Mercury in PDB 4o9x: Crystal Structure of TCDB2-TCCC3

The structure of Crystal Structure of TCDB2-TCCC3, PDB code: 4o9x was solved by D.Meusch, C.Gatsogiannis, R.G.Efremov, A.E.Lang, O.Hofnagel, I.R.Vetter, K.Aktories, S.Raunser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.77 / 2.17
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	232.360, 232.360, 143.570, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 21.5

The binding sites of Mercury atom in the Crystal Structure of TCDB2-TCCC3 (pdb code 4o9x). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the Crystal Structure of TCDB2-TCCC3, PDB code: 4o9x:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Mercury binding site 1 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2201 b:62.6 occ:1.00 SG A:CYS108 2.8 40.2 1.0 O A:CYS108 3.1 27.3 1.0 CB A:CYS108 3.2 29.8 1.0 C A:CYS108 3.4 32.5 1.0 CD1 A:PHE89 3.5 33.1 1.0 CE1 A:PHE89 3.7 33.4 1.0 CZ A:PHE296 3.7 28.9 1.0 CE1 A:PHE296 3.7 27.5 1.0 CA A:CYS108 3.9 33.0 1.0 CG A:PHE89 4.0 32.3 1.0 N A:ASN109 4.2 33.7 1.0 CZ A:PHE102 4.5 32.7 1.0 CZ A:PHE89 4.5 30.9 1.0 CB A:PHE89 4.5 32.0 1.0 CE2 A:PHE296 4.5 28.6 1.0 CD1 A:PHE296 4.6 29.2 1.0 CE2 A:PHE102 4.6 32.9 1.0 O A:ASN109 4.6 35.4 1.0 CD2 A:PHE89 4.7 29.8 1.0 CA A:ASN109 4.8 37.5 1.0 C A:ASN109 4.8 36.6 1.0 CE2 A:PHE89 4.9 28.9 1.0 CD2 A:LEU263 5.0 26.6 1.0 N A:CYS108 5.0 34.5 1.0

Mercury binding site 2 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2202 b:87.5 occ:1.00 SG A:CYS694 2.9 72.2 1.0 O A:ARG689 3.3 57.3 1.0 CB A:CYS694 3.4 40.9 1.0 CG2 A:VAL713 3.5 54.5 1.0 CA A:PHE690 3.6 56.1 1.0 C A:ARG689 3.9 59.8 1.0 CG1 A:VAL713 3.9 54.9 1.0 N A:PHE690 4.0 58.3 1.0 CD1 A:PHE690 4.1 59.8 1.0 CB A:VAL713 4.2 54.0 1.0 CD1 A:LEU711 4.2 47.5 1.0 CB A:PHE690 4.4 55.3 1.0 N A:ASP691 4.4 58.4 1.0 CA A:VAL713 4.5 53.4 1.0 C A:PHE690 4.6 56.7 1.0 CG A:PHE690 4.6 58.4 1.0 OD2 A:ASP691 4.7 71.7 1.0 O A:SER712 4.7 48.4 1.0 CA A:CYS694 4.8 45.1 1.0 CE1 A:PHE690 4.9 60.2 1.0 CG A:LEU711 4.9 46.7 1.0 CD A:PRO714 4.9 60.6 1.0

Mercury binding site 3 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2203 b:0.4 occ:1.00 SG A:CYS723 2.8 80.8 1.0 CB A:CYS723 3.2 41.1 1.0 CD1 A:LEU709 3.4 28.2 1.0 NE1 A:TRP415 3.5 51.1 1.0 CE2 A:TRP415 3.6 49.7 1.0 CZ2 A:TRP415 3.8 48.4 1.0 CB A:ALA413 3.9 77.2 1.0 CD2 A:LEU725 4.0 47.4 1.0 CD1 A:TRP415 4.2 54.1 1.0 CD2 A:LEU682 4.3 44.1 1.0 CD2 A:TRP415 4.4 51.1 1.0 CG A:LEU709 4.6 71.3 1.0 CH2 A:TRP415 4.6 50.6 1.0 CA A:CYS723 4.6 41.5 1.0 CG A:TRP415 4.7 54.9 1.0 CA A:ALA413 4.7 76.6 1.0 CB A:LEU682 4.8 44.5 1.0 CG A:LEU682 4.9 45.2 1.0 O A:ARG683 4.9 50.9 1.0 CB A:LEU709 5.0 45.6 1.0 N A:HIS414 5.0 76.7 1.0 C A:CYS723 5.0 41.8 1.0

