Gadolinium in PDB 4tws: Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution

All present enzymatic activity of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution:
3.2.1.17;

The structure of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution, PDB code: 4tws was solved by J.M.Holton, S.Classen, K.A.Frankel, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.61 / 1.45
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.220, 77.220, 38.810, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.1

The structure of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	13 atoms
Sodium	(Na)	5 atoms

The binding sites of Gadolinium atom in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution (pdb code 4tws). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 3 binding sites of Gadolinium where determined in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution, PDB code: 4tws:
Jump to Gadolinium binding site number: 1; 2; 3;

Gadolinium binding site 1 out of 3 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd201 b:14.1 occ:0.92 O4 A:DO3202 2.3 14.5 0.9 O5 A:DO3202 2.3 15.7 0.9 O1 A:DO3202 2.4 18.4 0.9 O7 A:DO3202 2.4 19.2 0.9 O A:HOH492 2.5 18.1 0.9 N4 A:DO3202 2.6 18.8 0.9 N1 A:DO3202 2.7 19.2 0.9 N2 A:DO3202 2.7 14.6 0.9 N3 A:DO3202 2.7 18.2 0.9 C13 A:DO3202 3.2 19.3 0.9 C11 A:DO3202 3.2 16.2 0.9 H161 A:DO3202 3.3 23.2 0.9 C16 A:DO3202 3.3 19.4 0.9 C9 A:DO3202 3.3 18.3 0.9 C14 A:DO3202 3.3 17.1 0.9 C12 A:DO3202 3.4 15.3 0.9 C10 A:DO3202 3.4 19.1 0.9 C15 A:DO3202 3.4 21.8 0.9 H121 A:DO3202 3.5 18.4 0.9 C5 A:DO3202 3.5 19.2 0.9 C7 A:DO3202 3.5 18.6 0.9 C8 A:DO3202 3.5 18.4 0.9 C6 A:DO3202 3.5 19.0 0.9 C3 A:DO3202 3.5 16.9 0.9 H142 A:DO3202 3.5 20.5 0.9 C1 A:DO3202 3.6 18.3 0.9 H101 A:DO3202 3.6 22.9 0.9 C4 A:DO3202 3.6 18.1 0.9 C2 A:DO3202 3.6 17.5 0.9 HC51 A:DO3202 3.7 23.0 0.9 H172 A:DO3206 3.7 41.5 0.4 HC32 A:DO3202 3.8 20.3 0.9 HC71 A:DO3202 3.8 22.3 0.9 HC11 A:DO3202 3.8 21.9 0.9 HC21 A:DO3202 3.8 21.0 0.9 HC62 A:DO3202 3.9 22.8 0.9 HC82 A:DO3202 3.9 22.1 0.9 HC41 A:DO3202 3.9 21.7 0.9 O A:HOH323 4.0 24.4 1.0 HA A:DO3202 4.1 26.2 0.9 H172 A:DO3202 4.2 26.7 0.9 O A:HOH493 4.2 11.9 0.6 H162 A:DO3202 4.2 23.2 0.9 H141 A:DO3202 4.2 20.5 0.9 H122 A:DO3202 4.2 18.4 0.9 H102 A:DO3202 4.3 22.9 0.9 O A:HOH539 4.3 25.4 1.0 HC52 A:DO3202 4.3 23.0 0.9 HC61 A:DO3202 4.3 22.8 0.9 C17 A:DO3202 4.3 22.2 0.9 O2 A:DO3202 4.4 27.7 0.9 O6 A:DO3202 4.4 24.2 0.9 HC81 A:DO3202 4.4 22.1 0.9 HC42 A:DO3202 4.4 21.7 0.9 HC72 A:DO3202 4.4 22.3 0.9 O2 A:DO3204 4.4 12.9 0.6 HC31 A:DO3202 4.4 20.3 0.9 HC12 A:DO3202 4.4 21.9 0.9 HC22 A:DO3202 4.4 21.0 0.9 H171 A:DO3206 4.4 41.5 0.4 O3 A:DO3202 4.4 15.3 0.9 O1 A:DO3204 4.4 10.8 0.6 C17 A:DO3206 4.5 34.6 0.4 H171 A:DO3202 4.6 26.7 0.9 O A:HOH494 4.6 28.2 0.4 C9 A:DO3204 4.7 11.7 0.6 H173 A:DO3206 5.0 41.5 0.4

