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Sodium in PDB 7fgv: H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution

Enzymatic activity of H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution

All present enzymatic activity of H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution:
3.2.1.17;

Protein crystallography data

The structure of H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution, PDB code: 7fgv was solved by A.Kita, Y.Morimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.15, 79.15, 37.902, 90, 90, 90
R / Rfree (%) 22.4 / 25

Other elements in 7fgv:

The structure of H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution (pdb code 7fgv). 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 H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution, PDB code: 7fgv:

Sodium binding site 1 out of 1 in 7fgv

Go back to Sodium Binding Sites List in 7fgv
Sodium binding site 1 out of 1 in the H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H/D Exchanged Hen Egg-White Lysozyme Denatured in Heat Condition and Refolded in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:37.2
occ:1.00
 HB2 A:SER72 2.1 38.6 1.0
OG A:SER72 2.2 36.4 1.0
D1 A:HOH351 2.3 26.1 1.0
O A:ARG73 2.4 37.8 1.0
O A:SER60 2.4 20.2 1.0
D2 A:HOH313 2.5 41.5 1.0
O A:CYS64 2.6 15.8 1.0
CB A:SER72 2.6 32.1 1.0
O A:HOH313 2.6 34.6 1.0
O A:HOH351 2.8 21.8 1.0
D2 A:HOH351 3.1 26.1 1.0
HA A:ASN65 3.2 23.0 1.0
HB3 A:SER72 3.3 38.6 1.0
C A:ARG73 3.3 31.8 1.0
D1 A:HOH313 3.4 41.5 1.0
C A:CYS64 3.5 13.4 1.0
C A:SER60 3.6 20.3 1.0
C A:SER72 3.6 31.1 1.0
CA A:SER72 3.7 34.6 1.0
N A:ARG73 3.7 22.4 1.0
HA A:ASN74 3.8 21.3 1.0
HB2 A:ASN74 3.8 21.9 1.0
D A:CYS64 3.9 17.3 1.0
H A:CYS64 3.9 17.3 0.0
D A:ARG73 3.9 26.8 0.5
H A:ARG73 3.9 26.8 0.5
O A:ARG61 4.0 26.1 1.0
HB A:THR69 4.0 19.8 1.0
HB2 A:SER60 4.1 15.6 1.0
CA A:ASN65 4.1 19.1 1.0
HA A:ARG61 4.1 25.7 1.0
HA A:SER60 4.1 19.4 1.0
C A:ARG61 4.2 23.9 1.0
CA A:ARG73 4.2 25.5 1.0
N A:ASN74 4.2 27.2 1.0
O A:SER72 4.2 27.0 1.0
HA A:SER72 4.2 41.5 1.0
N A:ASN65 4.2 14.5 1.0
CA A:ASN74 4.3 17.8 1.0
N A:CYS64 4.4 14.4 1.0
CA A:SER60 4.4 16.2 1.0
D1 A:HOH357 4.5 34.0 1.0
D A:ASP66 4.5 15.8 0.6
H A:ASP66 4.5 15.8 0.4
CA A:ARG61 4.5 21.4 1.0
N A:ARG61 4.5 17.4 1.0
CB A:ASN74 4.5 18.3 1.0
HB2 A:ASN65 4.6 19.1 1.0
N A:TRP62 4.6 21.4 1.0
CA A:CYS64 4.6 13.9 1.0
HA A:ARG73 4.6 30.6 1.0
D A:TRP63 4.7 18.0 1.0
H A:TRP63 4.7 18.0 0.0
H A:SER72 4.7 42.0 0.4
D A:SER72 4.7 42.0 0.6
CB A:SER60 4.7 13.0 1.0
N A:SER72 4.8 35.0 1.0
C A:TRP62 4.8 17.0 1.0
N A:TRP63 4.8 15.0 1.0
HG23 A:THR69 4.9 24.1 1.0
CB A:ASN65 4.9 15.9 1.0
OD1 A:ASN65 4.9 31.3 1.0
D A:ASN74 4.9 32.6 0.4
H A:ASN74 4.9 32.6 0.6
O A:HOH357 4.9 28.4 1.0
D A:TRP62 4.9 25.7 1.0
H A:TRP62 4.9 25.7 0.0
CB A:THR69 4.9 16.5 1.0
HA A:TRP62 4.9 24.9 1.0
O A:THR69 5.0 23.6 1.0
H A:ASN65 5.0 17.4 0.0
D A:ASN65 5.0 17.4 1.0
HA A:CYS64 5.0 16.6 1.0

Reference:

A.Kita, Y.Morimoto. Hydrogen/Deuterium Exchange Behavior During Denaturing/Refolding Processes Determined in Tetragonal Hen Egg-White Lysozyme Crystals. Mol Biotechnol. V. 64 590 2022.
ISSN: ESSN 1559-0305
PubMed: 35028904
DOI: 10.1007/S12033-022-00447-7
Page generated: Tue Oct 8 16:50:45 2024

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