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Sodium in PDB 6ro3: 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf

Enzymatic activity of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf

All present enzymatic activity of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf:
3.2.1.17;

Protein crystallography data

The structure of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf, PDB code: 6ro3 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) 39.97 / 1.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.940, 79.940, 36.460, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 11.8

Other elements in 6ro3:

The structure of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf also contains other interesting chemical elements:

Rhenium (Re) 16 atoms
Bromine (Br) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf (pdb code 6ro3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf, PDB code: 6ro3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6ro3

Go back to Sodium Binding Sites List in 6ro3
Sodium binding site 1 out of 2 in the 2YR-X: Lysozyme with Re Cluster 2 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 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:6.7
occ:1.00
O A:CYS64 2.4 6.5 1.0
O A:SER60 2.4 6.4 1.0
O A:ARG73 2.4 7.7 1.0
OG A:SER72 2.4 7.0 1.0
O A:HOH359 2.5 10.1 1.0
O A:HOH340 2.5 7.3 1.0
CB A:SER72 3.3 7.0 1.0
C A:CYS64 3.4 6.3 1.0
C A:ARG73 3.5 7.5 1.0
C A:SER60 3.5 6.2 1.0
N A:ARG73 3.9 7.8 1.0
CA A:ASN65 3.9 6.3 1.0
C A:SER72 4.0 7.3 1.0
N A:ASN65 4.1 6.5 1.0
CA A:SER60 4.1 6.3 1.0
CB A:SER60 4.2 6.2 1.0
CA A:ARG73 4.3 8.4 1.0
CA A:SER72 4.3 7.5 1.0
N A:CYS64 4.4 6.9 1.0
N A:ASN74 4.4 7.7 1.0
O A:ARG61 4.5 7.5 1.0
C A:ARG61 4.5 6.8 1.0
O A:SER72 4.5 8.1 1.0
CA A:CYS64 4.6 6.9 1.0
N A:ARG61 4.6 6.4 1.0
N A:ASP66 4.6 6.3 1.0
CA A:ASN74 4.6 7.8 1.0
CB A:THR69 4.7 6.2 1.0
OD1 A:ASN65 4.7 9.1 1.0
CL A:CL202 4.8 8.3 1.0
CB A:ASN74 4.8 8.3 1.0
CB A:ASN65 4.8 7.6 1.0
C A:ASN65 4.8 6.1 1.0
CA A:ARG61 4.8 7.0 1.0
O A:HOH388 4.8 15.6 1.0
N A:TRP62 4.8 7.7 0.5
N A:TRP62 4.9 6.8 0.5
O A:THR69 5.0 7.1 1.0

Sodium binding site 2 out of 2 in 6ro3

Go back to Sodium Binding Sites List in 6ro3
Sodium binding site 2 out of 2 in the 2YR-X: Lysozyme with Re Cluster 2 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 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na215

b:13.3
occ:1.00
O A:HOH328 2.3 13.8 1.0
OE1 A:GLU35 2.8 9.4 1.0
O A:HOH323 3.6 20.0 1.0
CD A:GLU35 3.8 8.3 1.0
CG1 A:VAL109 4.3 9.9 0.5
OE2 A:GLU35 4.3 9.1 1.0
O A:HOH372 4.3 26.6 1.0
O A:HOH302 4.4 14.6 1.0
OD2 A:ASP52 4.4 12.7 1.0
CG A:GLN57 4.5 6.6 1.0
CB A:GLN57 4.5 6.7 1.0
O A:GLU35 4.5 6.9 1.0
OE1 A:GLN57 4.6 7.6 1.0
CA A:GLU35 4.8 6.3 1.0
O A:HOH307 4.8 23.8 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 12:55:37 2020

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