Zinc in PDB 3dgd: Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6

The structure of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6, PDB code: 3dgd was solved by L.C.Palmieri, J.B.B.Freire, D.Foguel, L.M.T.R.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.37 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.950, 60.690, 82.990, 90.00, 89.98, 90.00
R / Rfree (%)	15.7 / 20.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 (pdb code 3dgd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6, PDB code: 3dgd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn128 b:16.3 occ:0.50 OD2 A:ASP74 1.9 23.3 1.0 NE2 A:HIS31 2.2 20.2 0.5 CE1 A:HIS31 2.2 14.9 0.5 O A:HOH238 2.5 30.0 1.0 CG A:ASP74 2.6 18.0 1.0 OD1 A:ASP74 2.6 21.8 1.0 CD2 A:HIS31 3.0 21.0 0.5 ND1 A:HIS31 3.0 19.1 0.5 NE2 A:HIS31 3.3 19.3 0.5 CE1 A:HIS31 3.3 20.1 0.5 CB A:ASP74 4.1 18.6 1.0 CG A:HIS31 4.2 19.6 0.5 CG A:HIS31 4.2 17.4 0.5 O A:HOH171 4.3 28.8 1.0 ND1 A:HIS31 4.3 19.6 0.5 CD2 A:HIS31 4.3 15.4 0.5 CB A:ALA29 4.4 17.7 1.0 O A:HOH155 4.8 33.6 1.0 NE2 A:HIS90 4.8 24.1 1.0 CD2 A:HIS90 4.9 23.6 1.0

Zinc binding site 2 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn129 b:29.5 occ:0.75 ND1 A:HIS56 2.0 23.7 1.0 O A:HOH233 2.1 40.3 1.0 SG A:CYS10 2.3 33.8 1.0 O A:HOH234 2.4 34.4 1.0 CE1 A:HIS56 2.9 24.0 1.0 CG A:HIS56 3.1 23.1 1.0 CB A:CYS10 3.3 29.6 1.0 CB A:HIS56 3.5 22.8 1.0 N A:CYS10 3.9 34.6 1.0 NE2 A:HIS56 4.1 24.9 1.0 CD2 A:HIS56 4.2 26.4 1.0 CA A:HIS56 4.2 20.7 1.0 CA A:CYS10 4.3 32.0 1.0 CG A:MET13 4.6 21.3 1.0 N A:GLY57 4.8 21.8 1.0 CB A:MET13 4.8 19.6 1.0

Zinc binding site 3 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn130 b:23.1 occ:1.00 OE1 A:GLU92 2.0 13.1 0.5 ND1 A:HIS90 2.0 19.5 1.0 NE2 A:HIS88 2.0 18.4 1.0 O A:HOH237 2.1 16.9 0.5 O A:HOH232 2.2 20.5 1.0 CE1 A:HIS90 2.9 24.4 1.0 CD2 A:HIS88 3.0 16.7 1.0 CE1 A:HIS88 3.1 21.7 1.0 CG A:HIS90 3.2 18.7 1.0 CD A:GLU92 3.2 26.1 0.5 CB A:HIS90 3.6 16.6 1.0 CG A:GLU92 4.0 25.7 0.5 NE2 A:HIS90 4.1 24.1 1.0 OE2 A:GLU92 4.1 34.2 0.5 CG A:HIS88 4.1 16.2 1.0 CG1 B:VAL94 4.2 17.1 1.0 ND1 A:HIS88 4.2 18.0 1.0 CD2 A:HIS90 4.2 23.6 1.0 OE2 A:GLU72 4.2 30.7 1.0 CG A:GLU89 4.4 24.1 0.5 N A:HIS90 4.4 17.4 1.0 CD A:GLU72 4.4 24.4 1.0 CA A:HIS90 4.6 16.6 1.0 O A:HOH168 4.7 37.5 1.0 OE1 A:GLU72 4.8 28.2 1.0 CB B:VAL94 4.8 15.6 1.0 CG A:GLU89 4.8 16.2 0.5 OE1 A:GLU89 4.9 34.0 0.5

