Sodium in PDB 5l31: Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds.

The structure of Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds., PDB code: 5l31 was solved by F.A.Tezcan, L.A.Churchfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.77 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.594, 77.534, 88.063, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.7

The structure of Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. (pdb code 5l31). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds., PDB code: 5l31:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds.


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 An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:51.7 occ:1.00 O B:HOH319 2.1 45.6 1.0 OD1 B:ASP50 2.8 56.9 1.0 O B:GLU49 3.2 59.9 1.0 C B:GLU49 4.0 58.8 1.0 CG B:ASP50 4.0 59.3 1.0 CA B:ASP50 4.3 57.3 1.0 N B:ASP50 4.4 57.3 1.0 CG B:GLU49 4.6 64.6 1.0 CB B:GLU49 4.7 63.2 1.0 CB B:ASP50 4.8 58.1 1.0 OD2 B:ASP50 4.9 61.0 1.0 CA B:GLU49 5.0 61.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds.


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 An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:63.6 occ:1.00 OE1 C:GLU4 2.8 91.0 1.0 CD C:GLU4 3.9 89.8 1.0 OE2 C:GLU4 4.4 89.1 1.0 O2A C:HEM201 4.8 73.7 1.0

L.A.Churchfield, A.Medina-Morales, J.D.Brodin, A.Perez, F.A.Tezcan. De Novo Design of An Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J.Am.Chem.Soc. V. 138 13163 2016.
ISSN: ESSN 1520-5126
PubMed: 27649076
DOI: 10.1021/JACS.6B08458