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Rhenium 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:

Sodium (Na) 1 atom
Bromine (Br) 1 atom
Chlorine (Cl) 5 atoms

Rhenium Binding Sites:

The binding sites of Rhenium 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 Rhenium atom.
In total 9 binding sites of Rhenium where determined in the Lysozyme Covalently Bound to Fac-[Re(Co)3-Imidazole] Complex, Incubated For 38 Weeks., PDB code: 8qcu:
Jump to Rhenium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Rhenium binding site 1 out of 9 in 8qcu

Go back to Rhenium Binding Sites List in 8qcu
Rhenium binding site 1 out of 9 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 Rhenium with other atoms in the Re 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:Re206

b:23.5
occ:0.43
 RE A:VHL206 0.0 23.5 0.4
C1 A:VHL206 1.9 22.8 0.4
C3 A:VHL206 1.9 25.6 0.4
C2 A:VHL206 1.9 24.6 0.4
N3 A:VHL206 2.2 22.8 0.4
N1 A:VHL206 2.2 23.4 0.4
OD2 A:ASP101 2.2 27.9 0.8
OD2 A:ASP101 2.2 24.8 0.2
CG A:ASP101 2.9 29.4 0.8
O3 A:VHL206 3.0 26.3 0.4
O1 A:VHL206 3.1 23.9 0.4
O2 A:VHL206 3.1 26.2 0.4
OD1 A:ASP101 3.1 32.8 0.8
C4 A:VHL206 3.1 22.0 0.4
C7 A:VHL206 3.1 24.6 0.4
C9 A:VHL206 3.2 24.9 0.4
C6 A:VHL206 3.2 22.5 0.4
H41 A:VHL206 3.3 26.4 0.4
H71 A:VHL206 3.3 29.5 0.4
H91 A:VHL206 3.4 29.9 0.4
CG A:ASP101 3.4 26.6 0.2
H61 A:VHL206 3.4 27.0 0.4
OD1 A:ASP101 4.0 27.9 0.2
HD12 A:LEU75 4.0 30.8 1.0
HH2 A:TRP63 4.0 24.2 1.0
HD13 A:LEU75 4.1 30.8 1.0
N4 A:VHL206 4.3 26.0 0.4
N2 A:VHL206 4.3 21.1 0.4
C8 A:VHL206 4.3 25.9 0.4
C5 A:VHL206 4.3 21.9 0.4
CB A:ASP101 4.4 27.2 0.8
HB2 A:ASP101 4.4 30.9 0.2
CD1 A:LEU75 4.5 25.7 1.0
CB A:ASP101 4.5 25.7 0.2
HB3 A:ASP101 4.5 32.7 0.8
HB2 A:ASP101 4.7 32.7 0.8
CH2 A:TRP63 4.7 20.1 1.0
HD11 A:LEU75 5.0 30.8 1.0

Rhenium binding site 2 out of 9 in 8qcu

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Rhenium binding site 2 out of 9 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 Rhenium with other atoms in the Re binding site number 2 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:Re207

b:34.0
occ:0.84
 RE A:REI207 0.0 34.0 0.8
C1 A:REI207 1.9 36.2 0.8
C3 A:REI207 1.9 31.3 0.8
C2 A:REI207 1.9 31.9 0.8
N1 A:REI207 2.2 36.3 0.8
OW A:REI207 2.2 34.6 0.8
NE2 A:HIS15 2.2 31.4 1.0
O3 A:REI207 3.0 32.6 0.8
O2 A:REI207 3.0 33.4 0.8
O1 A:REI207 3.0 37.2 0.8
CE1 A:HIS15 3.1 31.0 1.0
C5 A:REI207 3.2 37.9 0.8
C6 A:REI207 3.2 37.6 0.8
CD2 A:HIS15 3.2 30.1 1.0
HE1 A:HIS15 3.2 37.2 1.0
H5 A:REI207 3.3 45.5 0.8
H6 A:REI207 3.4 45.1 0.8
HD2 A:HIS15 3.4 36.1 1.0
OD2 A:ASP87 3.8 31.7 1.0
ND1 A:HIS15 4.2 30.1 1.0
HD3 A:ARG14 4.2 58.1 1.0
N2 A:REI207 4.3 38.9 0.8
CG A:HIS15 4.3 28.4 1.0
C7 A:REI207 4.3 38.1 0.8
HG1 A:THR89 4.4 33.5 1.0
HG12 A:ILE88 4.4 28.5 1.0
HG2 A:ARG14 4.6 51.0 1.0
H A:ILE88 4.6 29.3 1.0
HB3 A:ARG14 4.7 42.1 1.0
CG A:ASP87 4.7 31.7 1.0
HB1 A:ALA11 4.8 27.6 1.0
OG1 A:THR89 4.8 27.9 1.0
HG13 A:ILE88 4.9 28.5 1.0
HD1 A:HIS15 4.9 36.1 1.0
OD1 A:ASP87 5.0 35.0 1.0

