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Sodium in PDB 8qcu: Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks.

Enzymatic activity of Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks.

All present enzymatic activity of Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks.:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks., PDB code: 8qcu was solved by F.J.F.Jacobs, A.Brink, J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.28 / 1.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.12, 81.12, 37.19, 90, 90, 90
R / Rfree (%) 15.9 / 17.8

Other elements in 8qcu:

The structure of Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks. also contains other interesting chemical elements:

Bromine (Br) 1 atom
Rhenium (Re) 9 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks. (pdb code 8qcu). 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 Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks., PDB code: 8qcu:

Sodium binding site 1 out of 1 in 8qcu

Go back to Sodium Binding Sites List in 8qcu
Sodium binding site 1 out of 1 in the Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:21.8
occ:1.00
 O A:SER60 2.2 23.0 1.0
OG A:SER72 2.3 29.1 1.0
O A:HOH368 2.3 33.1 1.0
O A:ARG73 2.4 28.2 1.0
O A:HOH366 2.5 18.8 1.0
O A:CYS64 2.6 18.9 1.0
HB2 A:SER72 2.8 35.6 1.0
CB A:SER72 3.1 29.6 1.0
HA A:ASN65 3.1 21.4 1.0
C A:SER60 3.3 20.0 1.0
C A:ARG73 3.5 27.2 1.0
HB2 A:SER60 3.6 21.3 1.0
C A:CYS64 3.7 18.1 1.0
HB A:THR69 3.7 21.1 1.0
HB3 A:SER72 3.7 35.6 1.0
HA A:SER60 3.8 21.7 1.0
N A:ARG73 3.9 28.2 1.0
H A:ARG73 3.9 33.9 1.0
CA A:SER60 4.0 18.1 1.0
CA A:ASN65 4.0 17.8 1.0
C A:SER72 4.0 29.2 1.0
H A:ASP66 4.1 20.0 1.0
HB2 A:ASN74 4.1 26.4 1.0
H A:CYS64 4.1 21.2 1.0
CA A:SER72 4.2 29.7 1.0
HA A:ASN74 4.2 26.1 1.0
HA A:ARG61 4.2 28.4 1.0
CB A:SER60 4.3 17.8 1.0
N A:ASN65 4.3 18.3 1.0
CA A:ARG73 4.3 28.6 1.0
N A:ARG61 4.4 21.4 1.0
HG21 A:THR69 4.4 21.7 1.0
N A:ASN74 4.4 24.0 1.0
C A:ARG61 4.4 22.0 1.0
O A:ARG61 4.5 24.5 1.0
N A:CYS64 4.6 17.7 1.0
CA A:ARG61 4.6 23.6 1.0
O A:SER72 4.6 30.1 1.0
CB A:THR69 4.6 17.6 1.0
HB2 A:ASN65 4.6 23.8 1.0
CA A:ASN74 4.6 21.8 1.0
OD1 A:ASN65 4.7 22.9 1.0
HA A:ARG73 4.7 34.3 1.0
HA A:SER72 4.7 35.6 1.0
N A:TRP62 4.7 19.6 1.0
N A:ASP66 4.8 16.6 1.0
CL A:CL202 4.8 23.1 1.0
CA A:CYS64 4.8 17.4 1.0
O A:THR69 4.8 20.9 1.0
CB A:ASN74 4.8 22.0 1.0
CB A:ASN65 4.9 19.8 1.0
HB3 A:SER60 4.9 21.3 1.0
C A:ASN65 4.9 17.4 1.0
H A:SER72 5.0 35.1 1.0
H A:TRP62 5.0 23.6 1.0

Reference:

F.J.F.Jacobs, J.R.Helliwell, A.Brink. Time-Series Analysis of Rhenium(I) Organometallic Covalent Binding to A Model Protein For Drug Development. Iucrj 2024.
ISSN: ESSN 2052-2525
PubMed: 38639558
DOI: 10.1107/S2052252524002598
Page generated: Wed Oct 9 13:09:52 2024

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