Chlorine in PDB 7q0v: Lysozyme Soaked with V(IV)OSO4 and Phen

Enzymatic activity of Lysozyme Soaked with V(IV)OSO4 and Phen

All present enzymatic activity of Lysozyme Soaked with V(IV)OSO4 and Phen:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Soaked with V(IV)OSO4 and Phen, PDB code: 7q0v was solved by M.F.A.Santos, A.C.P.Fernandes, I.Correia, G.Sciortino, E.Garribba, T.Santos-Silva, J.C.Pessoa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.84 / 1.12
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.68, 77.68, 37.757, 90, 90, 90
R / Rfree (%) 14.7 / 17.6

Other elements in 7q0v:

The structure of Lysozyme Soaked with V(IV)OSO4 and Phen also contains other interesting chemical elements:

Vanadium (V) 4 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lysozyme Soaked with V(IV)OSO4 and Phen (pdb code 7q0v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Lysozyme Soaked with V(IV)OSO4 and Phen, PDB code: 7q0v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7q0v

Go back to Chlorine Binding Sites List in 7q0v
Chlorine binding site 1 out of 6 in the Lysozyme Soaked with V(IV)OSO4 and Phen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme Soaked with V(IV)OSO4 and Phen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:18.3
occ:0.80
 O A:HOH358 3.1 13.8 1.0
O A:HOH418 3.1 31.5 1.0
O A:HOH404 3.2 30.7 1.0
O A:HOH355 3.3 30.0 1.0
N A:THR69 3.3 15.1 1.0
O A:THR69 3.3 16.6 1.0
C A:THR69 3.6 15.2 1.0
CA A:GLY67 3.6 16.9 1.0
N A:ARG68 3.6 15.3 1.0
C A:GLY67 3.6 16.6 1.0
OD1 A:ASN65 3.7 15.8 1.0
N A:GLY67 3.7 14.9 1.0
OG A:SER72 3.7 16.3 1.0
CA A:THR69 3.9 14.6 1.0
O A:HOH386 4.0 17.9 1.0
CB A:THR69 4.2 14.2 1.0
O A:GLY67 4.3 19.6 1.0
N A:PRO70 4.3 16.7 1.0
OD1 A:ASP66 4.3 12.7 1.0
O A:HOH437 4.3 30.0 1.0
C A:ARG68 4.3 16.1 1.0
CA A:ARG68 4.3 15.3 0.5
CA A:ARG68 4.4 16.3 0.5
NA A:NA207 4.7 16.3 1.0
CA A:PRO70 4.8 18.1 1.0
C A:ASP66 4.8 13.5 1.0
CG A:ASN65 4.8 16.1 1.0
OG1 A:THR69 4.9 13.7 1.0
CB A:SER72 4.9 16.4 1.0
N A:ASP66 4.9 11.8 1.0
O A:HOH402 5.0 45.1 1.0

Chlorine binding site 2 out of 6 in 7q0v

Go back to Chlorine Binding Sites List in 7q0v
Chlorine binding site 2 out of 6 in the Lysozyme Soaked with V(IV)OSO4 and Phen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme Soaked with V(IV)OSO4 and Phen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:21.4
occ:1.00
 O A:HOH396 3.0 30.0 1.0
OG A:SER24 3.0 17.9 1.0
N A:GLY26 3.1 12.4 1.0
CA A:GLY26 3.5 12.4 1.0
CB A:SER24 3.5 15.4 1.0
CA A:GLN121 3.6 18.4 1.0
CB A:GLN121 3.9 20.8 1.0
CD1 A:ILE124 3.9 23.2 1.0
N A:GLN121 3.9 17.9 1.0
CG A:GLN121 4.1 25.3 1.0
N A:LEU25 4.2 13.7 1.0
CG2 A:VAL120 4.3 16.9 1.0
C A:VAL120 4.3 16.0 1.0
C A:LEU25 4.3 12.3 1.0
C A:SER24 4.3 13.7 1.0
CG1 A:ILE124 4.3 20.2 1.0
O A:VAL120 4.3 16.2 1.0
CA A:SER24 4.5 14.1 1.0
C A:GLY26 4.5 13.6 1.0
N A:ASN27 4.6 12.5 1.0
CA A:LEU25 4.7 12.9 1.0
O A:SER24 4.7 14.1 1.0
C A:GLN121 4.8 17.4 1.0