Gadolinium binding site 2 out of 3 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd203 b:10.6 occ:0.57 O7 A:DO3206 0.7 35.1 0.4 O A:HOH509 1.0 17.9 1.0 C15 A:DO3206 1.6 35.4 0.4 HA A:DO3206 1.9 42.5 0.4 HC81 A:DO3206 2.1 38.3 0.4 GD A:GD205 2.3 16.2 0.4 O4 A:DO3204 2.3 12.3 0.6 O5 A:DO3204 2.3 12.4 0.6 C16 A:DO3206 2.3 33.1 0.4 O1 A:DO3204 2.4 10.8 0.6 N1 A:DO3206 2.4 33.6 0.4 O7 A:DO3204 2.4 10.7 0.6 N4 A:DO3206 2.4 30.1 0.4 C8 A:DO3206 2.5 31.9 0.4 O A:HOH493 2.5 11.9 0.6 N1 A:DO3204 2.6 12.9 0.6 N3 A:DO3204 2.6 14.3 0.6 N2 A:DO3204 2.6 14.6 0.6 N4 A:DO3204 2.7 12.7 0.6 H101 A:DO3206 2.7 39.5 0.4 C10 A:DO3206 2.8 32.9 0.4 H161 A:DO3206 2.9 39.8 0.4 C17 A:DO3206 2.9 34.6 0.4 C7 A:DO3206 2.9 31.1 0.4 H172 A:DO3206 3.0 41.5 0.4 O1 A:DO3206 3.0 36.2 0.4 C9 A:DO3206 3.0 35.4 0.4 H162 A:DO3206 3.1 39.8 0.4 C13 A:DO3204 3.2 14.9 0.6 C11 A:DO3204 3.2 14.2 0.6 C9 A:DO3204 3.3 11.7 0.6 C14 A:DO3204 3.3 16.2 0.6 O A:HOH494 3.3 28.2 0.4 C12 A:DO3204 3.3 15.0 0.6 C10 A:DO3204 3.3 12.3 0.6 C16 A:DO3204 3.3 11.3 0.6 H161 A:DO3204 3.4 13.6 0.6 H173 A:DO3206 3.4 41.5 0.4 HC82 A:DO3206 3.4 38.3 0.4 HC71 A:DO3206 3.4 37.3 0.4 H121 A:DO3204 3.4 18.0 0.6 C15 A:DO3204 3.4 10.5 0.6 H142 A:DO3204 3.5 19.4 0.6 C5 A:DO3204 3.5 15.6 0.6 H171 A:DO3206 3.5 41.5 0.4 H101 A:DO3204 3.5 14.8 0.6 O5 A:DO3206 3.5 31.2 0.4 O2 A:DO3206 3.5 33.5 0.4 C3 A:DO3204 3.5 15.6 0.6 C8 A:DO3204 3.5 13.5 0.6 C1 A:DO3204 3.5 12.0 0.6 C7 A:DO3204 3.5 14.1 0.6 C4 A:DO3204 3.5 15.0 0.6 C2 A:DO3204 3.5 13.9 0.6 C6 A:DO3204 3.5 16.4 0.6 HC72 A:DO3206 3.7 37.3 0.4 H102 A:DO3206 3.7 39.5 0.4 HC11 A:DO3204 3.7 14.4 0.6 HC51 A:DO3204 3.8 18.7 0.6 HC32 A:DO3204 3.8 18.8 0.6 HC21 A:DO3204 3.8 16.7 0.6 HC82 A:DO3204 3.8 16.2 0.6 C6 A:DO3206 3.8 28.1 0.4 C1 A:DO3206 3.9 33.0 0.4 HC71 A:DO3204 3.9 16.9 0.6 HC41 A:DO3204 3.9 18.0 0.6 HC62 A:DO3204 4.0 19.7 0.6 O A:HOH323 4.1 24.4 1.0 HC61 A:DO3206 4.1 33.7 0.4 HA A:DO3204 4.1 12.6 0.6 HC12 A:DO3206 4.1 39.6 0.4 H141 A:DO3204 4.2 19.4 0.6 H172 A:DO3204 4.2 12.2 0.6 H122 A:DO3204 4.2 18.0 0.6 H102 A:DO3204 4.2 14.8 0.6 H162 A:DO3204 4.2 13.6 0.6 O6 A:DO3204 4.2 14.2 0.6 HC61 A:DO3204 4.3 19.7 0.6 HC52 A:DO3204 4.3 18.7 0.6 O A:HOH492 4.3 18.1 0.9 HC42 A:DO3204 4.3 18.0 0.6 HC31 A:DO3204 4.3 18.8 0.6 O3 A:DO3202 4.3 15.3 0.9 HC81 A:DO3204 4.3 16.2 0.6 HC22 A:DO3204 4.3 16.7 0.6 HC72 A:DO3204 4.4 16.9 0.6 HC12 A:DO3204 4.4 14.4 0.6 C17 A:DO3204 4.4 10.2 0.6 O3 A:DO3204 4.4 16.4 0.6 HC11 A:DO3206 4.4 39.6 0.4 N2 A:DO3206 4.4 33.4 0.4 HC62 A:DO3206 4.4 33.7 0.4 O4 A:DO3202 4.4 14.5 0.9 N3 A:DO3206 4.4 28.0 0.4 O2 A:DO3204 4.5 12.9 0.6 O4 A:DO3206 4.5 33.8 0.4 C2 A:DO3206 4.6 32.8 0.4 C5 A:DO3206 4.6 27.5 0.4 H171 A:DO3204 4.6 12.2 0.6 HC22 A:DO3206 4.6 39.3 0.4 HC52 A:DO3206 4.7 33.0 0.4 C13 A:DO3206 4.7 26.0 0.4 C11 A:DO3202 4.7 16.2 0.9

