:GLN32 3.7 19.3 1.0 C B:ARG78 3.7 19.5 1.0 CA B:GLU33 3.8 19.8 1.0 CB B:ARG78 3.8 21.1 1.0 CA B:LEU29 3.9 16.0 1.0 CG B:ARG78 3.9 22.0 1.0 CB B:LEU29 3.9 16.2 1.0 O B:TYR77 4.2 18.2 1.0 CD2 B:LEU29 4.2 17.9 1.0 CB B:GLU33 4.3 19.1 1.0 CA B:ALA79 4.4 18.2 1.0 CB B:GLN32 4.4 19.3 1.0 CA B:GLN32 4.4 19.1 1.0 CB B:ALA79 4.5 17.1 1.0 N B:ARG78 4.6 19.9 1.0 N B:VAL30 4.6 16.6 1.0 C B:GLY36 4.6 23.3 1.0 CG B:LEU29 4.7 17.2 1.0 C B:THR35 4.7 26.6 1.0 NE B:ARG78 4.8 23.7 1.0 C B:TYR77 4.8 20.4 1.0 N B:GLN32 4.8 17.6 1.0 OE1 B:GLU33 4.8 20.6 1.0 O B:ALA79 4.9 19.7 1.0 CD B:ARG78 4.9 22.6 1.0 N B:THR35 5.0 24.0 1.0

Sodium binding site 3 out of 3 in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:34.8 occ:1.00 O A:HOH361 2.5 32.1 1.0 OE1 B:GLU24 2.7 17.4 1.0 NE B:ARG27 3.0 16.9 0.9 CD B:GLU24 3.1 18.9 1.0 NH1 B:ARG27 3.2 18.4 0.1 NH1 B:ARG27 3.5 19.0 0.9 CZ B:ARG27 3.7 17.8 0.9 OE2 B:GLU24 3.7 18.3 1.0 CD B:ARG27 3.8 17.6 0.1 CA B:GLU24 3.8 18.8 1.0 CG B:GLU24 3.9 17.8 1.0 O B:HOH318 4.0 17.4 1.0 N B:GLU24 4.0 17.8 1.0 O B:LEU23 4.0 16.7 1.0 CD B:ARG27 4.0 17.1 0.9 CG B:ARG27 4.0 17.0 0.9 O B:HOH330 4.0 35.2 1.0 CG B:LEU23 4.1 21.9 1.0 CZ B:ARG27 4.1 18.2 0.1 CB B:ARG27 4.1 16.8 0.1 CB B:ARG27 4.1 16.6 0.9 C B:LEU23 4.1 18.2 1.0 CG B:ARG27 4.2 17.1 0.1 OH A:TYR90 4.3 22.9 1.0 NE B:ARG27 4.3 17.8 0.1 O B:HOH328 4.3 24.1 1.0 CB B:GLU24 4.3 18.4 1.0 CD2 B:LEU23 4.5 21.7 1.0 CE2 A:TYR90 4.5 19.6 1.0 CB B:LEU23 4.7 20.6 1.0 CZ A:TYR90 4.8 20.8 1.0 C B:GLU24 4.9 17.8 1.0 NH2 B:ARG27 5.0 16.2 0.9

C.Prabaharan, P.Kandavelu, C.Packianathan, B.P.Rosen, S.Thiyagarajan. Structures of Two Arsr As(III)-Responsive Transcriptional Repressors: Implications For the Mechanism of Derepression. J.Struct.Biol. V. 207 209 2019.
ISSN: ESSN 1095-8657
PubMed: 31136796
DOI: 10.1016/J.JSB.2019.05.009