Rhenium binding site 3 out of 9 in 8qcu

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Rhenium binding site 3 out of 9 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 Rhenium with other atoms in the Re binding site number 3 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:Re208

b:21.4
occ:0.53
 RE A:VHL208 0.0 21.4 0.5
C1 A:VHL208 1.9 22.5 0.5
C3 A:VHL208 1.9 21.0 0.5
C2 A:VHL208 1.9 21.4 0.5
N3 A:VHL208 2.2 21.9 0.5
N1 A:VHL208 2.2 23.0 0.5
OD2 A:ASP119 2.3 25.9 1.0
O3 A:VHL208 3.0 22.4 0.5
O1 A:VHL208 3.0 23.9 0.5
O2 A:VHL208 3.1 23.8 0.5
CG A:ASP119 3.1 24.3 1.0
C7 A:VHL208 3.2 23.2 0.5
C4 A:VHL208 3.2 24.5 0.5
C9 A:VHL208 3.2 23.8 0.5
C6 A:VHL208 3.2 24.7 0.5
H41 A:VHL208 3.3 29.4 0.5
H71 A:VHL208 3.3 27.9 0.5
OD1 A:ASP119 3.4 25.5 1.0
H61 A:VHL208 3.4 29.6 0.5
H91 A:VHL208 3.4 28.6 0.5
HB3 A:GLN121 4.0 35.9 1.0
O A:HOH306 4.0 33.5 1.0
N2 A:VHL208 4.3 25.4 0.5
N4 A:VHL208 4.3 24.4 0.5
C5 A:VHL208 4.3 25.0 0.5
C8 A:VHL208 4.3 23.9 0.5
CB A:ASP119 4.5 21.2 1.0
HG2 A:GLN121 4.6 45.5 1.0
HB2 A:ASP119 4.7 25.4 1.0
HB2 A:ALA122 4.8 26.2 1.0
HB3 A:ASP119 4.8 25.4 1.0
CB A:GLN121 4.9 29.9 1.0
H A:ALA122 4.9 23.4 1.0

Rhenium binding site 4 out of 9 in 8qcu

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Rhenium binding site 4 out of 9 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 Rhenium with other atoms in the Re binding site number 4 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:Re210

b:32.4
occ:0.17
 OD2 A:ASP18 2.1 29.6 1.0
HZ1 A:LYS13 2.8 50.6 1.0
HZ3 A:LYS13 2.8 50.6 1.0
CG A:ASP18 3.1 27.1 1.0
NZ A:LYS13 3.3 42.2 1.0
OD1 A:ASP18 3.4 27.0 1.0
HZ2 A:LYS13 3.9 50.6 1.0
HB2 A:LEU25 4.2 21.7 1.0
HE2 A:LYS13 4.4 46.2 1.0
CB A:ASP18 4.4 24.4 1.0
CE A:LYS13 4.4 38.5 1.0
HD22 A:LEU25 4.4 22.9 1.0
HB2 A:ASP18 4.5 29.4 1.0
HB3 A:LEU25 4.6 21.7 1.0
HD12 A:ILE124 4.6 31.3 1.0
HD2 A:LYS13 4.6 40.4 1.0
HB3 A:ASP18 4.7 29.4 1.0
H A:LEU25 4.7 20.6 1.0
HD13 A:ILE124 4.7 31.3 1.0
HD11 A:ILE124 4.8 31.3 1.0
HD23 A:LEU25 4.8 22.9 1.0
CB A:LEU25 4.9 18.1 1.0
OD1 A:ASN19 4.9 26.5 0.5
CD1 A:ILE124 4.9 26.1 1.0
HG3 A:LYS13 5.0 34.6 1.0

Rhenium binding site 5 out of 9 in 8qcu

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Rhenium binding site 5 out of 9 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 Rhenium with other atoms in the Re binding site number 5 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:Re211

b:34.2
occ:0.21
 OXT A:LEU129 3.8 41.2 1.0
HD3 A:LYS13 3.9 40.4 1.0
HE3 A:LYS13 4.5 46.2 1.0
HG2 A:LYS13 4.6 34.6 1.0
C A:LEU129 4.7 40.1 1.0
HB3 A:LYS13 4.8 29.6 1.0
CD A:LYS13 4.8 33.7 1.0
HA A:LEU129 5.0 44.2 1.0

