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Mercury in PDB 1edh: E-Cadherin Domains 1 and 2 in Complex with Calcium

Protein crystallography data

The structure of E-Cadherin Domains 1 and 2 in Complex with Calcium, PDB code: 1edh was solved by B.Nagar, M.Overduin, M.Ikura, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.657, 80.802, 72.635, 90.00, 116.65, 90.00
R / Rfree (%) 20.6 / 26.2

Other elements in 1edh:

The structure of E-Cadherin Domains 1 and 2 in Complex with Calcium also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the E-Cadherin Domains 1 and 2 in Complex with Calcium (pdb code 1edh). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the E-Cadherin Domains 1 and 2 in Complex with Calcium, PDB code: 1edh:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 1edh

Go back to Mercury Binding Sites List in 1edh
Mercury binding site 1 out of 2 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg300

b:33.4
occ:0.56
SG A:CYS9 2.6 40.6 1.0
CB A:CYS9 3.6 26.7 1.0
CD2 A:LEU21 3.9 30.0 1.0
CA A:CYS9 4.1 27.2 1.0
OE1 A:GLU13 4.2 42.1 1.0
CD A:PRO10 4.3 24.9 1.0
CG1 A:VAL62 4.3 18.4 1.0
O B:HOH488 4.5 30.6 1.0
O A:HOH421 4.7 26.7 1.0
CG A:GLU13 4.7 39.1 1.0
CD A:GLU13 4.7 42.7 1.0
O A:SER8 4.8 33.2 1.0
N A:PRO10 4.9 24.5 1.0
CD A:LYS19 4.9 31.8 1.0
C A:CYS9 4.9 25.2 1.0

Mercury binding site 2 out of 2 in 1edh

Go back to Mercury Binding Sites List in 1edh
Mercury binding site 2 out of 2 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg400

b:28.3
occ:0.66
SG B:CYS9 2.3 28.7 1.0
OE1 B:GLU13 3.1 40.3 1.0
CB B:CYS9 3.5 23.5 1.0
CD2 B:LEU21 3.7 30.4 1.0
CD B:GLU13 3.9 32.6 1.0
CA B:CYS9 4.0 19.1 1.0
CG1 B:VAL62 4.1 17.0 1.0
CD B:PRO10 4.1 20.7 1.0
OE2 B:GLU13 4.3 39.6 1.0
O B:HOH469 4.6 35.6 1.0
N B:PRO10 4.7 20.8 1.0
O B:SER8 4.8 27.3 1.0
C B:CYS9 4.8 21.0 1.0
CD B:LYS19 4.9 30.1 1.0
CB B:LYS19 4.9 26.7 1.0
CG B:GLU13 5.0 34.2 1.0

Reference:

B.Nagar, M.Overduin, M.Ikura, J.M.Rini. Structural Basis of Calcium-Induced E-Cadherin Rigidification and Dimerization. Nature V. 380 360 1996.
ISSN: ISSN 0028-0836
PubMed: 8598933
DOI: 10.1038/380360A0
Page generated: Wed Oct 28 18:39:12 2020

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