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Sodium in PDB 8pfy: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B, PDB code: 8pfy was solved by A.Teran, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.18 / 1.19
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.62, 76.62, 37.08, 90, 90, 90
R / Rfree (%) 19.5 / 21.2

Other elements in 8pfy:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B also contains other interesting chemical elements:

Ruthenium (Ru) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B (pdb code 8pfy). 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 X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B, PDB code: 8pfy:

Sodium binding site 1 out of 1 in 8pfy

Go back to Sodium Binding Sites List in 8pfy
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:19.0
occ:1.00
 O A:SER60 2.1 19.6 1.0
O A:HOH371 2.3 23.9 1.0
O A:ARG73 2.4 23.3 1.0
O A:HOH357 2.4 15.1 1.0
OG A:SER72 2.5 22.4 1.0
O A:CYS64 2.5 12.9 1.0
CB A:SER72 3.3 22.1 1.0
C A:SER60 3.3 15.1 1.0
C A:ARG73 3.5 21.4 1.0
C A:CYS64 3.6 13.2 1.0
N A:ARG73 3.9 23.6 1.0
CA A:ASN65 4.0 13.4 1.0
CA A:SER60 4.0 12.8 1.0
C A:SER72 4.1 24.2 1.0
N A:ASN65 4.2 12.9 1.0
O A:ARG61 4.3 21.5 1.0
C A:ARG61 4.3 18.7 1.0
CA A:SER72 4.3 24.8 1.0
N A:ARG61 4.3 15.1 1.0
N A:ASN74 4.3 18.3 1.0
CA A:ARG73 4.3 21.3 1.0
CB A:SER60 4.3 11.9 1.0
O A:HOH347 4.5 20.5 1.0
CA A:ARG61 4.5 19.4 1.0
N A:CYS64 4.5 13.2 1.0
OD1 A:ASN65 4.6 20.4 1.0
CA A:ASN74 4.6 15.9 1.0
CB A:THR69 4.7 12.9 1.0
N A:ASP66 4.7 12.2 1.0
CA A:CYS64 4.7 12.3 1.0
O A:SER72 4.7 26.6 1.0
CB A:ASN74 4.7 15.5 1.0
N A:TRP62 4.8 15.8 1.0
CB A:ASN65 4.9 14.7 1.0
C A:ASN65 4.9 11.8 1.0
O A:THR69 4.9 17.2 1.0

Reference:

S.Herrero Dominguez, A.Teran, G.Ferraro, A.E.Sanchez-Pelaez, A.Merlino. Charge Effect in Protein Metalation Reactions By Diruthenium Complexes Inorg Chem Front 2023.
DOI: 10.1039/D3QI01192E
Page generated: Wed Oct 9 12:55:58 2024

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