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Sodium in PDB 6ro5: 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf

Enzymatic activity of 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf

All present enzymatic activity of 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf:
3.2.1.17;

Protein crystallography data

The structure of 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf, PDB code: 6ro5 was solved by A.Brink, J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.43 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.880, 78.650, 80.670, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.3

Other elements in 6ro5:

The structure of 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf also contains other interesting chemical elements:

Rhenium (Re) 39 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf (pdb code 6ro5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf, PDB code: 6ro5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6ro5

Go back to Sodium Binding Sites List in 6ro5
Sodium binding site 1 out of 2 in the 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:34.6
occ:1.00
O A:HOH316 2.3 37.9 1.0
O A:SER60 2.3 29.2 1.0
O A:CYS64 2.4 30.0 1.0
OG A:SER72 2.4 36.3 1.0
O A:ARG73 2.6 41.5 1.0
O A:HOH315 2.6 41.2 1.0
CB A:SER72 3.4 42.3 1.0
C A:SER60 3.5 33.0 1.0
C A:CYS64 3.5 33.6 1.0
C A:ARG73 3.6 35.4 1.0
CA A:ASN65 3.9 36.9 1.0
N A:ARG73 4.0 37.9 1.0
CA A:SER60 4.1 27.7 1.0
N A:ASN65 4.1 32.0 1.0
C A:SER72 4.2 43.8 1.0
CB A:SER60 4.2 35.0 1.0
CA A:ARG73 4.4 38.5 1.0
CA A:SER72 4.4 42.2 1.0
N A:ASN74 4.5 31.8 1.0
O A:ARG61 4.5 35.5 1.0
C A:ARG61 4.5 36.7 1.0
N A:CYS64 4.5 29.5 1.0
N A:ARG61 4.6 33.0 1.0
CB A:THR69 4.6 42.3 1.0
CA A:ASN74 4.6 31.4 1.0
CA A:CYS64 4.7 33.6 1.0
CL A:CL204 4.7 49.0 1.0
CB A:ASN74 4.7 35.7 1.0
CB A:ASN65 4.7 32.5 1.0
O A:SER72 4.7 44.1 1.0
O A:THR69 4.8 46.0 1.0
CA A:ARG61 4.8 38.5 1.0
N A:ASP66 4.8 33.3 1.0
OD1 A:ASN65 4.9 40.0 1.0
N A:TRP62 4.9 28.9 1.0
C A:ASN65 4.9 34.1 1.0
CG2 A:THR69 5.0 36.1 1.0

Sodium binding site 2 out of 2 in 6ro5

Go back to Sodium Binding Sites List in 6ro5
Sodium binding site 2 out of 2 in the 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1YR-Y: Lysozyme with Re Cluster 1 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na207

b:27.2
occ:1.00
O B:CYS64 2.2 32.2 1.0
O B:SER60 2.4 34.9 1.0
O B:ARG73 2.5 40.9 1.0
OG B:SER72 2.6 39.3 1.0
C B:CYS64 3.3 30.2 1.0
CB B:SER72 3.4 38.7 1.0
C B:SER60 3.5 35.4 1.0
C B:ARG73 3.6 40.9 1.0
CA B:ASN65 3.8 28.2 1.0
N B:ASN65 4.0 32.1 1.0
CA B:SER60 4.0 30.1 1.0
N B:ARG73 4.0 44.5 1.0
CB B:SER60 4.2 28.7 1.0
C B:SER72 4.2 47.1 1.0
N B:CYS64 4.3 31.2 1.0
CA B:ARG73 4.4 37.4 1.0
CA B:CYS64 4.5 31.9 1.0
CA B:SER72 4.5 46.1 1.0
N B:ASN74 4.5 37.2 1.0
N B:ASP66 4.6 28.9 1.0
C B:ARG61 4.6 42.6 1.0
N B:ARG61 4.6 35.6 1.0
CA B:ASN74 4.6 38.4 1.0
ND2 B:ASN65 4.7 32.9 1.0
O B:SER72 4.7 43.1 1.0
CB B:ASN65 4.7 29.4 1.0
C B:ASN65 4.7 31.7 1.0
N B:TRP62 4.8 34.9 1.0
CL B:CL206 4.8 40.4 1.0
O B:ARG61 4.8 36.7 1.0
CB B:THR69 4.8 36.2 1.0
CB B:ASN74 4.8 32.5 1.0
CA B:ARG61 4.9 37.0 1.0
OG B:SER60 4.9 30.0 1.0

Reference:

A.Brink, J.R.Helliwell. Formation of A Highly Dense Tetra-Rhenium Cluster in A Protein Crystal and Its Implications in Medical Imaging. Iucrj V. 6 695 2019.
ISSN: ESSN 2052-2525
PubMed: 31316813
DOI: 10.1107/S2052252519006651
Page generated: Tue Dec 15 12:55:38 2020

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