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Sodium in PDB 6wrl: The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week

Enzymatic activity of The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week

All present enzymatic activity of The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week:
3.2.1.17;

Protein crystallography data

The structure of The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week, PDB code: 6wrl was solved by M.P.Sullivan, M.John, C.G.Hartinger, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.12 / 1.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.174, 78.174, 37.783, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.5

Other elements in 6wrl:

The structure of The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week also contains other interesting chemical elements:

Rhodium (Rh) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week (pdb code 6wrl). 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 The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week, PDB code: 6wrl:

Sodium binding site 1 out of 1 in 6wrl

Go back to Sodium Binding Sites List in 6wrl
Sodium binding site 1 out of 1 in the The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Interaction of Chlorido(1,5-Cyclooctadiene)([4-(2-((Tert- Butoxycarbonyl)Amino)-3-Methoxy-3-Oxopropyl)-1,3-Dimethyl-1H- Imidazol-3-Ide])Rhodium(I) with Hewl After 1 Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:18.5
occ:1.00
 O A:SER60 2.3 17.9 1.0
O A:HOH387 2.3 25.7 1.0
O A:CYS64 2.4 15.9 1.0
OG A:SER72 2.4 25.2 1.0
O A:ARG73 2.4 24.1 1.0
O A:ACT203 2.7 21.2 1.0
CB A:SER72 3.3 22.9 1.0
C A:CYS64 3.4 15.1 1.0
C A:ARG73 3.5 23.3 1.0
C A:SER60 3.5 17.5 1.0
C A:ACT203 3.5 24.3 1.0
CH3 A:ACT203 3.6 23.0 1.0
N A:ARG73 3.9 23.8 1.0
CA A:ASN65 4.0 18.6 0.7
CA A:ASN65 4.0 16.4 0.3
C A:SER72 4.1 26.5 1.0
CA A:SER60 4.1 15.5 1.0
N A:ASN65 4.1 16.5 1.0
CA A:SER72 4.3 26.6 1.0
CA A:ARG73 4.3 24.0 0.7
CA A:ARG73 4.3 24.1 0.3
N A:ASN74 4.3 20.6 1.0
CB A:SER60 4.3 15.5 1.0
N A:CYS64 4.3 15.7 1.0
O A:ARG61 4.5 21.1 1.0
C A:ARG61 4.5 21.7 1.0
CA A:CYS64 4.5 16.7 1.0
CA A:ASN74 4.6 20.3 1.0
N A:ARG61 4.6 19.0 1.0
O A:SER72 4.6 29.9 1.0
CB A:THR69 4.7 21.1 1.0
OXT A:ACT203 4.7 25.2 1.0
CB A:ASN74 4.7 20.2 1.0
O A:THR69 4.8 23.8 1.0
CA A:ARG61 4.8 20.5 0.7
N A:TRP62 4.8 18.8 1.0
CB A:ASN65 4.9 15.9 0.3
CA A:ARG61 4.9 19.6 0.3
CB A:ASN65 4.9 19.3 0.7
N A:ASP66 4.9 16.2 1.0
N A:TRP63 4.9 16.8 1.0
O A:HOH396 4.9 40.1 1.0
CG2 A:THR69 5.0 19.7 1.0
ND2 A:ASN65 5.0 20.9 0.7
C A:TRP62 5.0 18.8 1.0
C A:ASN65 5.0 15.0 1.0

Reference:

I.M.Daubit, M.P.Sullivan, M.John, D.C.Goldstone, C.G.Hartinger, N.Metzler-Nolte. A Combined Spectroscopic and Protein Crystallography Study Reveals Protein Interactions of Rh I (Nhc) Complexes at the Molecular Level. Inorg.Chem. V. 59 17191 2020.
ISSN: ISSN 0020-1669
PubMed: 33180473
DOI: 10.1021/ACS.INORGCHEM.0C02438
Page generated: Tue Oct 8 14:42:00 2024

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