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Chlorine in PDB 7bdm: The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.

Enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.

All present enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.:
3.2.1.17;

Protein crystallography data

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours., PDB code: 7bdm was solved by L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.93 / 1.07
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.022, 79.022, 37.567, 90, 90, 90
R / Rfree (%) 17 / 20.1

Other elements in 7bdm:

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Ruthenium (Ru) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. (pdb code 7bdm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours., PDB code: 7bdm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7bdm

Go back to Chlorine Binding Sites List in 7bdm
Chlorine binding site 1 out of 6 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:17.0
occ:0.79
 OH A:TYR23 3.0 15.2 1.0
O A:HOH346 3.2 19.3 1.0
CZ A:TYR23 3.7 14.9 1.0
CE2 A:TYR23 3.7 14.9 1.0
CA A:GLY104 4.2 15.7 1.0
O A:ARG21 4.6 18.8 1.0
N A:GLY104 4.8 16.2 1.0
CE1 A:TYR23 4.9 14.7 1.0
CD2 A:TYR23 4.9 14.8 1.0

Chlorine binding site 2 out of 6 in 7bdm

Go back to Chlorine Binding Sites List in 7bdm
Chlorine binding site 2 out of 6 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:81.5
occ:0.93
 NH1 A:ARG14 3.0 38.7 0.8
CZ A:ARG14 3.9 37.8 0.8
NH2 A:ARG14 4.1 38.8 0.8

Chlorine binding site 3 out of 6 in 7bdm

Go back to Chlorine Binding Sites List in 7bdm
Chlorine binding site 3 out of 6 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:80.5
occ:0.99
 O A:HOH423 3.1 26.6 1.0
CG2 A:THR118 3.9 20.5 1.0
O A:HOH364 4.8 40.8 1.0
CB A:THR118 4.8 20.4 1.0

Chlorine binding site 4 out of 6 in 7bdm

Go back to Chlorine Binding Sites List in 7bdm
Chlorine binding site 4 out of 6 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:91.4
occ:0.92
 NH1 A:ARG112 2.5 38.8 1.0
ND2 A:ASN113 2.8 17.7 1.0
CD A:ARG112 3.3 30.3 1.0
CG A:ARG112 3.6 25.9 1.0
CZ A:ARG112 3.6 37.5 1.0
CG A:ASN113 3.8 17.9 1.0
NE A:ARG112 3.9 33.9 1.0
OD1 A:ASN113 4.1 18.8 1.0
CB A:ARG112 4.3 21.4 1.0
NH2 A:ARG112 4.8 37.9 1.0

Chlorine binding site 5 out of 6 in 7bdm

Go back to Chlorine Binding Sites List in 7bdm
Chlorine binding site 5 out of 6 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:23.0
occ:1.00
 O A:HOH366 3.2 17.1 1.0
N A:THR69 3.2 19.4 1.0
O A:THR69 3.2 20.8 1.0
O A:HOH404 3.4 50.0 1.0
O A:HOH342 3.5 38.0 1.0
N A:ARG68 3.5 19.3 1.0
C A:THR69 3.6 20.2 1.0
C A:GLY67 3.6 20.6 1.0
OD1 A:ASN65 3.7 20.0 1.0
CA A:GLY67 3.7 19.9 1.0
N A:GLY67 3.7 18.2 1.0
OG A:SER72 3.8 21.9 1.0
CA A:THR69 3.8 18.4 1.0
O A:HOH382 4.0 20.5 1.0
CB A:THR69 4.2 17.7 1.0
C A:ARG68 4.2 20.8 1.0
O A:GLY67 4.3 22.9 1.0
OD1 A:ASP66 4.3 15.6 1.0
N A:PRO70 4.3 20.9 1.0
CA A:ARG68 4.3 20.4 1.0
NA A:NA201 4.7 14.9 0.7
CA A:PRO70 4.8 22.8 1.0
C A:ASP66 4.8 17.4 1.0
OG1 A:THR69 4.8 17.4 1.0
CG A:ASN65 4.9 19.1 1.0
N A:ASP66 4.9 14.8 1.0

Chlorine binding site 6 out of 6 in 7bdm

Go back to Chlorine Binding Sites List in 7bdm
Chlorine binding site 6 out of 6 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:60.0
occ:0.50
 NE1 A:TRP108 3.3 15.4 1.0
O A:HOH320 3.5 34.5 1.0
O A:GLN57 3.6 14.8 1.0
CD1 A:TRP108 3.7 15.2 1.0
CE2 A:TRP108 3.9 13.8 1.0
CA A:ILE58 4.0 13.4 1.0
O A:LEU56 4.2 15.5 1.0
O A:ALA107 4.2 18.4 1.0
C A:GLN57 4.3 13.4 1.0
CG A:TRP108 4.3 13.7 1.0
O A:HOH374 4.3 40.8 1.0
CD1 A:ILE98 4.3 16.3 1.0
N A:ASN59 4.4 13.6 1.0
CD2 A:TRP108 4.5 13.8 1.0
CZ2 A:TRP108 4.5 14.4 1.0
N A:ILE58 4.5 13.4 1.0
O A:HOH388 4.5 40.5 1.0
CG1 A:ILE58 4.6 16.6 1.0
C A:ILE58 4.7 13.1 1.0
C A:ALA107 4.7 16.4 1.0
CB A:ILE58 4.8 15.0 1.0
CG2 A:ILE98 4.8 16.0 1.0
O A:HOH375 4.9 35.7 1.0
CB A:ASN59 5.0 17.9 1.0
NE1 A:TRP63 5.0 18.0 1.0
CB A:ALA107 5.0 18.0 1.0
CD1 A:TRP63 5.0 16.8 1.0

Reference:

L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou. Insights Into the Protein Ruthenation Mechanism By Antimetastatic Metallodrugs: High-Resolution X-Ray Structures of the Adduct Formed Between Hen Egg-White Lysozyme and Nami-A at Various Time Points. Inorg.Chem. V. 60 10729 2021.
ISSN: ISSN 0020-1669
PubMed: 34197115
DOI: 10.1021/ACS.INORGCHEM.1C01441
Page generated: Mon Jul 29 19:05:06 2024

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