Zinc binding site 4 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn133 b:30.0 occ:1.00 OE1 A:GLU61 2.2 16.8 0.5 O A:HOH239 2.3 30.0 1.0 OE2 A:GLU61 2.8 17.2 0.5 CD A:GLU61 2.8 16.6 0.5 O A:GLU61 3.9 25.3 0.5 O A:GLU61 4.0 20.2 0.5 CA A:GLU62 4.3 25.8 1.0 O A:HOH223 4.3 37.2 1.0 CG A:GLU61 4.3 19.6 0.5 C A:GLU61 4.4 26.5 0.5 C A:GLU61 4.4 22.7 0.5 N A:GLU62 4.5 25.4 1.0 O A:GLU62 4.9 27.6 1.0

Zinc binding site 5 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn128 b:32.0 occ:0.75 O B:HOH221 2.1 48.2 1.0 SG B:CYS10 2.2 37.4 1.0 ND1 B:HIS56 2.3 19.6 0.5 CD2 B:HIS56 2.4 28.0 0.5 O B:HOH220 2.5 38.6 1.0 CG B:HIS56 3.2 21.2 0.5 CB B:CYS10 3.2 33.0 1.0 CB B:HIS56 3.3 22.8 0.5 CG B:HIS56 3.3 24.0 0.5 CE1 B:HIS56 3.4 17.4 0.5 NE2 B:HIS56 3.5 30.5 0.5 CB B:HIS56 3.7 24.2 0.5 N B:CYS10 3.8 37.3 1.0 CA B:CYS10 4.1 33.9 1.0 CA B:HIS56 4.2 22.8 0.5 CA B:HIS56 4.4 23.3 0.5 CD2 B:HIS56 4.4 18.9 0.5 NE2 B:HIS56 4.4 20.4 0.5 CG B:MET13 4.4 23.3 1.0 ND1 B:HIS56 4.5 30.2 0.5 CE1 B:HIS56 4.5 30.4 0.5 CB B:MET13 4.7 22.2 1.0 N B:GLY57 4.8 22.9 1.0

Zinc binding site 6 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn129 b:17.8 occ:0.50 OD2 B:ASP74 2.0 21.9 1.0 O B:HOH218 2.0 24.2 1.0 NE2 B:HIS31 2.2 20.1 0.5 CE1 B:HIS31 2.2 19.4 0.5 CG B:ASP74 2.9 21.9 1.0 CD2 B:HIS31 3.1 20.3 0.5 O B:HOH219 3.1 36.0 0.5 OD1 B:ASP74 3.2 24.7 1.0 NE2 B:HIS31 3.2 20.4 0.5 ND1 B:HIS31 3.2 22.4 0.5 CE1 B:HIS31 3.3 21.4 0.5 CB B:ALA29 4.1 22.6 1.0 O B:ACT131 4.1 28.4 1.0 CB B:ASP74 4.2 18.7 1.0 CG B:HIS31 4.3 18.7 0.5 ND1 B:HIS31 4.3 18.7 0.5 CD2 B:HIS31 4.4 17.3 0.5 CG B:HIS31 4.4 21.5 0.5

Zinc binding site 7 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn130 b:21.5 occ:0.75 O B:HOH217 2.2 29.9 1.0 OE2 B:GLU92 2.2 27.4 0.5 ND1 B:HIS90 2.2 17.3 0.5 NE2 B:HIS88 2.3 20.9 1.0 CD2 B:HIS90 2.3 16.3 0.5 CD2 B:HIS88 3.0 18.7 1.0 CE1 B:HIS90 3.1 20.2 0.5 CG B:HIS90 3.2 20.3 0.5 CG B:HIS90 3.3 19.2 0.5 NE2 B:HIS90 3.3 23.6 0.5 CE1 B:HIS88 3.4 20.6 1.0 CD B:GLU92 3.4 23.1 0.5 CB B:HIS90 3.6 17.7 0.5 CB B:HIS90 3.7 18.4 0.5 CG1 A:VAL94 4.1 18.3 1.0 CG B:HIS88 4.2 18.8 1.0 OE1 B:GLU92 4.3 26.5 0.5 NE2 B:HIS90 4.3 22.5 0.5 N B:HIS90 4.3 19.0 0.5 ND1 B:HIS88 4.4 19.4 1.0 OE1 B:GLU72 4.4 29.7 1.0 ND1 B:HIS90 4.4 22.0 0.5 CD2 B:HIS90 4.4 22.2 0.5 CE1 B:HIS90 4.4 22.1 0.5 CG B:GLU92 4.4 17.8 0.5 N B:HIS90 4.4 18.8 0.5 O B:HOH165 4.5 53.0 1.0 O B:HOH193 4.5 46.5 1.0 CG B:GLU89 4.6 20.7 0.5 CA B:HIS90 4.6 18.3 0.5 CA B:HIS90 4.6 17.6 0.5 CG B:GLU89 4.7 21.8 0.5 CB A:VAL94 4.8 17.6 1.0 CD B:GLU72 4.9 28.4 1.0 O B:HIS90 4.9 18.0 0.5

