Atomistry » Sodium » PDB 4nw9-4o9m » 4ny5
Atomistry »
  Sodium »
    PDB 4nw9-4o9m »
      4ny5 »

Sodium in PDB 4ny5: X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A

Enzymatic activity of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A, PDB code: 4ny5 was solved by L.Messori, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.15 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.772, 77.772, 37.316, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24

Other elements in 4ny5:

The structure of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A (pdb code 4ny5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A, PDB code: 4ny5:

Sodium binding site 1 out of 1 in 4ny5

Go back to Sodium Binding Sites List in 4ny5
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:24.1
occ:1.00
 O A:SER60 2.3 22.0 1.0
O A:HOH354 2.4 20.2 1.0
O A:HOH361 2.5 26.3 1.0
O A:CYS64 2.5 19.6 1.0
O A:ARG73 2.5 28.4 1.0
OG A:SER72 2.6 29.5 1.0
CB A:SER72 3.2 28.6 1.0
C A:SER60 3.4 21.6 1.0
C A:ARG73 3.5 28.8 1.0
C A:CYS64 3.5 19.2 1.0
CA A:ASN65 3.9 20.6 1.0
N A:ARG73 3.9 29.6 1.0
CA A:SER60 4.1 18.6 1.0
C A:SER72 4.1 31.3 1.0
N A:ASN65 4.1 18.2 1.0
CB A:SER60 4.2 18.5 1.0
CA A:SER72 4.3 31.2 1.0
CA A:ARG73 4.3 30.3 1.0
N A:ASN74 4.4 24.8 1.0
N A:CYS64 4.4 21.0 1.0
N A:ARG61 4.5 22.9 1.0
O A:HOH382 4.5 48.9 1.0
C A:ARG61 4.6 26.7 1.0
CA A:ASN74 4.6 26.8 1.0
CA A:CYS64 4.6 19.0 1.0
N A:ASP66 4.6 18.3 1.0
O A:ARG61 4.6 29.0 1.0
O A:SER72 4.7 28.2 1.0
OD1 A:ASN65 4.7 28.0 1.0
CB A:THR69 4.7 26.6 1.0
CL A:CL204 4.7 30.5 1.0
CB A:ASN74 4.8 27.7 1.0
C A:ASN65 4.8 17.1 1.0
CA A:ARG61 4.8 26.9 1.0
N A:TRP62 4.8 25.3 1.0
CB A:ASN65 4.9 22.8 1.0
OG A:SER60 5.0 18.9 1.0
O A:THR69 5.0 22.8 1.0

Reference:

L.Messori, A.Merlino. Ruthenium Metalation of Proteins: the X-Ray Structure of the Complex Formed Between Nami-A and Hen Egg White Lysozyme. Dalton Trans V. 43 6128 2014.
ISSN: ISSN 1477-9226
PubMed: 24553967
DOI: 10.1039/C3DT53582G
Page generated: Tue Dec 15 06:56:08 2020

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy