Chlorine in PDB 6ro3: 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf

Enzymatic activity of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf

All present enzymatic activity of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf:
3.2.1.17;

Protein crystallography data

The structure of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf, PDB code: 6ro3 was solved by A.Brink, J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.97 / 1.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.940, 79.940, 36.460, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 11.8

Other elements in 6ro3:

The structure of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf also contains other interesting chemical elements:

Rhenium (Re) 16 atoms
Bromine (Br) 1 atom
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf (pdb code 6ro3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf, PDB code: 6ro3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6ro3

Go back to Chlorine Binding Sites List in 6ro3
Chlorine binding site 1 out of 4 in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:9.7
occ:1.00
OH A:TYR23 3.0 7.3 1.0
O A:HOH344 3.4 15.3 1.0
CE2 A:TYR23 3.7 6.9 1.0
CZ A:TYR23 3.7 7.0 1.0
CA A:GLY104 4.1 8.5 1.0
N A:GLY104 4.7 9.3 1.0
O A:HOH310 4.7 18.0 1.0
O A:ARG21 4.8 11.3 1.0
CD2 A:TYR23 4.9 6.8 1.0
CE1 A:TYR23 4.9 7.0 1.0

Chlorine binding site 2 out of 4 in 6ro3

Go back to Chlorine Binding Sites List in 6ro3
Chlorine binding site 2 out of 4 in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:8.3
occ:1.00
O A:HOH409 3.1 21.4 1.0
O A:HOH340 3.2 7.3 1.0
O A:HOH374 3.2 13.1 1.0
O A:THR69 3.3 7.1 1.0
N A:THR69 3.4 6.8 1.0
CA A:GLY67 3.5 8.3 1.0
C A:GLY67 3.6 8.6 1.0
N A:GLY67 3.6 7.3 1.0
OD1 A:ASN65 3.6 9.1 1.0
N A:ARG68 3.6 7.3 1.0
C A:THR69 3.6 6.9 1.0
OG A:SER72 3.6 7.0 1.0
O A:HOH346 3.8 15.4 1.0
O A:HOH359 3.9 10.1 1.0
CA A:THR69 4.0 6.4 1.0
O A:GLY67 4.2 10.1 1.0
N A:PRO70 4.3 7.4 1.0
OD1 A:ASP66 4.3 6.3 1.0
CB A:THR69 4.3 6.2 1.0
C A:ARG68 4.4 6.7 1.0
O A:HOH417 4.4 24.7 1.0
CA A:ARG68 4.5 7.1 1.0
CA A:PRO70 4.5 7.9 1.0
O A:HOH382 4.6 14.7 1.0
C A:ASP66 4.7 6.8 1.0
O A:HOH364 4.7 10.4 0.5
NA A:NA204 4.8 6.7 1.0
CG A:ASN65 4.8 8.3 1.0
N A:ASP66 4.8 6.3 1.0
CB A:SER72 4.9 7.0 1.0
OG1 A:THR69 5.0 6.2 1.0

Chlorine binding site 3 out of 4 in 6ro3

Go back to Chlorine Binding Sites List in 6ro3
Chlorine binding site 3 out of 4 in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:24.9
occ:1.00
O A:HOH418 2.8 30.6 1.0
O A:HOH396 3.0 15.3 1.0
ND2 A:ASN65 3.2 9.3 1.0
CA A:PRO79 3.7 7.8 1.0
CB A:PRO79 3.7 9.3 1.0
CB A:ASN65 3.8 7.6 1.0
N A:PRO79 3.8 8.1 1.0
CG A:ASN65 4.0 8.3 1.0
CD A:PRO79 4.2 9.4 1.0
O A:ASN65 4.3 6.7 1.0
C A:ILE78 4.3 8.0 1.0
CG A:PRO79 4.4 10.6 1.0
O A:ILE78 4.5 8.2 1.0
ND2 A:ASN74 4.7 9.0 1.0
CA A:ASN65 4.9 6.3 1.0
C A:ASN65 4.9 6.1 1.0

Chlorine binding site 4 out of 4 in 6ro3

Go back to Chlorine Binding Sites List in 6ro3
Chlorine binding site 4 out of 4 in the 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 2YR-X: Lysozyme with Re Cluster 2 Year on Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:14.5
occ:0.75
O A:HOH415 2.9 18.6 1.0
N A:GLY26 3.0 6.8 1.0
OG A:SER24 3.2 11.4 1.0
CA A:GLN121 3.5 14.3 1.0
CA A:GLY26 3.5 7.0 1.0
CB A:SER24 3.5 9.5 1.0
CB A:GLN121 3.9 16.5 1.0
CD1 A:ILE124 3.9 11.8 1.0
N A:LEU25 3.9 7.1 1.0
N A:GLN121 3.9 12.4 1.0
C A:LEU25 4.1 6.9 1.0
C A:SER24 4.2 7.5 1.0
O A:VAL120 4.2 10.2 1.0
CG A:GLN121 4.2 16.8 0.0
C A:VAL120 4.3 10.8 1.0
O A:HOH308 4.4 11.5 1.0
CG1 A:ILE124 4.4 11.2 1.0
CA A:LEU25 4.4 7.2 1.0
CA A:SER24 4.5 8.1 1.0
CG2 A:VAL120 4.6 12.4 1.0
C A:GLY26 4.6 6.5 1.0
CB A:LEU25 4.6 8.2 1.0
C A:GLN121 4.6 13.7 1.0
O A:SER24 4.7 8.0 1.0
N A:ASN27 4.7 6.6 1.0
O A:GLN121 4.8 14.3 1.0
CG2 A:ILE124 4.9 10.1 1.0

Reference:

A.Brink, J.R.Helliwell. Formation of A Highly Dense Tetra-Rhenium Cluster in A Protein Crystal and Its Implications in Medical Imaging. Iucrj V. 6 695 2019.
ISSN: ESSN 2052-2525
PubMed: 31316813
DOI: 10.1107/S2052252519006651
Page generated: Sat Dec 12 13:37:12 2020

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