Zinc binding site 8 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn134 b:30.0 occ:1.00 O B:HOH223 2.2 25.0 0.5 O B:GLU62 2.3 16.9 0.5 OE2 B:GLU62 2.3 17.4 0.5 OE2 B:GLU62 2.4 23.3 0.5 CD B:GLU62 3.0 24.7 0.5 CG B:GLU62 3.0 25.0 0.5 CD B:GLU62 3.3 24.9 0.5 C B:GLU62 3.3 20.2 0.5 O B:GLU62 3.4 27.8 0.5 CG B:GLU62 3.5 22.3 0.5 C B:GLU62 3.6 25.4 0.5 CA B:GLU62 3.7 25.9 0.5 CA B:GLU62 3.7 21.8 0.5 CB B:GLU62 3.9 25.5 0.5 O B:HOH173 4.1 33.3 1.0 OE1 B:GLU62 4.2 24.6 0.5 CB B:GLU62 4.2 20.2 0.5 OE1 B:GLU62 4.4 26.5 0.5 N B:GLU63 4.5 20.0 1.0 CA B:GLU63 5.0 20.0 1.0 O B:GLU61 5.0 27.2 1.0

Zinc binding site 9 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn128 b:20.3 occ:1.00 NE2 C:HIS88 2.0 18.9 1.0 OE1 C:GLU92 2.0 9.0 0.5 ND1 C:HIS90 2.1 19.5 1.0 O C:HOH135 2.3 20.4 1.0 CE1 C:HIS90 2.9 23.1 1.0 CD2 C:HIS88 2.9 17.0 1.0 CD C:GLU92 3.0 19.5 0.5 CE1 C:HIS88 3.0 20.3 1.0 CG C:HIS90 3.1 20.4 1.0 OE2 C:GLU92 3.4 24.8 0.5 CB C:HIS90 3.5 16.7 1.0 NE2 C:HIS90 4.1 21.2 1.0 CG C:HIS88 4.1 16.6 1.0 ND1 C:HIS88 4.1 17.5 1.0 CG1 D:VAL94 4.2 18.4 1.0 CD2 C:HIS90 4.2 22.9 1.0 OE2 C:GLU72 4.3 31.2 1.0 CG C:GLU92 4.4 22.1 0.5 N C:HIS90 4.4 16.9 1.0 CD C:GLU72 4.5 23.4 1.0 CA C:HIS90 4.6 16.9 1.0 O C:HOH208 4.6 35.3 1.0 CG C:GLU89 4.7 23.4 1.0 CB D:VAL94 4.8 15.7 1.0 OE1 C:GLU72 4.8 27.8 1.0

Zinc binding site 10 out of 15 in the Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the F87M/L110M Mutant of Human Transthyretin at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn129 b:29.2 occ:0.75 ND1 C:HIS56 2.0 24.7 1.0 O C:HOH225 2.1 38.4 1.0 SG C:CYS10 2.3 34.1 1.0 O C:HOH209 2.3 36.3 1.0 CE1 C:HIS56 2.9 25.2 1.0 CG C:HIS56 3.1 22.7 1.0 CB C:CYS10 3.3 29.9 1.0 CB C:HIS56 3.5 23.1 1.0 N C:CYS10 3.9 33.1 1.0 NE2 C:HIS56 4.0 25.1 1.0 CD2 C:HIS56 4.2 28.0 1.0 CA C:CYS10 4.2 31.6 1.0 CA C:HIS56 4.2 21.2 1.0 CG C:MET13 4.5 22.6 1.0 N C:GLY57 4.8 21.7 1.0 CB C:MET13 4.8 19.6 1.0

L.De.C.Palmieri, L.M.Lima, J.B.Freire, L.Bleicher, I.Polikarpov, F.C.Almeida, D.Foguel. Novel ZN2+-Binding Sites in Human Transthyretin: Implications For Amyloidogenesis and Retinol-Binding Protein Recognition. J.Biol.Chem. V. 285 31731 2010.
ISSN: ISSN 0021-9258
PubMed: 20659897
DOI: 10.1074/JBC.M110.157206