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Rhodium in PDB 6wrm: 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 Month

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 Month

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 Month:
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 Month, PDB code: 6wrm 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) 40.51 / 1.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.952, 80.952, 35.824, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.9

Other elements in 6wrm:

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 Month also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Rhodium Binding Sites:

The binding sites of Rhodium 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 Month (pdb code 6wrm). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 3 binding sites of Rhodium where 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 Month, PDB code: 6wrm:
Jump to Rhodium binding site number: 1; 2; 3;

Rhodium binding site 1 out of 3 in 6wrm

Go back to Rhodium Binding Sites List in 6wrm
Rhodium binding site 1 out of 3 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 Month


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh 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 Month within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh204

b:39.0
occ:0.50
 O A:HOH341 1.3 16.6 0.5
O A:HOH370 1.5 36.5 0.5
NE2 A:HIS15 2.0 31.8 1.0
O A:HOH397 2.3 32.9 0.5
O A:HOH383 2.5 28.9 0.5
O A:HOH388 2.8 32.9 0.5
CE1 A:HIS15 2.9 41.9 1.0
CD2 A:HIS15 3.1 38.8 1.0
ND1 A:HIS15 4.0 45.2 1.0
CG A:HIS15 4.2 37.0 1.0
OD1 A:ASP87 4.4 39.7 1.0
OG1 A:THR89 4.6 37.3 1.0

Rhodium binding site 2 out of 3 in 6wrm

Go back to Rhodium Binding Sites List in 6wrm
Rhodium binding site 2 out of 3 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 Month


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 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 Month within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh205

b:24.1
occ:0.35
 RH01 A:U8G205 0.0 24.1 0.3
RH01 A:U8G205 0.7 23.8 0.2
O A:HOH382 1.0 1.7 0.2
O A:HOH304 1.4 15.5 0.3
O A:HOH357 2.0 16.9 0.2
O A:HOH389 2.0 17.1 0.2
C31 A:U8G205 2.0 21.8 0.2
C31 A:U8G205 2.1 19.3 0.3
O A:HOH389 2.3 20.4 0.3
NZ A:LYS33 2.4 36.1 1.0
O A:HOH382 2.5 25.2 0.3
O A:HOH357 3.0 24.4 0.3
N04 A:U8G205 3.0 26.6 0.2
O A:HOH304 3.1 12.6 0.2
N04 A:U8G205 3.1 23.2 0.3
N07 A:U8G205 3.1 25.6 0.2
N07 A:U8G205 3.2 23.2 0.3
C32 A:U8G205 3.3 26.9 0.2
C36 A:U8G205 3.5 23.1 0.3
C32 A:U8G205 3.6 23.6 0.3
C36 A:U8G205 3.6 25.0 0.2
CE A:LYS33 3.7 35.6 1.0
C42 A:U8G205 4.2 26.1 0.2
C40 A:U8G205 4.3 26.6 0.2
C42 A:U8G205 4.4 22.4 0.3
C40 A:U8G205 4.4 22.9 0.3
CD A:LYS33 4.8 32.3 1.0

Rhodium binding site 3 out of 3 in 6wrm

Go back to Rhodium Binding Sites List in 6wrm
Rhodium binding site 3 out of 3 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 Month


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 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 Month within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh205

b:23.8
occ:0.25
 RH01 A:U8G205 0.0 23.8 0.2
RH01 A:U8G205 0.7 24.1 0.3
O A:HOH304 1.2 15.5 0.3
O A:HOH382 1.3 1.7 0.2
O A:HOH357 1.5 16.9 0.2
C31 A:U8G205 2.0 19.3 0.3
C31 A:U8G205 2.1 21.8 0.2
O A:HOH357 2.3 24.4 0.3
NZ A:LYS33 2.3 36.1 1.0
O A:HOH389 2.6 17.1 0.2
O A:HOH304 2.8 12.6 0.2
O A:HOH389 2.8 20.4 0.3
N04 A:U8G205 2.9 23.2 0.3
O A:HOH382 3.0 25.2 0.3
N07 A:U8G205 3.1 23.2 0.3
N07 A:U8G205 3.1 25.6 0.2
N04 A:U8G205 3.2 26.6 0.2
C32 A:U8G205 3.3 23.6 0.3
C36 A:U8G205 3.5 25.0 0.2
C32 A:U8G205 3.6 26.9 0.2
CE A:LYS33 3.6 35.6 1.0
C36 A:U8G205 3.6 23.1 0.3
C42 A:U8G205 4.2 22.4 0.3
C40 A:U8G205 4.3 22.9 0.3
C40 A:U8G205 4.4 26.6 0.2
C42 A:U8G205 4.4 26.1 0.2
CD A:LYS33 4.8 32.3 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: Thu Oct 10 12:37:07 2024

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