Chlorine 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
Rhenium (Re) 9 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 5 in 8qcu

Go back to Chlorine Binding Sites List in 8qcu
Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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:Cl201

b:24.7
occ:1.00
 H A:GLY26 2.4 18.7 1.0
HG A:SER24 2.7 26.1 1.0
HA A:GLN121 2.8 27.8 1.0
HA3 A:GLY26 3.0 18.3 1.0
HB2 A:SER24 3.0 23.8 1.0
OG A:SER24 3.1 21.8 1.0
N A:GLY26 3.2 15.6 1.0
HG23 A:VAL120 3.3 26.0 1.0
OE1 A:GLN121 3.4 46.4 1.0
HD11 A:ILE124 3.4 31.3 1.0
CB A:SER24 3.6 19.8 1.0
CA A:GLY26 3.6 15.2 1.0
CA A:GLN121 3.6 23.1 1.0
HG12 A:ILE124 3.7 29.8 1.0
HB2 A:GLN121 3.8 35.9 1.0
HD13 A:ILE124 3.8 31.3 1.0
N A:GLN121 3.9 20.8 1.0
CD A:GLN121 3.9 43.9 1.0
CD1 A:ILE124 3.9 26.1 1.0
CB A:GLN121 4.1 29.9 1.0
O A:VAL120 4.1 20.0 1.0
C A:VAL120 4.2 19.5 1.0
H A:LEU25 4.2 20.6 1.0
HA2 A:GLY26 4.2 18.3 1.0
HB3 A:SER24 4.2 23.8 1.0
N A:LEU25 4.2 17.1 1.0
H A:GLN121 4.2 24.9 1.0
CG2 A:VAL120 4.2 21.6 1.0
H A:ASN27 4.2 17.9 1.0
HB3 A:LEU25 4.3 21.7 1.0
CG1 A:ILE124 4.3 24.8 1.0
C A:SER24 4.4 16.7 1.0
C A:LEU25 4.4 16.2 1.0
HE22 A:GLN121 4.4 55.5 1.0
NE2 A:GLN121 4.4 46.3 1.0
HG21 A:VAL120 4.5 26.0 1.0
CA A:SER24 4.6 17.8 1.0
C A:GLY26 4.6 14.8 1.0
CG A:GLN121 4.6 37.9 1.0
HG23 A:ILE124 4.7 26.6 1.0
N A:ASN27 4.7 14.9 1.0
HB A:VAL120 4.7 24.2 1.0
CA A:LEU25 4.7 16.2 1.0
O A:SER24 4.8 17.3 1.0
HG22 A:VAL120 4.8 26.0 1.0
C A:GLN121 4.8 20.7 1.0
HD12 A:ILE124 4.8 31.3 1.0
HG13 A:ILE124 4.9 29.8 1.0
CB A:VAL120 4.9 20.2 1.0

Chlorine binding site 2 out of 5 in 8qcu

Go back to Chlorine Binding Sites List in 8qcu
Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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:Cl202

b:23.1
occ:1.00
 H A:THR69 2.4 21.8 1.0
HA2 A:GLY67 3.2 23.5 1.0
H A:GLY67 3.2 22.3 1.0
O A:HOH366 3.2 18.8 1.0
N A:THR69 3.2 18.1 1.0
O A:THR69 3.3 20.9 1.0
O A:HOH385 3.3 37.4 1.0
H A:ARG68 3.5 23.2 0.5
C A:GLY67 3.5 20.2 1.0
H A:ARG68 3.5 22.4 0.6
N A:ARG68 3.5 19.4 0.5
N A:ARG68 3.6 18.7 0.6
CA A:GLY67 3.6 19.5 1.0
C A:THR69 3.6 18.9 1.0
OD1 A:ASN65 3.6 22.9 1.0
HB A:THR69 3.7 21.1 1.0
N A:GLY67 3.7 18.6 1.0
OG A:SER72 3.7 29.1 1.0
CA A:THR69 3.9 18.3 1.0
O A:HOH368 4.0 33.1 1.0
O A:GLY67 4.1 22.5 1.0
CB A:THR69 4.2 17.6 1.0
C A:ARG68 4.3 19.4 0.6
C A:ARG68 4.3 19.9 0.5
HA A:PRO70 4.3 27.0 1.0
H A:ASP66 4.3 20.0 1.0
OD1 A:ASP66 4.3 16.7 1.0
CA A:ARG68 4.4 18.3 0.6
CA A:ARG68 4.4 19.4 0.5
N A:PRO70 4.4 19.8 1.0
HA A:ARG68 4.5 22.0 0.6
HG1 A:THR69 4.5 20.0 1.0
HA3 A:GLY67 4.5 23.5 1.0
HA A:ARG68 4.5 23.3 0.5
H A:SER72 4.6 35.1 1.0
NA A:NA205 4.8 21.8 1.0
HA A:THR69 4.8 21.9 1.0
C A:ASP66 4.8 17.8 1.0
CA A:PRO70 4.8 22.5 1.0
CG A:ASN65 4.8 21.6 1.0
HB3 A:SER72 4.8 35.6 1.0
O A:HOH317 4.9 28.2 0.5
OG1 A:THR69 4.9 16.6 1.0
CB A:SER72 4.9 29.6 1.0
HA A:ASN65 4.9 21.4 1.0
N A:ASP66 5.0 16.6 1.0

