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Sodium in PDB 5fst: Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

Enzymatic activity of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

All present enzymatic activity of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure:
3.2.1.17;

Protein crystallography data

The structure of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fst was solved by B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Derlinden, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.86 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.001, 79.001, 37.053, 90.00, 90.00, 90.00
R / Rfree (%) 10.9 / 13.4

Other elements in 5fst:

The structure of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure also contains other interesting chemical elements:

Krypton (Kr) 5 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure (pdb code 5fst). 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 Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fst:

Sodium binding site 1 out of 1 in 5fst

Go back to Sodium Binding Sites List in 5fst
Sodium binding site 1 out of 1 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:11.9
occ:1.00
HG A:SER72 2.1 14.4 0.0
O A:SER60 2.3 11.8 1.0
O A:ARG73 2.4 13.6 1.0
O A:CYS64 2.4 10.0 1.0
O A:HOH2118 2.4 14.7 1.0
O A:HOH2117 2.5 11.1 1.0
OG A:SER72 2.5 14.4 1.0
HB2 A:SER72 2.9 14.4 1.0
HA A:ASN65 3.0 9.5 1.0
CB A:SER72 3.2 14.4 1.0
C A:SER60 3.4 10.1 1.0
HB2 A:SER60 3.4 9.6 1.0
C A:ARG73 3.5 13.1 1.0
C A:CYS64 3.5 9.1 1.0
H A:ASP66 3.7 9.1 1.0
HB A:THR69 3.7 10.8 1.0
HA A:SER60 3.8 9.2 1.0
HB3 A:SER72 3.9 14.4 1.0
H A:CYS64 3.9 9.6 1.0
CA A:ASN65 3.9 9.5 1.0
N A:ARG73 3.9 14.4 1.0
H A:ARG73 3.9 14.4 1.0
HB2 A:ASN74 4.0 12.4 1.0
CA A:SER60 4.0 9.2 1.0
HA A:ASN74 4.1 11.9 1.0
N A:ASN65 4.1 9.4 1.0
CB A:SER60 4.2 9.6 1.0
C A:SER72 4.2 14.8 1.0
CA A:ARG73 4.3 14.8 1.0
CA A:SER72 4.4 14.4 1.0
N A:ASN74 4.4 13.0 1.0
N A:CYS64 4.5 9.6 1.0
O A:HOH2130 4.5 47.4 1.0
N A:ARG61 4.5 10.9 1.0
C A:ARG61 4.6 12.1 1.0
CA A:ASN74 4.6 11.9 1.0
O A:ARG61 4.6 15.4 1.0
N A:ASP66 4.6 9.1 1.0
CA A:CYS64 4.6 9.5 1.0
HB2 A:ASN65 4.6 10.9 1.0
HA A:ARG61 4.6 13.3 1.0
CB A:THR69 4.6 10.8 1.0
OD1 A:ASN65 4.7 13.6 1.0
CL A:CL203 4.7 15.1 1.0
HG1 A:THR69 4.7 10.6 0.0
HA A:ARG73 4.7 14.8 1.0
CB A:ASN74 4.7 12.4 1.0
H A:TRP63 4.8 10.0 1.0
HG22 A:THR69 4.8 11.8 1.0
O A:SER72 4.8 17.7 1.0
C A:ASN65 4.8 8.7 1.0
CB A:ASN65 4.8 10.9 1.0
CA A:ARG61 4.8 13.3 1.0
HB3 A:SER60 4.8 9.6 1.0
HA A:SER72 4.9 14.4 1.0
N A:TRP62 4.9 11.8 1.0

Reference:

B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Der Linden, P.Carpentier. Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using A Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. V. 49 1478 2016.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576716010992
Page generated: Tue Dec 15 10:59:55 2020

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