Mercury binding site 4 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2204 b:0.5 occ:1.00 SG A:CYS964 3.2 50.4 1.0 NE A:ARG989 3.4 32.3 1.0 CZ A:PHE866 3.7 29.8 1.0 NH2 A:ARG989 3.8 33.2 1.0 CE2 A:PHE866 3.8 31.2 1.0 CG A:ARG989 4.1 29.6 1.0 CZ A:ARG989 4.1 33.1 1.0 CE1 A:PHE866 4.3 29.7 1.0 CD A:ARG989 4.4 31.4 1.0 O A:GLN864 4.5 31.7 1.0 CD2 A:PHE866 4.6 29.6 1.0 CB A:CYS964 4.9 31.3 1.0 CE1 A:TYR953 4.9 29.7 1.0 CD1 A:PHE866 5.0 28.4 1.0 CG A:PRO962 5.0 27.5 1.0

Mercury binding site 5 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2205 b:0.8 occ:1.00 CB A:CYS1285 2.8 30.8 1.0 N A:CYS1285 3.3 28.9 1.0 CG2 A:VAL1282 3.4 27.1 1.0 CB A:LEU1360 3.4 32.8 1.0 SG A:CYS1285 3.5 0.2 1.0 CA A:CYS1285 3.6 30.0 1.0 C A:GLN1284 3.7 31.7 1.0 O A:LEU1360 3.7 33.7 1.0 CD1 A:LEU1360 3.8 32.3 1.0 CD1 A:LEU1280 3.9 41.7 1.0 O A:GLN1284 4.1 34.3 1.0 CG A:LEU1360 4.2 34.5 1.0 C A:LEU1360 4.2 35.8 1.0 CA A:GLN1284 4.4 34.7 1.0 CE2 A:PHE1264 4.4 44.7 1.0 CZ A:PHE1264 4.4 46.3 1.0 CA A:LEU1360 4.4 35.4 1.0 C A:CYS1285 4.5 31.8 1.0 O A:CYS1285 4.5 32.5 1.0 N A:GLN1284 4.9 33.0 1.0 CB A:VAL1282 4.9 29.1 1.0

Mercury binding site 6 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2206 b:0.6 occ:1.00 SG A:CYS1601 2.8 83.9 1.0 CB A:CYS1601 3.3 31.8 1.0 OE1 A:GLN1592 3.4 45.0 1.0 OE2 A:GLU1603 3.5 58.5 1.0 O A:ALA1121 3.6 30.9 1.0 CD A:ARG1609 4.2 50.8 1.0 O A:HOH3069 4.2 41.7 1.0 NE A:ARG1609 4.2 58.9 1.0 CD A:GLU1603 4.3 58.6 1.0 CZ A:ARG1609 4.4 65.7 1.0 C A:ALA1121 4.4 32.6 1.0 NH1 A:ARG1609 4.5 68.8 1.0 CA A:ALA1121 4.5 32.0 1.0 CG A:GLU1603 4.5 49.1 1.0 CD A:GLN1592 4.5 45.7 1.0 CG2 A:VAL1611 4.7 33.1 1.0 CG A:ARG1609 4.7 43.1 1.0 CA A:CYS1601 4.8 33.6 1.0

