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Sodium in PDB 1yik: Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam

Enzymatic activity of Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam

All present enzymatic activity of Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam:
3.2.1.17;

Protein crystallography data

The structure of Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam, PDB code: 1yik was solved by T.M.Hunter, I.W.Mcnae, X.Liang, J.Bella, S.Parsons, M.D.Walkinshaw, P.J.Sadler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.00 / 1.75
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.906, 77.906, 37.762, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.3

Other elements in 1yik:

The structure of Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam (pdb code 1yik). 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 Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam, PDB code: 1yik:

Sodium binding site 1 out of 1 in 1yik

Go back to Sodium Binding Sites List in 1yik
Sodium binding site 1 out of 1 in the Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hen Egg White Lysozyme Soaked with Cu-Cyclam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:22.5
occ:1.00
O A:HOH527 2.2 14.8 1.0
O A:SER60 2.3 18.2 1.0
O A:CYS64 2.4 13.1 1.0
OG A:SER72 2.4 25.5 1.0
O A:HOH528 2.5 18.5 1.0
O A:ARG73 2.5 19.8 1.0
CB A:SER72 3.2 26.9 1.0
C A:SER60 3.4 16.4 1.0
C A:CYS64 3.5 12.9 1.0
C A:ARG73 3.6 20.1 1.0
CA A:ASN65 3.8 14.0 1.0
CA A:SER60 4.0 15.8 1.0
N A:ARG73 4.0 24.1 1.0
N A:ASN65 4.1 13.2 1.0
C A:SER72 4.2 25.9 1.0
CB A:SER60 4.2 16.3 1.0
CA A:SER72 4.3 26.4 1.0
CA A:ARG73 4.4 21.9 1.0
CB A:THR69 4.4 17.0 1.0
N A:ASP66 4.4 13.6 1.0
CL A:CL503 4.5 33.0 1.0
N A:ASN74 4.5 17.0 1.0
N A:ARG61 4.5 17.9 1.0
N A:CYS64 4.5 13.4 1.0
ND2 A:ASN65 4.6 19.1 1.0
C A:ARG61 4.6 18.9 1.0
CA A:CYS64 4.6 13.4 1.0
O A:ARG61 4.6 19.2 1.0
CB A:ASN65 4.7 14.8 1.0
C A:ASN65 4.7 13.9 1.0
CA A:ASN74 4.7 15.7 1.0
O A:SER72 4.8 26.4 1.0
CA A:ARG61 4.8 19.6 1.0
O A:THR69 4.8 19.3 1.0
CB A:ASN74 4.9 16.0 1.0
CG2 A:THR69 4.9 19.1 1.0
N A:TRP62 4.9 17.4 1.0
O A:HOH663 5.0 41.5 1.0
OG1 A:THR69 5.0 14.5 1.0

Reference:

T.M.Hunter, I.W.Mcnae, X.Liang, J.Bella, S.Parsons, M.D.Walkinshaw, P.J.Sadler. Protein Recognition of Macrocycles: Binding of Anti-Hiv Metallocyclams to Lysozyme Proc.Natl.Acad.Sci.Usa V. 102 2288 2005.
ISSN: ISSN 0027-8424
PubMed: 15701702
DOI: 10.1073/PNAS.0407595102
Page generated: Tue Dec 15 05:43:04 2020

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