Atomistry » Sodium » PDB 8oyf-8ph7 » 8pfu
Atomistry »
  Sodium »
    PDB 8oyf-8ph7 »
      8pfu »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy