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Sodium in PDB 3ru5: Silver Metallated Hen Egg White Lysozyme at 1.35 A

Enzymatic activity of Silver Metallated Hen Egg White Lysozyme at 1.35 A

All present enzymatic activity of Silver Metallated Hen Egg White Lysozyme at 1.35 A:
3.2.1.17;

Protein crystallography data

The structure of Silver Metallated Hen Egg White Lysozyme at 1.35 A, PDB code: 3ru5 was solved by T.C.Leeper, M.J.Panzner, S.M.Bilinovich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.55 / 1.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.798, 77.798, 37.629, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.5

Other elements in 3ru5:

The structure of Silver Metallated Hen Egg White Lysozyme at 1.35 A also contains other interesting chemical elements:

Silver (Ag) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Silver Metallated Hen Egg White Lysozyme at 1.35 A (pdb code 3ru5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Silver Metallated Hen Egg White Lysozyme at 1.35 A, PDB code: 3ru5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3ru5

Go back to Sodium Binding Sites List in 3ru5
Sodium binding site 1 out of 5 in the Silver Metallated Hen Egg White Lysozyme at 1.35 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Silver Metallated Hen Egg White Lysozyme at 1.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na133

b:13.8
occ:1.00
 O A:SER60 2.3 13.3 1.0
O A:CYS64 2.4 11.2 1.0
O A:HOH152 2.4 16.6 1.0
OG A:SER72 2.4 16.4 1.0
O A:ARG73 2.5 16.8 1.0
O3 A:NO3132 2.7 15.3 1.0
CB A:SER72 3.4 18.2 1.0
C A:ARG73 3.4 17.3 1.0
C A:SER60 3.4 12.8 1.0
C A:CYS64 3.4 11.5 1.0
N A:NO3132 3.6 16.2 1.0
O1 A:NO3132 3.6 16.4 1.0
N A:ARG73 3.9 18.1 1.0
CA A:ASN65 4.0 12.6 1.0
CA A:SER60 4.1 11.9 1.0
N A:ASN65 4.1 12.2 1.0
C A:SER72 4.1 18.8 1.0
CA A:ARG73 4.2 18.3 1.0
N A:ASN74 4.3 16.6 1.0
CB A:SER60 4.3 12.0 1.0
N A:CYS64 4.3 11.5 1.0
CA A:SER72 4.4 18.5 1.0
CA A:ASN74 4.5 16.2 1.0
C A:ARG61 4.5 14.8 1.0
N A:ARG61 4.5 13.4 1.0
CA A:CYS64 4.5 11.7 1.0
O A:ARG61 4.6 15.5 1.0
CB A:THR69 4.7 14.9 1.0
O A:SER72 4.7 19.8 1.0
O A:THR69 4.7 15.4 1.0
CB A:ASN74 4.7 15.7 1.0
N A:TRP62 4.8 14.3 1.0
CB A:ASN65 4.8 13.3 1.0
CA A:ARG61 4.8 14.4 1.0
N A:TRP63 4.9 12.7 1.0
O2 A:NO3132 4.9 16.1 1.0
N A:ASP66 5.0 12.4 1.0
O A:HOH206 5.0 29.3 1.0

Sodium binding site 2 out of 5 in 3ru5

Go back to Sodium Binding Sites List in 3ru5
Sodium binding site 2 out of 5 in the Silver Metallated Hen Egg White Lysozyme at 1.35 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Silver Metallated Hen Egg White Lysozyme at 1.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na134

b:17.1
occ:1.00
 OG A:SER91 2.8 11.8 1.0
O A:TYR53 2.8 9.8 1.0
N A:LEU56 2.9 11.5 1.0
N A:ILE55 3.3 11.8 1.0
C A:GLY54 3.4 11.3 1.0
CB A:SER91 3.5 11.5 1.0
N A:GLN57 3.6 10.6 1.0
CA A:GLY54 3.6 11.5 1.0
CA A:LEU56 3.6 11.4 1.0
C A:LEU56 3.7 10.9 1.0
CD1 A:ILE58 3.8 15.6 1.0
CB A:LEU56 3.8 12.2 1.0
C A:TYR53 3.8 10.7 1.0
CG1 A:ILE58 3.8 12.8 1.0
C A:ILE55 4.0 11.7 1.0
CG2 A:ILE55 4.0 15.2 1.0
O A:GLY54 4.0 10.7 1.0
N A:ILE58 4.0 10.1 1.0
CA A:ILE55 4.1 12.6 1.0
O A:LEU83 4.1 18.4 1.0
N A:GLY54 4.2 10.3 1.0
CB A:ILE58 4.3 10.9 1.0
CB A:LEU83 4.3 17.8 1.0
CD2 A:LEU83 4.3 17.9 1.0
CA A:SER91 4.4 11.6 1.0
O A:HOH173 4.5 17.3 1.0
O A:LEU56 4.5 10.8 1.0
CA A:GLN57 4.6 10.7 1.0
CB A:ILE55 4.7 14.2 1.0
CG A:LEU83 4.8 17.4 1.0
C A:GLN57 4.8 10.5 1.0
CA A:ILE58 4.8 10.7 1.0
CG A:LEU56 4.8 12.1 1.0

