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Sodium in PDB 1yap: Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants

Enzymatic activity of Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants

All present enzymatic activity of Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants:
3.2.1.17;

Protein crystallography data

The structure of Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants, PDB code: 1yap was solved by Y.Yamagata, H.Kaneda, S.Fujii, K.Takano, K.Ogasahara, E.Kanaya, M.Kikuchi, M.Oobatake, K.Yutani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.918, 61.072, 33.741, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants (pdb code 1yap). 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 Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants, PDB code: 1yap:

Sodium binding site 1 out of 1 in 1yap

Go back to Sodium Binding Sites List in 1yap
Sodium binding site 1 out of 1 in the Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:27.9
occ:1.00
 O A:SER61 2.1 16.9 1.0
O A:HOH545 2.2 19.4 1.0
O A:CYS65 2.3 14.2 1.0
O A:HOH541 2.4 13.9 1.0
O A:VAL74 2.5 20.7 1.0
H1 A:HOH541 2.8 0.0 1.0
H1 A:HOH545 2.8 0.0 1.0
H2 A:HOH541 2.9 0.0 1.0
H2 A:HOH545 2.9 0.0 1.0
CB A:ALA73 3.2 23.5 1.0
C A:SER61 3.3 17.2 1.0
C A:CYS65 3.3 11.3 1.0
C A:VAL74 3.5 21.5 1.0
CA A:ASN66 3.7 12.3 1.0
H A:ASP67 3.8 15.0 1.0
H A:VAL74 3.9 15.0 1.0
H A:CYS65 3.9 15.0 1.0
N A:ASN66 3.9 10.8 1.0
N A:VAL74 3.9 23.5 1.0
C A:ALA73 4.1 23.9 1.0
C A:ARG62 4.1 16.4 1.0
CA A:SER61 4.1 14.3 1.0
O A:ARG62 4.2 15.9 1.0
N A:ARG62 4.3 17.5 1.0
CA A:ALA73 4.3 23.7 1.0
N A:CYS65 4.3 12.5 1.0
CA A:ARG62 4.3 17.6 1.0
O A:HOH537 4.4 17.8 1.0
CA A:VAL74 4.4 23.2 1.0
N A:ASN75 4.4 19.3 1.0
H2 A:HOH574 4.4 0.0 1.0
CA A:CYS65 4.4 11.1 1.0
CB A:ASN66 4.5 11.9 1.0
CA A:ASN75 4.5 18.6 1.0
OD1 A:ASN66 4.5 13.3 1.0
N A:TYR63 4.5 15.7 1.0
CB A:SER61 4.6 11.4 1.0
N A:ASP67 4.6 11.0 1.0
CB A:ASN75 4.7 17.5 1.0
C A:ASN66 4.7 11.5 1.0
H A:TYR63 4.8 15.0 1.0
O A:HOH574 4.8 31.0 1.0
O A:ALA73 4.8 23.2 1.0
H A:ASN66 4.8 15.0 1.0
H1 A:HOH537 4.9 0.0 1.0
H2 A:HOH571 4.9 35.0 1.0
C A:TYR63 4.9 16.0 1.0
CG A:ASN66 5.0 13.0 1.0

Reference:

K.Takano, K.Ogasahara, H.Kaneda, Y.Yamagata, S.Fujii, E.Kanaya, M.Kikuchi, M.Oobatake, K.Yutani. Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants. J.Mol.Biol. V. 254 62 1995.
ISSN: ISSN 0022-2836
PubMed: 7473760
DOI: 10.1006/JMBI.1995.0599
Page generated: Sun Aug 17 09:15:51 2025

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