Gadolinium binding site 3 out of 3 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd205 b:16.2 occ:0.40 N2 A:DO3204 0.9 14.6 0.6 C12 A:DO3204 1.4 15.0 0.6 H121 A:DO3204 1.6 18.0 0.6 C2 A:DO3204 1.7 13.9 0.6 O A:HOH509 2.0 17.9 1.0 C1 A:DO3204 2.1 12.0 0.6 HC11 A:DO3204 2.2 14.4 0.6 H122 A:DO3204 2.2 18.0 0.6 HC22 A:DO3204 2.2 16.7 0.6 GD A:GD203 2.3 10.6 0.6 O4 A:DO3206 2.3 33.8 0.4 C3 A:DO3204 2.3 15.6 0.6 O5 A:DO3206 2.3 31.2 0.4 C11 A:DO3204 2.4 14.2 0.6 O1 A:DO3206 2.4 36.2 0.4 HC21 A:DO3204 2.4 16.7 0.6 O1 A:DO3204 2.4 10.8 0.6 O7 A:DO3206 2.4 35.1 0.4 N1 A:DO3204 2.5 12.9 0.6 O A:HOH494 2.5 28.2 0.4 O4 A:DO3204 2.5 12.3 0.6 N1 A:DO3206 2.6 33.6 0.4 N2 A:DO3206 2.6 33.4 0.4 N4 A:DO3206 2.7 30.1 0.4 N3 A:DO3206 2.7 28.0 0.4 HC32 A:DO3204 2.7 18.8 0.6 HC31 A:DO3204 2.8 18.8 0.6 HC12 A:DO3204 3.1 14.4 0.6 C13 A:DO3206 3.2 26.0 0.4 C11 A:DO3206 3.2 35.3 0.4 C9 A:DO3204 3.3 11.7 0.6 C9 A:DO3206 3.3 35.4 0.4 C4 A:DO3204 3.3 15.0 0.6 C12 A:DO3206 3.4 33.0 0.4 C16 A:DO3206 3.4 33.1 0.4 N3 A:DO3204 3.4 14.3 0.6 C10 A:DO3204 3.4 12.3 0.6 C14 A:DO3206 3.4 25.1 0.4 C10 A:DO3206 3.4 32.9 0.4 C5 A:DO3206 3.4 27.5 0.4 H161 A:DO3206 3.5 39.8 0.4 C15 A:DO3206 3.5 35.4 0.4 C3 A:DO3206 3.5 31.0 0.4 C8 A:DO3206 3.5 31.9 0.4 C6 A:DO3206 3.5 28.1 0.4 C4 A:DO3206 3.5 28.1 0.4 C2 A:DO3206 3.5 32.8 0.4 C1 A:DO3206 3.5 33.0 0.4 C7 A:DO3206 3.5 31.1 0.4 H121 A:DO3206 3.5 39.7 0.4 O3 A:DO3204 3.5 16.4 0.6 HC82 A:DO3204 3.6 16.2 0.6 C8 A:DO3204 3.6 13.5 0.6 HC41 A:DO3204 3.6 18.0 0.6 HC52 A:DO3206 3.7 33.0 0.4 HC22 