Sodium binding site 3 out of 5 in 3ru5

Go back to Sodium Binding Sites List in 3ru5
Sodium binding site 3 out of 5 in the Silver Metallated Hen Egg White Lysozyme at 1.35 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Silver Metallated Hen Egg White Lysozyme at 1.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na135

b:16.9
occ:1.00
 O A:GLN41 2.8 10.6 1.0
OG1 A:THR43 2.8 12.5 1.0
N A:THR43 3.0 10.8 1.0
CB A:THR43 3.6 11.4 1.0
C A:ALA42 3.7 10.2 1.0
CG2 A:THR43 3.8 11.9 1.0
C A:GLN41 3.8 10.2 1.0
CA A:THR43 3.8 11.4 1.0
CA A:ALA42 3.8 10.4 1.0
O A:THR43 4.1 12.3 1.0
N A:ALA42 4.3 9.9 1.0
C A:THR43 4.5 11.6 1.0
O A:ALA42 4.6 10.3 1.0
CB A:GLN41 5.0 10.7 1.0
CA A:GLN41 5.0 10.2 1.0

Sodium binding site 4 out of 5 in 3ru5

Go back to Sodium Binding Sites List in 3ru5
Sodium binding site 4 out of 5 in the Silver Metallated Hen Egg White Lysozyme at 1.35 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Silver Metallated Hen Egg White Lysozyme at 1.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na136

b:18.1
occ:1.00
 OG1 A:THR51 2.7 10.3 1.0
OD2 A:ASP66 2.7 11.5 1.0
O A:GLY49 2.9 13.7 1.0
NE A:ARG68 3.0 15.6 1.0
OG1 A:THR69 3.1 13.3 1.0
N A:THR51 3.4 10.1 1.0
C A:SER50 3.5 10.9 1.0
CB A:THR51 3.5 10.2 1.0
CG A:ARG68 3.5 16.1 1.0
NE A:ARG45 3.6 21.1 1.0
CG A:ASP66 3.6 11.8 1.0
CA A:SER50 3.7 11.8 1.0
CD A:ARG68 3.8 16.3 1.0
OD1 A:ASP66 3.9 12.2 1.0
NH2 A:ARG68 3.9 14.7 1.0
CZ A:ARG68 3.9 14.3 1.0
C A:GLY49 3.9 14.0 1.0
OG A:SER60 3.9 10.7 1.0
O A:SER50 4.0 11.5 1.0
O A:ARG68 4.0 16.6 1.0
NH2 A:ARG45 4.0 22.2 1.0
CA A:THR51 4.0 10.2 1.0
CZ A:ARG45 4.1 21.3 1.0
C A:ARG68 4.3 15.7 1.0
N A:SER50 4.3 12.4 1.0
OH A:TYR53 4.3 11.2 1.0
CD A:ARG45 4.3 18.5 1.0
CB A:THR69 4.4 14.9 1.0
N A:THR69 4.7 15.3 1.0
CB A:ARG68 4.7 16.1 1.0
CA A:THR69 4.8 14.9 1.0
CG2 A:THR51 4.8 10.0 1.0
O A:HOH209 4.9 25.0 1.0
CG2 A:THR69 4.9 14.6 1.0
CB A:SER60 4.9 12.0 1.0
CB A:ASP66 5.0 12.1 1.0
CB A:SER50 5.0 11.8 1.0
CA A:ARG68 5.0 15.4 1.0

Sodium binding site 5 out of 5 in 3ru5

Go back to Sodium Binding Sites List in 3ru5
Sodium binding site 5 out of 5 in the Silver Metallated Hen Egg White Lysozyme at 1.35 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Silver Metallated Hen Egg White Lysozyme at 1.35 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na137

b:17.8
occ:1.00
 O A:HOH153 2.9 16.1 1.0
NE A:ARG114 3.0 10.6 1.0
NH2 A:ARG114 3.6 11.4 1.0
CB A:ARG114 3.7 11.1 1.0
CZ A:ARG114 3.7 10.9 1.0
CG A:ARG114 3.8 11.6 1.0
CD A:ARG114 4.0 11.8 1.0
CZ A:PHE34 4.0 12.0 1.0
CE1 A:PHE34 4.3 13.0 1.0
CA A:ARG114 4.3 10.3 1.0
O A:ARG114 4.3 10.3 1.0
CE2 A:PHE34 4.5 10.7 1.0
C A:ARG114 4.8 9.9 1.0
O A:HOH188 4.8 23.0 1.0
CD1 A:PHE34 4.9 11.1 1.0

Reference:

M.J.Panzner, S.M.Bilinovich, W.J.Youngs, T.C.Leeper. Silver Metallation of Hen Egg White Lysozyme: X-Ray Crystal Structure and uc(Nmr) Studies. Chem.Commun.(Camb.) V. 47 12479 2011.
ISSN: ISSN 1359-7345
PubMed: 22042312
DOI: 10.1039/C1CC15908A
Page generated: Sun Aug 17 17:18:05 2025

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