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Sodium in PDB 7qq1: X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl, PDB code: 7qq1 was solved by D.Loreto, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.86 / 1.48
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.58, 77.58, 37.93, 90, 90, 90
R / Rfree (%) 18.6 / 22.4

Other elements in 7qq1:

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl also contains other interesting chemical elements:

Rhodium (Rh) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl (pdb code 7qq1). 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 Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl, PDB code: 7qq1:

Sodium binding site 1 out of 1 in 7qq1

Go back to Sodium Binding Sites List in 7qq1
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl


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 Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:27.5
occ:1.00
HG A:SER72 2.0 29.4 0.0
O A:SER60 2.1 20.1 1.0
OG A:SER72 2.3 29.5 1.0
O A:HOH355 2.3 30.1 1.0
O A:HOH379 2.3 19.6 1.0
O A:ARG73 2.4 31.8 1.0
O A:CYS64 2.6 18.1 1.0
HB2 A:SER72 2.8 33.7 1.0
HA A:ASN65 3.0 18.3 1.0
CB A:SER72 3.1 34.6 1.0
C A:SER60 3.3 19.9 1.0
C A:ARG73 3.5 30.0 1.0
C A:CYS64 3.6 15.7 1.0
HB2 A:SER60 3.6 16.6 1.0
HB A:THR69 3.6 20.1 1.0
HA A:SER60 3.7 17.4 1.0
HB3 A:SER72 3.8 33.8 1.0
O A:ARG61 3.9 17.2 0.5
N A:ARG73 3.9 30.1 1.0
CA A:ASN65 3.9 18.8 1.0
H A:ASP66 4.0 16.5 1.0
CA A:SER60 4.0 16.4 1.0
HA A:ARG61 4.0 21.6 0.5
HB2 A:ASN74 4.0 22.8 1.0
H A:ARG73 4.0 31.0 1.0
H A:CYS64 4.1 19.4 1.0
C A:SER72 4.1 34.6 1.0
C A:ARG61 4.2 21.4 0.5
CA A:SER72 4.2 37.5 1.0
N A:ASN65 4.2 17.5 1.0
HA A:ASN74 4.2 23.4 1.0
HA A:ARG61 4.3 21.6 0.5
CB A:SER60 4.3 17.0 1.0
N A:ARG61 4.3 19.6 0.5
CA A:ARG73 4.3 30.2 1.0
N A:ARG61 4.4 19.5 0.5
N A:ASN74 4.4 25.5 1.0
O A:HOH388 4.4 26.4 1.0
CA A:ARG61 4.4 21.8 0.5
O A:HOH438 4.4 39.5 1.0
C A:ARG61 4.6 21.3 0.5
CB A:THR69 4.6 21.0 1.0
HG22 A:THR69 4.6 21.1 1.0
N A:CYS64 4.6 20.6 1.0
CA A:ARG61 4.6 21.9 0.5
HB2 A:ASN65 4.7 20.4 1.0
N A:ASP66 4.7 16.4 1.0
CA A:ASN74 4.7 23.4 1.0
HA A:ARG73 4.7 30.7 1.0
OD1 A:ASN65 4.7 26.6 1.0
HG1 A:THR69 4.7 18.4 0.0
HA A:SER72 4.7 36.2 1.0
CA A:CYS64 4.8 18.6 1.0
N A:TRP62 4.8 18.5 1.0
CB A:ASN74 4.8 23.2 1.0
O A:ARG61 4.8 18.6 0.5
O A:SER72 4.8 33.9 1.0
CB A:ASN65 4.9 19.9 1.0
C A:ASN65 4.9 16.4 1.0
H A:TRP63 4.9 17.9 1.0
O A:THR69 4.9 22.2 1.0
H A:TRP62 5.0 20.2 1.0
CG2 A:THR69 5.0 21.1 1.0

Reference:

D.Loreto, A.Esposito, N.Demitri, A.Guaragna, A.Merlino. Reactivity of A Fluorine-Containing Dirhodium Tetracarboxylate Compound with Proteins. Dalton Trans V. 51 3695 2022.
ISSN: ESSN 1477-9234
PubMed: 35166290
DOI: 10.1039/D2DT00082B
Page generated: Wed Oct 9 08:23:23 2024

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