A:DO3206 3.7 39.3 0.4 HC12 A:DO3206 3.7 39.6 0.4 HC42 A:DO3206 3.7 33.7 0.4 HC61 A:DO3206 3.7 33.7 0.4 HC31 A:DO3206 3.7 37.2 0.4 HC81 A:DO3206 3.8 38.3 0.4 HC72 A:DO3206 3.8 37.3 0.4 H142 A:DO3206 3.9 30.1 0.4 H102 A:DO3204 3.9 14.8 0.6 H101 A:DO3206 3.9 39.5 0.4 O A:HOH307 4.0 37.1 1.0 H142 A:DO3204 4.0 19.4 0.6 HA A:DO3206 4.0 42.5 0.4 H101 A:DO3204 4.1 14.8 0.6 HC42 A:DO3204 4.1 18.0 0.6 O A:HOH493 4.1 11.9 0.6 O6 A:DO3206 4.1 21.3 0.4 N4 A:DO3204 4.1 12.7 0.6 H141 A:DO3206 4.1 30.1 0.4 H102 A:DO3206 4.2 39.5 0.4 O A:HOH492 4.2 18.1 0.9 O2 A:DO3206 4.2 33.5 0.4 O A:HOH539 4.2 25.4 1.0 H122 A:DO3206 4.2 39.7 0.4 C14 A:DO3204 4.2 16.2 0.6 O2 A:DO3204 4.2 12.9 0.6 H162 A:DO3206 4.3 39.8 0.4 HC51 A:DO3206 4.3 33.0 0.4 HC81 A:DO3204 4.3 16.2 0.6 O7 A:DO3204 4.3 10.7 0.6 HC32 A:DO3206 4.3 37.2 0.4 HC41 A:DO3206 4.3 33.7 0.4 HC62 A:DO3206 4.3 33.7 0.4 HC82 A:DO3206 4.3 38.3 0.4 HC21 A:DO3206 4.3 39.3 0.4 HC11 A:DO3206 4.4 39.6 0.4 HC71 A:DO3206 4.4 37.3 0.4 O5 A:DO3204 4.4 12.4 0.6 O3 A:DO3206 4.4 37.7 0.4 H172 A:DO3206 4.4 41.5 0.4 C7 A:DO3204 4.5 14.1 0.6 C5 A:DO3204 4.5 15.6 0.6 C17 A:DO3206 4.5 34.6 0.4 O A:HOH323 4.6 24.4 1.0 C6 A:DO3204 4.7 16.4 0.6 HC62 A:DO3204 4.8 19.7 0.6 C13 A:DO3204 4.8 14.9 0.6 H171 A:DO3206 4.8 41.5 0.4 HC52 A:DO3204 5.0 18.7 0.6

J.M.Holton, S.Classen, K.A.Frankel, J.A.Tainer. The R-Factor Gap in Macromolecular Crystallography: An Untapped Potential For Insights on Accurate Structures. Febs J. V. 281 4046 2014.
ISSN: ISSN 1742-464X
PubMed: 25040949
DOI: 10.1111/FEBS.12922