Sodium in PDB 6jsc: Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum

The structure of Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum, PDB code: 6jsc was solved by N.Muraki, S.Aono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.19 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.040, 43.150, 199.440, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 20.2

The structure of Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum (pdb code 6jsc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum, PDB code: 6jsc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum


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 the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:22.1 occ:1.00 O A:HOH666 2.3 22.9 1.0 OG A:SER448 2.4 17.7 1.0 O A:HOH672 2.4 26.0 1.0 O A:HOH674 2.4 27.1 1.0 OG A:SER422 2.5 21.2 1.0 O A:GLY421 2.6 13.2 1.0 C A:GLY421 3.3 12.4 1.0 CB A:SER448 3.4 15.1 1.0 CB A:SER422 3.5 17.4 1.0 N A:SER422 3.8 11.9 1.0 CA A:SER448 3.8 12.6 1.0 CA A:SER422 3.8 13.3 1.0 N A:PHE449 4.2 13.2 1.0 CA A:GLY421 4.3 13.8 1.0 C A:SER448 4.4 14.6 1.0 N A:GLY421 4.5 13.5 1.0 O A:PHE449 4.5 14.4 1.0 OE2 A:GLU446 4.6 16.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum


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 the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:25.0 occ:1.00 O A:VAL367 2.3 18.3 1.0 O A:ASN410 2.4 14.6 1.0 O A:HOH673 2.4 39.3 1.0 O A:HOH670 2.4 37.8 1.0 O A:HOH628 2.5 18.9 1.0 O A:HOH653 2.5 31.2 1.0 C A:ASN410 3.5 12.5 1.0 C A:VAL367 3.5 13.9 1.0 CA A:SER411 4.0 15.2 1.0 N A:SER411 4.1 12.6 1.0 O A:THR368 4.3 14.8 1.0 N A:THR368 4.4 14.0 1.0 CA A:THR368 4.4 13.7 1.0 N A:VAL367 4.4 13.9 1.0 CA A:VAL367 4.4 13.1 1.0 CA A:ASN410 4.5 12.1 1.0 O A:HOH608 4.6 29.8 1.0 CB A:ASN410 4.6 15.7 1.0 CB A:VAL367 4.8 13.4 1.0 C A:THR368 4.8 12.2 1.0 CB A:SER411 4.8 21.0 1.0 C A:SER411 4.9 13.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum


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 the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:19.5 occ:1.00 O B:HOH664 2.3 25.8 1.0 OG B:SER422 2.4 20.2 1.0 OG B:SER448 2.4 18.8 1.0 O B:HOH678 2.5 27.8 1.0 O B:GLY421 2.5 14.1 1.0 O B:HOH679 2.5 24.2 1.0 C B:GLY421 3.2 13.8 1.0 CB B:SER448 3.5 14.9 1.0 CB B:SER422 3.5 17.0 1.0 N B:SER422 3.7 13.7 1.0 CA B:SER448 3.8 13.2 1.0 CA B:SER422 3.8 13.1 1.0 N B:PHE449 4.1 14.7 1.0 CA B:GLY421 4.2 14.3 1.0 N B:GLY421 4.3 14.7 1.0 C B:SER448 4.4 15.4 1.0 O B:PHE449 4.4 16.4 1.0 OE2 B:GLU446 4.5 17.6 1.0 O B:HOH668 4.6 32.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum


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 the H434A Variant of the C-Terminal Domain of Htaa From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:25.3 occ:1.00 O B:VAL367 2.3 18.5 1.0 O B:HOH669 2.4 41.7 1.0 O B:HOH647 2.4 21.9 1.0 O B:ASN410 2.4 14.3 1.0 O B:HOH670 2.4 27.1 1.0 C B:ASN410 3.5 13.4 1.0 C B:VAL367 3.5 14.7 1.0 CA B:SER411 3.9 14.5 1.0 N B:SER411 4.1 12.2 1.0 O B:THR368 4.3 14.2 1.0 N B:THR368 4.4 13.1 1.0 N B:VAL367 4.4 13.2 1.0 CA B:VAL367 4.5 13.5 1.0 CA B:THR368 4.5 14.1 1.0 CA B:ASN410 4.5 12.3 1.0 O B:HOH661 4.7 28.1 1.0 CB B:ASN410 4.7 16.9 1.0 CB B:VAL367 4.7 15.5 1.0 CB B:SER411 4.7 24.2 1.0 C B:THR368 4.8 14.5 1.0 C B:SER411 4.9 14.4 1.0

N.Muraki, C.Kitatsuji, Y.Okamoto, T.Uchida, K.Ishimori, S.Aono. Structural Basis For the Heme Transfer Reaction in Heme Uptake Machinery From Corynebacteria. Chem.Commun.(Camb.) V. 55 13864 2019.
ISSN: ESSN 1364-548X
PubMed: 31670736
DOI: 10.1039/C9CC07369H