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Sodium in PDB 1wqm: Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme

Enzymatic activity of Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme

All present enzymatic activity of Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme, PDB code: 1wqm was solved by Y.Yamagata, M.Kubota, Y.Sumikawa, J.Funahashi, S.Fujii, 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 (°) 56.720, 61.120, 33.740, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / n/a

Other elements in 1wqm:

The structure of Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme (pdb code 1wqm). 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 Hydrogen Bonds to the Conformational Stability of Human Lysozyme, PDB code: 1wqm:

Sodium binding site 1 out of 1 in 1wqm

Go back to Sodium Binding Sites List in 1wqm
Sodium binding site 1 out of 1 in the Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na131

b:22.3
occ:1.00
 O A:SER61 2.1 14.6 1.0
O A:CYS65 2.2 11.8 1.0
O A:HOH148 2.2 21.0 1.0
O A:VAL74 2.4 18.2 1.0
O A:HOH142 2.4 14.4 1.0
C A:CYS65 3.2 10.5 1.0
C A:SER61 3.3 15.2 1.0
CB A:ALA73 3.3 22.9 1.0
C A:VAL74 3.5 18.6 1.0
CA A:ASN66 3.7 12.0 1.0
N A:VAL74 3.8 21.3 1.0
N A:ASN66 3.9 9.7 1.0
CA A:SER61 4.1 13.3 1.0
C A:ALA73 4.1 22.8 1.0
C A:ARG62 4.1 14.4 1.0
O A:ARG62 4.2 14.0 1.0
N A:CYS65 4.2 11.4 1.0
N A:ARG62 4.2 16.3 1.0
CA A:VAL74 4.3 20.8 1.0
CA A:ALA73 4.3 23.3 1.0
N A:ASN75 4.3 17.9 1.0
CA A:ARG62 4.4 15.6 1.0
CA A:CYS65 4.4 10.8 1.0
CA A:ASN75 4.4 17.9 1.0
OD1 A:ASN66 4.5 13.5 1.0
CB A:ASN66 4.5 12.0 1.0
CB A:SER61 4.5 10.1 1.0
N A:TYR63 4.5 15.7 1.0
O A:HOH154 4.6 17.3 1.0
N A:ASP67 4.6 11.9 1.0
CB A:ASN75 4.6 16.4 1.0
C A:ASN66 4.7 10.7 1.0
O A:ALA73 4.8 22.3 1.0
N A:TRP64 4.9 13.5 1.0
C A:TYR63 4.9 16.6 1.0
O A:HOH218 5.0 38.5 1.0
CG A:ASN66 5.0 12.9 1.0

Reference:

Y.Yamagata, M.Kubota, Y.Sumikawa, J.Funahashi, K.Takano, S.Fujii, K.Yutani. Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyrosine --> Phenylalanine Mutants. Biochemistry V. 37 9355 1998.
ISSN: ISSN 0006-2960
PubMed: 9649316
DOI: 10.1021/BI980431I
Page generated: Sun Aug 17 09:07:40 2025

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