Atomistry » Rhodium » PDB 165d-8oqd » 6wrm
Atomistry »
  Rhodium »
    PDB 165d-8oqd »
      6wrm »

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

Last articles

Zn in 4LK0
Zn in 4LJZ
Zn in 4LJO
Zn in 4LJN
Zn in 4LJP
Zn in 4LIM
Zn in 4LFY
Zn in 4LGR
Zn in 4LI8
Zn in 4LIK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy