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Sodium in PDB 6f1p: Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound

Enzymatic activity of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound

All present enzymatic activity of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound:
3.2.1.17;

Protein crystallography data

The structure of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound, PDB code: 6f1p was solved by A.Camara-Artigas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.69 / 1.12
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.056, 77.056, 38.387, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 16.8

Other elements in 6f1p:

The structure of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound (pdb code 6f1p). 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 Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound, PDB code: 6f1p:

Sodium binding site 1 out of 1 in 6f1p

Go back to Sodium Binding Sites List in 6f1p
Sodium binding site 1 out of 1 in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:52.9
occ:0.65
 HB2 A:SER72 1.8 41.2 0.5
O A:HOH307 2.0 19.8 0.5
HB2 A:SER72 2.1 40.0 0.6
O A:HOH371 2.3 16.8 1.0
O A:SER60 2.3 19.6 1.0
O A:HOH301 2.3 22.2 0.7
OG A:SER72 2.4 33.7 0.6
O A:CYS64 2.4 16.6 1.0
CB A:SER72 2.6 34.3 0.5
O A:ARG73 2.6 27.4 0.6
CB A:SER72 2.6 33.3 0.6
HA A:ASN65 2.8 18.6 1.0
OG A:SER72 2.9 34.8 0.5
HB3 A:SER72 2.9 41.2 0.5
HB3 A:SER72 3.2 40.0 0.6
HG A:SER72 3.2 40.4 0.6
H A:ASN74 3.3 28.6 0.5
H A:ARG73 3.4 37.5 0.5
C A:CYS64 3.4 15.4 1.0
C A:SER60 3.5 16.5 1.0
C A:ARG73 3.7 27.5 0.6
CA A:ASN65 3.7 15.5 1.0
HB2 A:ASN74 3.7 24.0 0.5
HG A:SER72 3.7 41.8 0.5
HB2 A:SER60 3.8 17.5 1.0
N A:ARG73 3.8 31.2 0.5
HA A:SER60 3.8 17.6 1.0
CA A:SER72 3.8 33.8 0.5
CA A:SER72 3.9 33.2 0.6
H A:ASP66 3.9 17.3 1.0
HB A:THR69 3.9 21.1 1.0
N A:ASN74 3.9 23.8 0.5
HB2 A:ASN74 4.0 23.3 0.6
N A:ASN65 4.0 15.1 1.0
C A:SER72 4.0 31.4 0.6
HA A:ASN74 4.0 25.1 0.6
H A:CYS64 4.1 19.1 1.0
C A:SER72 4.1 32.2 0.5
HA A:SER72 4.1 40.6 0.5
CA A:SER60 4.1 14.6 1.0
N A:ARG73 4.1 30.6 0.6
HA A:SER72 4.2 39.8 0.6
HA A:ASN74 4.2 25.4 0.5
HA A:ARG61 4.2 23.8 1.0
H A:ARG73 4.3 36.8 0.6
HB2 A:ASN65 4.4 21.4 1.0
CB A:SER60 4.4 14.6 1.0
CA A:ASN74 4.5 21.2 0.5
OD1 A:ASN65 4.5 22.1 1.0
N A:ARG61 4.5 16.7 1.0
C A:ARG61 4.5 19.3 1.0
N A:CYS64 4.5 15.9 1.0
N A:ASN74 4.5 24.1 0.6
N A:ASP66 4.5 14.4 1.0
CB A:ASN74 4.5 20.0 0.5
O A:ARG61 4.5 20.9 1.0
CA A:ARG73 4.6 30.9 0.6
CL A:CL204 4.6 36.9 1.0
CB A:ASN65 4.6 17.8 1.0
O A:SER72 4.6 30.6 0.6
CA A:ASN74 4.6 20.9 0.6
CA A:CYS64 4.6 15.4 1.0
CA A:ARG61 4.6 19.9 1.0
C A:ASN65 4.7 14.8 1.0
CB A:ASN74 4.7 19.4 0.6
C A:ARG73 4.8 27.7 0.5
CB A:THR69 4.8 17.6 1.0
H A:ASN65 4.8 18.1 1.0
HG21 A:THR69 4.9 21.9 1.0
CA A:ARG73 4.9 31.2 0.5
H A:TRP63 4.9 19.0 1.0
N A:TRP62 4.9 18.5 1.0
H A:SER72 5.0 41.3 0.6
H A:SER72 5.0 41.7 0.5
HA A:ARG73 5.0 37.0 0.6
O A:SER72 5.0 31.7 0.5

Reference:

M.Plaza-Garrido, M.C.Salinas-Garcia, A.Camara-Artigas. Orthorhombic Lysozyme Crystallization at Acidic pH Values Driven By Phosphate Binding. Acta Crystallogr D Struct V. 74 480 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29717719
DOI: 10.1107/S205979831800517X
Page generated: Tue Oct 8 08:39:38 2024

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