Chlorine binding site 3 out of 6 in 7q0v

Go back to Chlorine Binding Sites List in 7q0v
Chlorine binding site 3 out of 6 in the Lysozyme Soaked with V(IV)OSO4 and Phen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme Soaked with V(IV)OSO4 and Phen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:18.3
occ:1.00
 OH A:TYR23 3.0 12.0 1.0
O A:HOH342 3.3 29.2 1.0
O A:HOH337 3.3 19.6 1.0
CE2 A:TYR23 3.6 11.2 1.0
CZ A:TYR23 3.7 11.1 1.0
CA A:GLY104 4.1 14.7 1.0
O A:ARG21 4.5 17.8 1.0
N A:GLY104 4.7 17.5 1.0
CD2 A:TYR23 4.9 11.3 1.0
CE1 A:TYR23 5.0 10.9 1.0

Chlorine binding site 4 out of 6 in 7q0v

Go back to Chlorine Binding Sites List in 7q0v
Chlorine binding site 4 out of 6 in the Lysozyme Soaked with V(IV)OSO4 and Phen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme Soaked with V(IV)OSO4 and Phen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:17.7
occ:0.50
 O A:HOH310 3.0 26.6 1.0
C1A A:PHN201 3.5 25.7 0.8
N1 A:PHN201 3.7 26.7 0.8
C4A A:PHN201 3.8 24.8 0.8
C10 A:PHN201 3.9 26.3 0.8
CG A:ASN44 4.0 16.0 1.0
C2 A:PHN201 4.0 23.5 0.8
CB A:ASN44 4.0 14.2 1.0
OD1 A:ASN44 4.1 17.8 1.0
C4 A:PHN201 4.3 23.9 0.8
N10 A:PHN201 4.3 27.6 0.8
C3 A:PHN201 4.3 24.5 0.8
C5 A:PHN201 4.4 24.8 0.8
C6A A:PHN201 4.5 26.3 0.8
ND2 A:ASN44 4.5 18.3 1.0
V A:V202 4.6 23.2 0.8
C6 A:PHN201 4.7 23.7 0.8
O A:ARG45 5.0 20.6 0.5

Chlorine binding site 5 out of 6 in 7q0v

Go back to Chlorine Binding Sites List in 7q0v
Chlorine binding site 5 out of 6 in the Lysozyme Soaked with V(IV)OSO4 and Phen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme Soaked with V(IV)OSO4 and Phen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:29.7
occ:1.00
 O A:HOH311 2.8 40.9 1.0
N A:ILE88 3.3 15.4 1.0
O A:HOH317 3.4 28.1 1.0
CG1 A:ILE88 3.7 15.7 1.0
CA A:ASP87 3.8 19.4 1.0
C A:ASP87 4.0 16.5 1.0
CZ A:PHE3 4.0 17.9 1.0
O A:SER86 4.1 19.9 1.0
OD1 A:ASP87 4.2 23.4 1.0
NH2 A:ARG14 4.2 31.0 1.0
CB A:ILE88 4.2 15.1 1.0
CG2 A:ILE88 4.2 16.1 1.0
CB A:ALA11 4.2 16.9 1.0
CA A:ILE88 4.3 14.9 1.0
NE2 A:HIS15 4.6 23.0 1.0
CD1 A:ILE88 4.6 17.5 1.0
CG A:ASP87 4.6 23.1 1.0
CE2 A:PHE3 4.6 17.1 1.0
CB A:ASP87 4.7 20.6 1.0
N A:ASP87 4.8 17.8 1.0
C A:SER86 4.8 17.4 1.0
CD2 A:HIS15 4.9 20.5 1.0

Chlorine binding site 6 out of 6 in 7q0v

Go back to Chlorine Binding Sites List in 7q0v
Chlorine binding site 6 out of 6 in the Lysozyme Soaked with V(IV)OSO4 and Phen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lysozyme Soaked with V(IV)OSO4 and Phen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:22.6
occ:0.75
 O A:HOH438 2.6 33.5 1.0
ND2 A:ASN65 3.2 17.4 1.0
CA A:GLY67 3.6 16.9 1.0
N A:GLY67 4.0 14.9 1.0
CG A:ASN65 4.2 16.1 1.0
OD1 A:ASN65 4.3 15.8 1.0
O A:HOH355 4.4 30.0 1.0
C A:ASP66 4.6 13.5 1.0
O A:HOH315 4.7 32.5 1.0
O A:ASP66 4.8 15.0 1.0
C A:GLY67 5.0 16.6 1.0

Reference:

M.F.A.Santos, G.Sciortino, I.Correia, A.C.P.Fernandes, T.Santos-Silva, F.Pisanu, E.Garribba, J.Costa Pessoa. Binding of V IV O 2+ , V IV Ol, V IV Ol 2 and V V O 2 L Moieties to Proteins: X-Ray/Theoretical Characterization and Biological Implications. Chemistry V. 28 00105 2022.
ISSN: ISSN 0947-6539
PubMed: 35486702
DOI: 10.1002/CHEM.202200105
Page generated: Tue Jul 30 02:56:36 2024

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