Atomistry » Chlorine » PDB 7bab-7bhk » 7bdm
Atomistry »
  Chlorine »
    PDB 7bab-7bhk »
      7bdm »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy