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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: Mon Oct 7 17:19:59 2024

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