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Sodium in PDB 1gwd: Tri-Iodide Derivative of Hen Egg-White Lysozyme

Enzymatic activity of Tri-Iodide Derivative of Hen Egg-White Lysozyme

All present enzymatic activity of Tri-Iodide Derivative of Hen Egg-White Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Tri-Iodide Derivative of Hen Egg-White Lysozyme, PDB code: 1gwd was solved by G.Evans, G.Bricogne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.09 / 1.77
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.050, 79.050, 36.820, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.1

Other elements in 1gwd:

The structure of Tri-Iodide Derivative of Hen Egg-White Lysozyme also contains other interesting chemical elements:

Iodine (I) 5 atoms
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Tri-Iodide Derivative of Hen Egg-White Lysozyme (pdb code 1gwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Tri-Iodide Derivative of Hen Egg-White Lysozyme, PDB code: 1gwd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1gwd

Go back to Sodium Binding Sites List in 1gwd
Sodium binding site 1 out of 3 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1144

b:9.6
occ:1.00
O A:SER60 2.3 9.6 1.0
O A:HOH2053 2.5 5.5 1.0
O A:ARG73 2.5 12.9 1.0
O A:HOH2051 2.5 9.6 1.0
O A:CYS64 2.5 8.5 1.0
OG A:SER72 2.5 13.9 1.0
CB A:SER72 3.2 11.4 1.0
C A:SER60 3.4 10.0 1.0
C A:ARG73 3.6 13.6 1.0
C A:CYS64 3.6 8.5 1.0
N A:ARG73 3.9 9.9 1.0
CA A:ASN65 4.0 6.1 1.0
CA A:SER60 4.1 4.1 1.0
C A:SER72 4.1 14.3 1.0
CB A:SER60 4.2 6.2 1.0
CA A:SER72 4.3 10.2 1.0
N A:ASN65 4.3 6.1 1.0
CA A:ARG73 4.4 9.5 1.0
O A:ARG61 4.4 14.5 1.0
N A:ASN74 4.5 9.9 1.0
N A:CYS64 4.5 4.7 1.0
C A:ARG61 4.5 15.2 1.0
N A:ARG61 4.5 8.9 1.0
CA A:ASN74 4.6 9.2 1.0
OD1 A:ASN65 4.6 10.8 1.0
CB A:THR69 4.6 11.0 1.0
N A:ASP66 4.6 5.5 1.0
O A:SER72 4.7 14.2 1.0
CL A:CL1138 4.7 8.1 0.8
CA A:CYS64 4.7 4.0 1.0
CA A:ARG61 4.7 10.0 1.0
O A:HOH2061 4.7 23.2 1.0
CB A:ASN74 4.8 7.7 1.0
C A:ASN65 4.8 8.7 1.0
CB A:ASN65 4.9 6.3 1.0
OG1 A:THR69 4.9 9.1 1.0
OG A:SER60 4.9 7.4 1.0
N A:TRP62 4.9 13.0 1.0

Sodium binding site 2 out of 3 in 1gwd

Go back to Sodium Binding Sites List in 1gwd
Sodium binding site 2 out of 3 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1145

b:11.5
occ:1.00
OG A:SER91 2.9 6.9 1.0
O A:TYR53 2.9 5.1 1.0
N A:LEU56 2.9 4.6 1.0
N A:ILE55 3.4 5.0 1.0
C A:GLY54 3.4 7.6 1.0
CA A:GLY54 3.5 4.2 1.0
N A:GLN57 3.5 2.6 1.0
CA A:LEU56 3.6 3.9 1.0
CB A:SER91 3.6 4.9 1.0
CD1 A:ILE58 3.7 6.6 1.0
C A:LEU56 3.7 6.1 1.0
CB A:LEU56 3.7 3.6 1.0
CG1 A:ILE58 3.8 5.6 1.0
C A:TYR53 3.9 6.8 1.0
O A:HOH2070 3.9 11.0 1.0
N A:ILE58 4.0 3.0 1.0
C A:ILE55 4.0 8.1 1.0
CG1 A:ILE55 4.0 9.0 1.0
O A:GLY54 4.0 6.6 1.0
CA A:ILE55 4.1 5.4 1.0
CB A:ILE58 4.2 5.7 1.0
N A:GLY54 4.2 4.3 1.0
O A:LEU83 4.4 7.4 1.0
CA A:SER91 4.4 3.3 1.0
CB A:LEU83 4.4 5.5 1.0
CD2 A:LEU83 4.5 12.2 1.0
CA A:GLN57 4.5 2.3 1.0
O A:LEU56 4.5 5.0 1.0
CB A:ILE55 4.7 9.0 1.0
C A:GLN57 4.7 5.6 1.0
CG A:LEU56 4.7 7.5 1.0
CA A:ILE58 4.8 3.1 1.0
CG A:LEU83 5.0 9.1 1.0

Sodium binding site 3 out of 3 in 1gwd

Go back to Sodium Binding Sites List in 1gwd
Sodium binding site 3 out of 3 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1146

b:16.2
occ:1.00
OG1 A:THR51 2.7 6.8 1.0
OD2 A:ASP66 2.7 8.4 1.0
O A:GLY49 2.9 14.4 1.0
NE A:ARG68 2.9 21.4 1.0
OG1 A:THR69 3.0 9.1 1.0
N A:THR51 3.3 4.6 1.0
CB A:THR51 3.3 7.0 1.0
C A:SER50 3.5 8.7 1.0
CG A:ASP66 3.6 8.4 1.0
OG A:SER60 3.7 7.4 1.0
CG A:ARG68 3.7 11.9 1.0
CD A:ARG68 3.7 15.7 1.0
CA A:SER50 3.7 6.4 1.0
OD1 A:ASP66 3.8 7.9 1.0
CZ A:ARG68 3.9 35.0 1.0
O A:ARG68 3.9 11.5 1.0
NH2 A:ARG68 3.9 21.6 1.0
CA A:THR51 4.0 3.9 1.0
NE A:ARG45 4.0 22.7 1.0
C A:GLY49 4.0 14.1 1.0
O A:SER50 4.1 8.2 1.0
NH2 A:ARG45 4.1 17.8 1.0
OH A:TYR53 4.3 8.1 1.0
C A:ARG68 4.3 11.5 1.0
CB A:THR69 4.3 11.0 1.0
CZ A:ARG45 4.4 36.7 1.0
N A:SER50 4.4 7.7 1.0
CB A:SER60 4.6 6.2 1.0
N A:THR69 4.7 7.5 1.0
CA A:THR69 4.7 7.2 1.0
CB A:ARG68 4.7 8.9 1.0
CG2 A:THR51 4.7 4.0 1.0
CD A:ARG45 4.8 16.8 1.0
CG2 A:THR69 4.8 7.0 1.0
CB A:ASP66 4.9 5.6 1.0
CB A:SER50 4.9 7.8 1.0

Reference:

G.Evans, G.Bricogne. Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods For Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment Acta Crystallogr.,Sect.D V. 58 976 2002.
ISSN: ISSN 0907-4449
PubMed: 12037300
DOI: 10.1107/S0907444902005486
Page generated: Tue Dec 15 05:25:05 2020

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