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Sodium in PDB 6g5c: Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme

Enzymatic activity of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme

All present enzymatic activity of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme, PDB code: 6g5c was solved by H.I.Sbirkova-Dimitrova, G.Radoslavov, P.Hristov, V.Ganev, L.Dimowa, R.Rusev, B.L.Shivachev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.50 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.866, 78.866, 36.893, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.4

Other elements in 6g5c:

The structure of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme also contains other interesting chemical elements:

Titanium (Ti) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme (pdb code 6g5c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme, PDB code: 6g5c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6g5c

Go back to Sodium Binding Sites List in 6g5c
Sodium binding site 1 out of 5 in the Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:8.3
occ:1.00
 O A:SER60 2.3 7.4 1.0
O A:CYS64 2.4 4.7 1.0
O A:ARG73 2.4 9.8 1.0
O A:HOH355 2.4 6.5 1.0
O A:HOH347 2.5 3.9 1.0
OG A:SER72 2.6 9.7 1.0
CB A:SER72 3.3 10.2 1.0
C A:CYS64 3.4 4.9 1.0
C A:SER60 3.5 7.6 1.0
C A:ARG73 3.5 9.8 1.0
CA A:ASN65 3.8 5.6 1.0
N A:ARG73 4.0 10.4 1.0
N A:ASN65 4.0 5.6 1.0
CA A:SER60 4.1 6.7 1.0
C A:SER72 4.2 11.6 1.0
CB A:SER60 4.2 6.6 1.0
CA A:ARG73 4.4 10.4 1.0
CA A:SER72 4.4 11.0 1.0
N A:ASN74 4.4 8.6 1.0
N A:CYS64 4.4 5.5 1.0
O A:ARG61 4.5 11.2 1.0
C A:ARG61 4.5 11.3 1.0
CA A:ASN74 4.5 8.5 1.0
N A:ARG61 4.5 9.3 1.0
CA A:CYS64 4.6 5.3 1.0
N A:ASP66 4.6 5.8 1.0
OD1 A:ASN65 4.6 7.1 1.0
TI A:4TI207 4.7 15.5 1.0
O A:SER72 4.7 12.2 1.0
CB A:THR69 4.7 8.0 1.0
CA A:ARG61 4.7 11.7 1.0
CB A:ASN74 4.8 8.2 1.0
CB A:ASN65 4.8 6.0 1.0
C A:ASN65 4.8 5.3 1.0
N A:TRP62 5.0 10.6 1.0

Sodium binding site 2 out of 5 in 6g5c

Go back to Sodium Binding Sites List in 6g5c
Sodium binding site 2 out of 5 in the Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:3.3
occ:1.00
 ND2 A:ASN113 3.4 7.2 1.0
CB A:ASN113 3.7 6.8 1.0
CA A:ALA110 3.8 6.2 1.0
CB A:ALA110 4.1 6.3 1.0
CG A:ASN113 4.1 7.1 1.0
N A:ALA110 4.2 6.5 1.0
O A:VAL109 4.3 7.7 1.0
CG1 A:VAL109 4.3 9.7 1.0
CD A:ARG114 4.4 6.2 1.0
C A:VAL109 4.4 7.1 1.0
CG A:ARG114 4.6 6.0 1.0
C A:ALA110 4.9 5.9 1.0
O A:ALA110 4.9 5.9 1.0

Sodium binding site 3 out of 5 in 6g5c

Go back to Sodium Binding Sites List in 6g5c
Sodium binding site 3 out of 5 in the Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:11.5
occ:1.00
 O A:HOH389 3.2 16.8 1.0
N A:ILE88 3.3 9.0 1.0
O A:HOH318 3.4 19.8 1.0
CG1 A:ILE88 3.8 8.8 1.0
CA A:ASP87 3.8 10.9 1.0
NE2 A:HIS15 4.0 15.5 1.0
O A:SER86 4.0 12.8 1.0
C A:ASP87 4.1 8.9 1.0
OD1 A:ASP87 4.1 13.7 1.0
CB A:ALA11 4.2 9.4 1.0
CZ A:PHE3 4.3 7.6 1.0
CB A:ILE88 4.3 8.4 1.0
CA A:ILE88 4.3 8.1 1.0
CG2 A:ILE88 4.4 8.5 1.0
CG A:ASP87 4.5 15.7 1.0
CD2 A:HIS15 4.6 14.8 1.0
CB A:ASP87 4.7 12.4 1.0
CD1 A:ILE88 4.7 9.5 1.0
CE1 A:PHE3 4.8 7.8 1.0
N A:ASP87 4.8 10.5 1.0
C A:SER86 4.8 11.7 1.0
CE1 A:HIS15 5.0 15.9 1.0

Sodium binding site 4 out of 5 in 6g5c

Go back to Sodium Binding Sites List in 6g5c
Sodium binding site 4 out of 5 in the Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:13.7
occ:1.00
 NZ A:LYS33 3.7 12.6 1.0
CE2 A:PHE38 3.8 5.6 1.0
CZ3 A:TRP123 3.9 7.7 1.0
CE A:LYS33 4.1 11.0 1.0
CD A:ARG5 4.1 11.7 1.0
CD A:LYS33 4.2 8.8 1.0
CB A:ARG5 4.4 11.0 1.0
CZ A:PHE38 4.4 5.4 1.0
CG A:ARG5 4.7 11.4 1.0
CD2 A:PHE38 4.7 5.4 1.0
CE3 A:TRP123 4.7 7.8 1.0
NE A:ARG5 4.8 12.1 1.0
CH2 A:TRP123 4.8 7.9 1.0
O A:HOH393 4.9 31.1 1.0

Sodium binding site 5 out of 5 in 6g5c

Go back to Sodium Binding Sites List in 6g5c
Sodium binding site 5 out of 5 in the Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Interaction of TIO2 Nanoparticles (Nm-101) with Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:6.7
occ:1.00
 OG A:SER24 3.0 8.4 1.0
N A:GLY26 3.2 6.0 1.0
CA A:GLY26 3.5 5.8 1.0
CB A:SER24 3.6 7.9 1.0
CA A:GLN121 3.6 13.2 1.0
CD1 A:ILE124 3.8 14.7 1.0
CB A:GLN121 3.8 18.6 1.0
N A:GLN121 3.9 11.4 1.0
CG1 A:ILE124 4.2 12.2 1.0
O A:VAL120 4.2 9.0 1.0
C A:VAL120 4.2 9.9 1.0
CG2 A:VAL120 4.3 9.4 1.0
N A:LEU25 4.4 7.5 1.0
C A:LEU25 4.4 7.0 1.0
C A:SER24 4.5 7.5 1.0
C A:GLY26 4.5 5.4 1.0
N A:ASN27 4.6 5.2 1.0
CA A:SER24 4.6 7.5 1.0
C A:GLN121 4.8 11.1 1.0
CA A:LEU25 4.8 7.2 1.0
O A:SER24 4.9 7.3 1.0

Reference:

B.L.Shivachev, H.I.Sbirkova-Dimitrova. Crystallization and Crystal Structure of Lysozyme in the Presence of Nanosized Titanium Dioxide Bul.Chem.Commn. V. 50 2018.
ISSN: ISSN 0324-1130
Page generated: Tue Dec 15 12:16:44 2020

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