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Sodium in PDB 4j1b: X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Black Crystal)

Enzymatic activity of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Black Crystal)

All present enzymatic activity of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Black Crystal):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Black Crystal), PDB code: 4j1b was solved by A.Vergara, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.57 / 1.66
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.009, 78.009, 37.192, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.6

Other elements in 4j1b:

The structure of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Black Crystal) also contains other interesting chemical elements:

Ruthenium (Ru) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Black Crystal) (pdb code 4j1b). 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 Between Hen Egg White Lysozyme and Aziru (Black Crystal), PDB code: 4j1b:

Sodium binding site 1 out of 1 in 4j1b

Go back to Sodium Binding Sites List in 4j1b
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Black Crystal)


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 Between Hen Egg White Lysozyme and Aziru (Black Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:26.2
occ:1.00
 O A:HOH324 2.3 23.5 1.0
O A:SER60 2.4 23.8 1.0
O A:ARG73 2.5 27.1 0.5
O A:HOH319 2.5 20.4 1.0
OG A:SER72 2.5 28.3 1.0
O A:ARG73 2.5 27.4 0.5
O A:CYS64 2.6 20.7 1.0
CB A:SER72 3.2 30.2 1.0
C A:ARG73 3.5 28.2 0.5
C A:SER60 3.5 22.3 1.0
C A:ARG73 3.5 28.2 0.5
C A:CYS64 3.6 20.5 1.0
N A:ARG73 3.8 29.8 0.5
N A:ARG73 3.8 29.8 0.5
CA A:ASN65 3.9 20.2 1.0
CA A:SER60 4.1 19.8 1.0
C A:SER72 4.1 31.5 1.0
N A:ASN65 4.2 21.0 1.0
CB A:SER60 4.2 18.8 1.0
CA A:ARG73 4.3 28.4 0.5
CA A:ARG73 4.3 28.5 0.5
CA A:SER72 4.3 31.2 1.0
N A:ASN74 4.4 26.0 1.0
O A:HOH414 4.5 50.5 1.0
CA A:ASN74 4.6 25.5 1.0
CL A:CL202 4.6 31.1 1.0
N A:ARG61 4.6 23.6 1.0
N A:CYS64 4.6 20.3 1.0
C A:ARG61 4.6 26.4 1.0
O A:ARG61 4.6 26.9 1.0
OD1 A:ASN65 4.6 25.3 1.0
O A:SER72 4.6 32.2 1.0
CB A:THR69 4.7 23.1 1.0
N A:ASP66 4.7 18.1 1.0
CB A:ASN74 4.7 24.7 1.0
CB A:ASN65 4.7 23.1 1.0
CA A:CYS64 4.8 21.5 1.0
O A:THR69 4.8 25.6 1.0
C A:ASN65 4.8 18.3 1.0
CA A:ARG61 4.9 25.5 1.0
N A:TRP62 4.9 24.5 1.0

Reference:

A.Vergara, G.D'errico, D.Montesarchio, G.Mangiapia, L.Paduano, A.Merlino. Interaction of Anticancer Ruthenium Compounds with Proteins: High-Resolution X-Ray Structures and Raman Microscopy Studies of the Adduct Between Hen Egg White Lysozyme and Aziru. Inorg.Chem. V. 52 4157 2013.
ISSN: ISSN 0020-1669
PubMed: 23517183
DOI: 10.1021/IC4004142
Page generated: Tue Dec 15 06:45:34 2020

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