Rhenium binding site 6 out of 9 in 8qcu

Go back to Rhenium Binding Sites List in 8qcu
Rhenium binding site 6 out of 9 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 Rhenium with other atoms in the Re binding site number 6 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:Re212

b:20.6
occ:0.10
 BR A:BR217 3.3 24.6 0.2
HD2 A:ARG14 3.5 58.1 1.0
O2 A:REI207 4.0 33.4 0.8
HD3 A:ARG14 4.0 58.1 1.0
HE A:ARG14 4.1 62.6 1.0
CD A:ARG14 4.2 48.4 1.0
C2 A:REI207 4.6 31.9 0.8
NE A:ARG14 4.6 52.2 1.0
O1 A:REI207 4.9 37.2 0.8

Rhenium binding site 7 out of 9 in 8qcu

Go back to Rhenium Binding Sites List in 8qcu
Rhenium binding site 7 out of 9 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 Rhenium with other atoms in the Re binding site number 7 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:Re213

b:20.8
occ:0.23
 HH A:TYR23 2.4 19.8 1.0
OH A:TYR23 3.1 16.5 1.0
HE2 A:TYR23 3.2 18.4 1.0
O A:HOH336 3.3 22.9 1.0
HA3 A:GLY104 3.3 18.3 1.0
CE2 A:TYR23 3.7 15.4 1.0
CZ A:TYR23 3.7 15.6 1.0
HA2 A:GLY104 4.0 18.3 1.0
CA A:GLY104 4.1 15.2 1.0
O A:ARG21 4.5 20.1 1.0
N A:GLY104 4.7 16.6 1.0
HE A:ARG21 4.7 50.8 1.0
HH21 A:ARG21 4.7 56.7 1.0
H A:MET105 4.8 17.2 1.0
H A:GLY104 4.8 19.9 1.0
CD2 A:TYR23 4.9 15.0 1.0
HB3 A:ARG21 4.9 29.6 1.0
CE1 A:TYR23 5.0 15.1 1.0

Rhenium binding site 8 out of 9 in 8qcu

Go back to Rhenium Binding Sites List in 8qcu
Rhenium binding site 8 out of 9 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 Rhenium with other atoms in the Re binding site number 8 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:Re214

b:101.9
occ:0.26
 HN1 A:IMD209 2.0 121.4 1.0
H21 A:VHL208 2.0 30.4 0.5
O A:HOH383 2.5 26.8 1.0
N2 A:VHL208 2.8 25.4 0.5
N1 A:IMD209 2.8 101.2 1.0
H41 A:VHL208 3.1 29.4 0.5
H2 A:IMD209 3.2 55.3 1.0
C4 A:VHL208 3.3 24.5 0.5
C2 A:IMD209 3.4 46.0 1.0
C5 A:IMD209 4.0 72.7 1.0
C5 A:VHL208 4.0 25.0 0.5
HA A:ASP119 4.3 23.7 1.0
H5 A:IMD209 4.3 87.2 1.0
H51 A:VHL208 4.4 30.0 0.5
N1 A:VHL208 4.6 23.0 0.5
N3 A:IMD209 4.6 74.0 1.0
HB2 A:GLN121 4.7 35.9 1.0
OD1 A:ASP119 4.9 25.5 1.0
H A:GLN121 4.9 24.9 1.0
C6 A:VHL208 4.9 24.7 0.5
C4 A:IMD209 4.9 56.4 1.0

Rhenium binding site 9 out of 9 in 8qcu

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Rhenium binding site 9 out of 9 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 Rhenium with other atoms in the Re binding site number 9 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:Re215

b:33.0
occ:0.13
 HD3 A:ARG61 3.0 45.0 1.0
O A:PRO70 3.3 29.1 1.0
HE A:ARG61 3.6 47.6 1.0
CD A:ARG61 3.7 37.5 1.0
NE A:ARG61 3.9 39.6 1.0
HD2 A:ARG61 4.0 45.0 1.0
HG22 A:THR69 4.1 21.7 1.0
C A:PRO70 4.5 25.6 1.0
HA3 A:GLY71 4.8 36.0 1.0
CG2 A:THR69 4.9 18.1 1.0
HG2 A:ARG61 4.9 41.0 1.0
HB3 A:SER72 4.9 35.6 1.0
CG A:ARG61 4.9 34.1 1.0
HG21 A:THR69 4.9 21.7 1.0
CZ A:ARG61 4.9 39.1 1.0
O A:ASP48 5.0 29.1 1.0
HB2 A:ARG61 5.0 34.2 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: Thu Oct 10 12:29:12 2024

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