Sodium in PDB 8pfu: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A, PDB code: 8pfu 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) 55.20 / 1.18
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.06, 78.06, 37.47, 90, 90, 90
R / Rfree (%) 17.9 / 20.2

Other elements in 8pfu:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A also contains other interesting chemical elements:

Ruthenium (Ru) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A (pdb code 8pfu). 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 K3[RU2(CO3)4] in Condition A, PDB code: 8pfu:

Sodium binding site 1 out of 1 in 8pfu

Go back to Sodium Binding Sites List in 8pfu
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


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 K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:18.3
occ:1.00
 O A:SER60 2.3 17.6 1.0
O A:HOH308 2.4 23.1 1.0
O A:ARG73 2.4 21.1 0.5
O A:CYS64 2.4 14.4 1.0
O A:ARG73 2.5 23.0 0.5
OG A:SER72 2.5 23.2 1.0
O3 A:NO3202 2.6 21.3 1.0
CB A:SER72 3.3 22.9 1.0
C A:ARG73 3.4 21.3 0.5
C A:ARG73 3.4 22.1 0.5
C A:CYS64 3.4 14.0 1.0
C A:SER60 3.4 16.4 1.0
N A:NO3202 3.5 27.1 1.0
O1 A:NO3202 3.5 30.5 1.0
N A:ARG73 3.8 21.8 0.5
N A:ARG73 3.9 22.5 0.5
CA A:ASN65 3.9 15.1 0.5
N A:ASN65 4.1 15.7 0.5
CA A:ASN65 4.1 15.5 0.5
CA A:SER60 4.1 14.8 1.0
N A:ASN65 4.1 16.0 0.5
C A:SER72 4.1 25.5 1.0
CA A:ARG73 4.2 21.9 0.5
N A:ASN74 4.2 19.8 1.0
CA A:ARG73 4.3 22.9 0.5
N A:CYS64 4.3 14.7 1.0
CB A:SER60 4.3 14.6 1.0
CA A:SER72 4.4 24.6 1.0
C A:ARG61 4.5 19.6 1.0
CA A:ASN74 4.5 19.8 1.0
CA A:CYS64 4.5 15.3 1.0
N A:ARG61 4.5 16.4 1.0
O A:ARG61 4.6 21.9 1.0
CB A:THR69 4.6 18.8 1.0
O2 A:NO3202 4.7 24.3 1.0
CB A:ASN65 4.7 16.6 0.5
CB A:ASN74 4.7 20.4 1.0
O A:SER72 4.7 27.5 1.0
N A:TRP62 4.8 18.3 1.0
O A:HOH422 4.8 37.2 1.0
CA A:ARG61 4.8 18.7 1.0
O A:THR69 4.9 21.8 1.0
N A:TRP63 4.9 14.7 1.0
N A:ASP66 4.9 14.7 1.0
C A:TRP62 5.0 16.5 1.0
C A:ASN65 5.0 14.2 0.5
OD1 A:ASN65 5.0 17.0 0.5

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 12:55:49 2024

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