Atomistry » Sodium » PDB 5kvc-5l4i » 5l31
Atomistry »
  Sodium »
    PDB 5kvc-5l4i »
      5l31 »

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

Protein crystallography data

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

Other elements in 5l31:

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

Sodium Binding Sites:

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 5l31

Go back to Sodium Binding Sites List in 5l31
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 5l31

Go back to Sodium Binding Sites List in 5l31
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

Reference:

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
Page generated: Tue Dec 15 11:12:25 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy