Atomistry » Sodium » PDB 3rnx-3si4 » 3ru5
Atomistry »
  Sodium »
    PDB 3rnx-3si4 »
      3ru5 »

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: Mon Oct 7 12:51:54 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