Chlorine binding site 3 out of 5 in 8qcu

Go back to Chlorine Binding Sites List in 8qcu
Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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:Cl203

b:40.4
occ:1.00
 HD22 A:ASN65 2.5 29.6 1.0
HB3 A:PRO79 2.8 24.6 1.0
HB3 A:ASN65 3.0 23.8 1.0
O A:HOH382 3.0 32.5 1.0
HA A:PRO79 3.2 23.0 1.0
ND2 A:ASN65 3.3 24.7 1.0
CB A:PRO79 3.6 20.5 1.0
HD3 A:PRO79 3.7 26.9 1.0
CA A:PRO79 3.7 19.1 1.0
HD21 A:ASN65 3.8 29.6 1.0
CB A:ASN65 3.9 19.8 1.0
N A:PRO79 3.9 21.1 1.0
CG A:ASN65 4.1 21.6 1.0
CD A:PRO79 4.2 22.4 1.0
HG3 A:PRO79 4.3 28.1 1.0
CG A:PRO79 4.3 23.4 1.0
O A:ASN65 4.3 17.9 1.0
HB2 A:ASN65 4.3 23.8 1.0
HB2 A:PRO79 4.4 24.6 1.0
HD21 A:ASN74 4.4 28.0 1.0
C A:ILE78 4.5 21.2 0.7
O A:ILE78 4.6 20.6 0.7
C A:ILE78 4.6 21.4 0.3
HD22 A:ASN74 4.8 28.0 1.0
H A:ASN65 4.9 21.9 1.0
ND2 A:ASN74 4.9 23.3 1.0
O A:ILE78 4.9 21.0 0.3
C A:ASN65 4.9 17.4 1.0
CA A:ASN65 5.0 17.8 1.0

Chlorine binding site 4 out of 5 in 8qcu

Go back to Chlorine Binding Sites List in 8qcu
Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl 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:Cl204

b:40.6
occ:1.00
 HH11 A:ARG68 2.3 20.4 0.6
HH11 A:ARG68 2.3 24.9 0.5
HD2 A:ARG68 3.0 23.5 0.5
NH1 A:ARG68 3.0 17.0 0.6
NH1 A:ARG68 3.1 20.7 0.5
O A:HOH391 3.1 42.2 1.0
HD3 A:ARG68 3.2 21.3 0.6
HD2 A:ARG68 3.2 21.3 0.6
HH12 A:ARG68 3.3 20.4 0.6
HH12 A:ARG68 3.4 24.9 0.5
CD A:ARG68 3.6 17.8 0.6
HH12 A:ARG45 3.9 29.7 0.5
CD A:ARG68 4.0 19.6 0.5
CZ A:ARG68 4.1 17.6 0.6
CZ A:ARG68 4.2 19.5 0.5
HD3 A:ARG68 4.2 23.5 0.5
NE A:ARG68 4.3 17.6 0.6
HH12 A:ARG45 4.4 28.9 0.5
HH22 A:ARG45 4.4 28.6 0.5
NE A:ARG68 4.5 19.6 0.5
NH1 A:ARG45 4.6 24.8 0.5
HB3 A:ARG68 4.6 23.8 0.5
HB2 A:ARG68 4.6 23.8 0.5
HB2 A:ARG68 4.6 21.4 0.6
HB3 A:ARG68 4.6 21.4 0.6
HH11 A:ARG45 4.8 29.7 0.5
CG A:ARG68 4.9 17.2 0.6
CB A:ARG68 4.9 19.8 0.5
CB A:ARG68 4.9 17.8 0.6
CG A:ARG68 5.0 19.9 0.5
HH22 A:ARG45 5.0 30.1 0.5

Chlorine binding site 5 out of 5 in 8qcu

Go back to Chlorine Binding Sites List in 8qcu
Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl 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:Cl216

b:40.5
occ:1.00
 HE2 A:PHE38 2.9 22.2 1.0
HZ2 A:LYS33 3.0 33.0 1.0
HZ3 A:TRP123 3.1 28.9 1.0
HB2 A:ARG5 3.4 29.4 1.0
HD3 A:ARG5 3.4 32.2 1.0
HD3 A:LYS33 3.6 26.9 1.0
CE2 A:PHE38 3.8 18.5 1.0
NZ A:LYS33 3.9 27.5 1.0
HE2 A:LYS33 4.0 30.5 1.0
CZ3 A:TRP123 4.0 24.0 1.0
HZ3 A:LYS33 4.2 33.0 1.0
CE A:LYS33 4.3 25.4 1.0
CB A:ARG5 4.3 24.5 1.0
HZ A:PHE38 4.3 21.9 1.0
CD A:ARG5 4.3 26.8 1.0
CD A:LYS33 4.4 22.4 1.0
HE A:ARG5 4.4 33.1 1.0
HZ1 A:LYS33 4.4 33.0 1.0
CZ A:PHE38 4.5 18.2 1.0
HB3 A:ARG5 4.6 29.4 1.0
HD2 A:PHE38 4.6 22.7 1.0
HH2 A:TRP123 4.7 29.6 1.0
CD2 A:PHE38 4.7 18.9 1.0
HE3 A:TRP123 4.7 26.0 1.0
CG A:ARG5 4.8 25.1 1.0
NE A:ARG5 4.8 27.6 1.0
CH2 A:TRP123 4.9 24.7 1.0
CE3 A:TRP123 4.9 21.7 1.0
H A:ARG5 4.9 26.8 1.0
HG3 A:ARG5 4.9 30.1 1.0
HD2 A:LYS33 4.9 26.9 1.0
HD2 A:ARG5 4.9 32.2 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: Tue Jul 30 11:54:43 2024

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