Mercury binding site 7 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2207 b:60.3 occ:1.00 SG A:CYS1681 2.8 39.3 1.0 O A:CYS1681 3.0 24.3 1.0 C A:CYS1681 3.3 25.0 1.0 CB A:CYS1681 3.4 23.3 1.0 O A:HOH2700 3.6 45.2 1.0 CB A:HIS1684 3.6 29.0 1.0 N A:ARG1683 3.7 30.7 1.0 N A:HIS1684 3.7 29.4 1.0 N A:VAL1682 3.7 27.8 1.0 C A:VAL1682 3.8 32.6 1.0 C A:ARG1683 3.9 31.6 1.0 CA A:CYS1681 4.0 25.4 1.0 CA A:VAL1682 4.0 31.6 1.0 CA A:ARG1683 4.1 32.5 1.0 CA A:HIS1684 4.2 29.8 1.0 O A:VAL1682 4.3 34.8 1.0 O A:ARG1683 4.4 32.1 1.0 O A:THR1691 4.5 30.9 1.0 CG A:HIS1684 4.7 34.8 1.0

Mercury binding site 8 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2208 b:96.0 occ:1.00 SG A:CYS771 3.2 82.1 1.0 N A:TYR772 3.2 62.1 1.0 CB A:CYS771 3.3 61.8 1.0 O A:GLY437 3.3 56.3 1.0 O A:LYS436 3.3 51.5 1.0 C A:CYS771 3.3 61.4 1.0 O A:CYS771 3.7 60.0 1.0 CA A:TYR772 3.7 63.9 1.0 CA A:CYS771 3.8 62.5 1.0 C A:GLY437 3.9 54.9 1.0 C A:TYR772 4.1 72.1 1.0 O A:TYR772 4.1 76.4 1.0 CA A:GLY437 4.2 54.3 1.0 C A:LYS436 4.4 54.5 1.0 CD A:PRO774 4.6 79.3 1.0 N A:CYS771 4.7 64.7 1.0 N A:GLU438 4.7 52.7 1.0 N A:GLY437 4.8 55.2 1.0 N A:LEU773 4.9 75.3 1.0

Mercury binding site 9 out of 9 in the Crystal Structure of TCDB2-TCCC3


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of TCDB2-TCCC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg2209 b:0.6 occ:1.00 O A:ASP691 2.8 59.2 1.0 O A:CYS694 2.8 45.4 1.0 CZ A:PHE690 3.0 61.7 1.0 C A:CYS694 3.2 43.9 1.0 CE2 A:PHE690 3.3 60.9 1.0 N A:CYS694 3.6 47.4 1.0 CE1 A:PHE690 3.6 60.2 1.0 CA A:CYS694 3.6 45.1 1.0 CB A:CYS694 3.7 40.9 1.0 C A:ASP691 3.8 61.0 1.0 N A:GLN695 3.9 42.5 1.0 CA A:GLN695 4.1 42.4 1.0 CA A:HIS692 4.1 62.7 1.0 CD2 A:PHE690 4.2 59.7 1.0 O A:HOH2984 4.2 47.9 1.0 C A:HIS692 4.2 61.0 1.0 CD1 A:PHE690 4.4 59.8 1.0 N A:HIS692 4.4 61.1 1.0 O A:HIS692 4.5 61.9 1.0 N A:THR693 4.6 57.8 1.0 CG A:PHE690 4.6 58.4 1.0 NE2 A:GLN428 4.6 53.3 1.0 N A:ASP691 4.7 58.4 1.0 C A:GLN695 4.7 42.2 1.0 C A:THR693 4.7 52.0 1.0 SG A:CYS694 4.8 72.2 1.0 N A:LEU696 4.8 41.7 1.0 CA A:ASP691 4.9 61.6 1.0

D.Meusch, C.Gatsogiannis, R.G.Efremov, A.E.Lang, O.Hofnagel, I.R.Vetter, K.Aktories, S.Raunser. Mechanism of Tc Toxin Action Revealed in Molecular Detail Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13015