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Gadolinium in PDB 1h87: Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 A Resolution

Enzymatic activity of Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 A Resolution

All present enzymatic activity of Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 A Resolution:
3.2.1.17;

Protein crystallography data

The structure of Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 A Resolution, PDB code: 1h87 was solved by E.Girard, L.Chantalat, J.Vicat, R.Kahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.33 / 1.72
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.250, 77.250, 38.660, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21

Other elements in 1h87:

The structure of Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 A Resolution (pdb code 1h87). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 2 binding sites of Gadolinium where determined in the Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 A Resolution, PDB code: 1h87:
Jump to Gadolinium binding site number: 1; 2;

Gadolinium binding site 1 out of 2 in 1h87

Go back to Gadolinium Binding Sites List in 1h87
Gadolinium binding site 1 out of 2 in the Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 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-White Lysozyme at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd290

b:15.3
occ:0.81
O7 A:DO3284 2.2 17.0 0.8
O1 A:DO3284 2.2 21.4 0.8
O3 A:DO3284 2.3 14.6 0.8
O A:HOH2150 2.3 19.8 1.0
O5 A:DO3284 2.6 17.9 0.8
N4 A:DO3284 2.7 18.8 0.8
N1 A:DO3284 2.8 20.0 0.8
N3 A:DO3284 2.8 18.3 0.8
N2 A:DO3284 2.8 17.7 0.8
C9 A:DO3284 3.1 21.5 0.8
C16 A:DO3284 3.2 18.2 0.8
C15 A:DO3284 3.2 17.8 0.8
C11 A:DO3284 3.2 16.3 0.8
C10 A:DO3284 3.2 20.5 0.8
C12 A:DO3284 3.4 16.5 0.8
C13 A:DO3284 3.4 18.9 0.8
C14 A:DO3284 3.4 18.6 0.8
C7 A:DO3284 3.6 19.1 0.8
C5 A:DO3284 3.6 18.2 0.8
C8 A:DO3284 3.6 19.7 0.8
C3 A:DO3284 3.6 17.5 0.8
C6 A:DO3284 3.6 18.6 0.8
C4 A:DO3284 3.7 18.1 0.8
C1 A:DO3284 3.7 19.2 0.8
C2 A:DO3284 3.8 17.9 0.8
O A:HOH2152 4.1 28.9 1.0
C17 A:DO3284 4.1 17.2 0.8
O A:HOH2153 4.2 24.7 1.0
O2 A:DO3284 4.3 22.9 0.8
O4 A:DO3284 4.4 15.5 0.8
O1 A:DO3285 4.4 14.2 0.7
O2 A:DO3285 4.5 15.9 0.7
O6 A:DO3284 4.5 19.3 0.8
C9 A:DO3285 4.8 15.4 0.7

Gadolinium binding site 2 out of 2 in 1h87

Go back to Gadolinium Binding Sites List in 1h87
Gadolinium binding site 2 out of 2 in the Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.7 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-White Lysozyme at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd291

b:15.8
occ:0.73
O3 A:DO3285 2.3 17.2 0.7
O5 A:DO3285 2.3 17.7 0.7
O7 A:DO3285 2.4 15.9 0.7
O1 A:DO3285 2.5 14.2 0.7
O A:HOH2153 2.6 24.7 1.0
N3 A:DO3285 2.6 18.9 0.7
N4 A:DO3285 2.7 18.1 0.7
N2 A:DO3285 2.7 17.8 0.7
N1 A:DO3285 2.7 17.8 0.7
C13 A:DO3285 3.1 18.6 0.7
C14 A:DO3285 3.2 18.6 0.7
C11 A:DO3285 3.2 18.1 0.7
C10 A:DO3285 3.3 16.3 0.7
C16 A:DO3285 3.3 17.7 0.7
C9 A:DO3285 3.3 15.4 0.7
C12 A:DO3285 3.3 18.7 0.7
C15 A:DO3285 3.4 17.0 0.7
C5 A:DO3285 3.4 18.9 0.7
C4 A:DO3285 3.5 18.4 0.7
C6 A:DO3285 3.5 19.1 0.7
C3 A:DO3285 3.5 18.7 0.7
C7 A:DO3285 3.6 18.1 0.7
C8 A:DO3285 3.6 17.9 0.7
C1 A:DO3285 3.7 17.5 0.7
C2 A:DO3285 3.7 18.3 0.7
O6 A:DO3285 4.2 18.3 0.7
O A:HOH2152 4.2 28.9 1.0
O A:HOH2150 4.3 19.8 1.0
C17 A:DO3285 4.3 16.6 0.7
O4 A:DO3285 4.4 19.4 0.7
O4 A:DO3284 4.4 15.5 0.8
O3 A:DO3284 4.5 14.6 0.8
O2 A:DO3285 4.5 15.9 0.7
C11 A:DO3284 4.9 16.3 0.8

Reference:

E.Girard, L.Chantalat, J.Vicat, R.Kahn. Gd-Hp-DO3A, A Complex to Obtain High-Phasing-Power Heavy Atom Derivatives For Sad and Mad Experiments. Results with Tetragonal Hen Egg-White Lysozyme Acta Crystallogr.,Sect.D V. 58 1 2001.
ISSN: ISSN 0907-4449
PubMed: 11752774
DOI: 10.1107/S0907444901016444
Page generated: Sun Dec 13 18:59:10 2020

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