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Chlorine in PDB 4j1a: X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal)

Enzymatic activity of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal)

All present enzymatic activity of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal), PDB code: 4j1a was solved by A.Vergara, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.84 / 1.79
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.189, 78.189, 37.157, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.7

Other elements in 4j1a:

The structure of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal) also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal) (pdb code 4j1a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal), PDB code: 4j1a:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4j1a

Go back to Chlorine Binding Sites List in 4j1a
Chlorine binding site 1 out of 3 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:21.9
occ:1.00
 OH A:TYR23 3.0 15.2 1.0
O A:HOH327 3.4 19.6 1.0
CZ A:TYR23 3.7 16.6 1.0
CE2 A:TYR23 3.8 16.4 1.0
CA A:GLY104 4.1 16.4 1.0
O A:ARG21 4.6 17.9 1.0
N A:GLY104 4.7 17.1 1.0
CE1 A:TYR23 4.9 16.5 1.0
CD2 A:TYR23 5.0 15.6 1.0

Chlorine binding site 2 out of 3 in 4j1a

Go back to Chlorine Binding Sites List in 4j1a
Chlorine binding site 2 out of 3 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:24.1
occ:1.00
 O A:HOH350 3.0 32.1 1.0
O A:HOH317 3.1 17.6 1.0
N A:THR69 3.1 18.3 1.0
O A:THR69 3.3 19.7 1.0
O A:HOH414 3.3 30.3 1.0
N A:ARG68 3.4 18.8 1.0
C A:GLY67 3.5 21.3 1.0
CA A:GLY67 3.6 17.5 1.0
C A:THR69 3.7 20.8 1.0
N A:GLY67 3.7 16.5 1.0
OG A:SER72 3.7 28.9 1.0
OD1 A:ASN65 3.8 17.3 1.0
CA A:THR69 3.9 19.7 1.0
C A:ARG68 4.1 19.3 1.0
O A:HOH322 4.1 18.8 1.0
CA A:ARG68 4.2 19.8 1.0
CB A:THR69 4.2 19.5 1.0
O A:GLY67 4.2 20.0 1.0
OD1 A:ASP66 4.2 15.2 1.0
N A:PRO70 4.5 22.4 1.0
OG1 A:THR69 4.7 16.8 1.0
NA A:NA203 4.7 23.7 1.0
C A:ASP66 4.8 15.7 1.0
O A:HOH328 4.8 14.3 0.5
N A:ASP66 4.9 13.6 1.0
CG A:ASN65 4.9 19.0 1.0

Chlorine binding site 3 out of 3 in 4j1a

Go back to Chlorine Binding Sites List in 4j1a
Chlorine binding site 3 out of 3 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Aziru (Green Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:33.8
occ:0.30
 RU A:RU204 2.6 39.8 0.3
O A:HOH303 2.9 36.0 0.3
N A:ILE88 3.3 20.1 1.0
OD2 A:ASP87 3.3 29.6 0.3
O A:HOH351 3.6 34.9 1.0
CG1 A:ILE88 3.7 15.8 1.0
O A:HOH302 3.7 36.9 0.3
CA A:ASP87 3.7 21.3 0.3
NE2 A:HIS15 3.7 27.9 1.0
OD1 A:ASP87 3.8 23.8 0.7
CG A:ASP87 3.9 24.8 0.3
CA A:ASP87 3.9 20.2 0.7
NH2 A:ARG14 4.0 28.3 0.7
C A:ASP87 4.1 20.2 0.3
C A:ASP87 4.1 19.0 0.7
CB A:ALA11 4.1 21.1 1.0
CB A:ASP87 4.2 23.2 0.3
CD2 A:HIS15 4.3 25.1 1.0
CB A:ILE88 4.3 16.7 1.0
CA A:ILE88 4.3 18.3 1.0
CG2 A:ILE88 4.3 16.6 1.0
O A:SER86 4.4 23.9 1.0
CG A:ASP87 4.5 24.4 0.7
CD1 A:ILE88 4.5 18.8 1.0
CZ A:PHE3 4.5 20.1 1.0
CB A:ASP87 4.7 22.6 0.7
OD1 A:ASP87 4.7 23.6 0.3
CE1 A:HIS15 4.9 26.6 1.0
N A:ASP87 4.9 21.5 0.3
N A:THR89 4.9 18.2 1.0
N A:ASP87 5.0 20.4 0.7
C A:ILE88 5.0 19.7 1.0

Reference:

A.Vergara, G.D'errico, D.Montesarchio, G.Mangiapia, L.Paduano, A.Merlino. Interaction of Anticancer Ruthenium Compounds with Proteins: High-Resolution X-Ray Structures and Raman Microscopy Studies of the Adduct Between Hen Egg White Lysozyme and Aziru. Inorg.Chem. V. 52 4157 2013.
ISSN: ISSN 0020-1669
PubMed: 23517183
DOI: 10.1021/IC4004142
Page generated: Sat Dec 12 10:47:21 2020

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