Zinc in PDB 5t93: Immunoglobulin Light Chain Variable Domain Al-T05

The structure of Immunoglobulin Light Chain Variable Domain Al-T05, PDB code: 5t93 was solved by M.Ramirez-Alvarado, L.M.Blancas-Mejia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.43 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.459, 42.118, 64.995, 80.66, 86.24, 63.02
R / Rfree (%)	17.1 / 22.3

The binding sites of Zinc atom in the Immunoglobulin Light Chain Variable Domain Al-T05 (pdb code 5t93). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Immunoglobulin Light Chain Variable Domain Al-T05, PDB code: 5t93:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Immunoglobulin Light Chain Variable Domain Al-T05


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Immunoglobulin Light Chain Variable Domain Al-T05 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:51.7 occ:1.00 O A:ACT202 1.8 10.2 1.0 O A:HOH301 2.0 31.1 1.0 O A:ACT203 2.3 20.9 1.0 ND1 A:HIS39 2.4 28.9 1.0 OXT A:ACT203 2.4 32.5 1.0 C A:ACT203 2.8 21.0 1.0 HB3 A:HIS39 2.9 30.4 1.0 C A:ACT202 3.0 32.5 1.0 CG A:HIS39 3.2 26.4 1.0 CE1 A:HIS39 3.3 34.7 1.0 CB A:HIS39 3.4 25.3 1.0 HD11 C:LEU99 3.5 27.2 1.0 OXT A:ACT202 3.5 27.6 1.0 HE1 A:HIS39 3.6 41.6 1.0 HB2 A:HIS39 3.6 30.4 1.0 HD21 C:LEU99 3.6 32.0 1.0 HE2 A:TYR88 3.8 17.1 1.0 H1 A:ACT202 3.8 37.0 1.0 HH A:TYR37 3.9 22.5 1.0 HE1 A:TYR37 3.9 21.2 1.0 CH3 A:ACT202 4.0 30.8 1.0 OH A:TYR88 4.0 17.3 1.0 CH3 A:ACT203 4.2 25.8 1.0 CE2 A:TYR88 4.3 14.2 1.0 CD1 C:LEU99 4.3 22.6 1.0 HD13 C:LEU99 4.4 27.2 1.0 CD2 A:HIS39 4.4 27.9 1.0 NE2 A:HIS39 4.4 26.6 1.0 CD2 C:LEU99 4.5 26.6 1.0 CZ A:TYR88 4.5 16.3 1.0 HD22 C:LEU99 4.5 32.0 1.0 HH A:TYR88 4.6 20.8 1.0 H2 A:ACT203 4.6 31.0 1.0 H3 A:ACT202 4.7 37.0 1.0 H2 A:ACT202 4.7 37.0 1.0 H1 A:ACT203 4.7 31.0 1.0 OH A:TYR37 4.7 18.7 1.0 HG3 A:PRO45 4.7 28.9 1.0 H3 A:ACT203 4.8 31.0 1.0 CE1 A:TYR37 4.8 17.6 1.0 CA A:HIS39 4.8 19.5 1.0 O A:HIS39 4.9 21.2 1.0 HB3 A:PRO45 5.0 22.2 1.0 CG C:LEU99 5.0 25.8 1.0 HB2 A:ASP86 5.0 28.1 1.0

Zinc binding site 2 out of 7 in the Immunoglobulin Light Chain Variable Domain Al-T05


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Immunoglobulin Light Chain Variable Domain Al-T05 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:57.6 occ:1.00 HD1 B:HIS39 1.7 38.0 1.0 OXT B:ACT202 1.9 23.2 1.0 OXT B:ACT204 2.4 28.1 1.0 O B:HOH332 2.4 32.2 1.0 ND1 B:HIS39 2.4 31.6 1.0 O B:ACT204 2.7 35.8 1.0 C B:ACT204 2.9 23.4 1.0 C B:ACT202 3.1 48.6 1.0 HB3 B:HIS39 3.2 30.6 1.0 CG B:HIS39 3.3 23.2 1.0 HD11 D:LEU99 3.3 30.4 1.0 CE1 B:HIS39 3.3 39.0 1.0 HE1 B:HIS39 3.5 46.8 1.0 CB B:HIS39 3.6 25.5 1.0 HB2 B:HIS39 3.6 30.6 1.0 O B:ACT202 3.8 30.6 1.0 HD21 D:LEU99 3.8 27.3 1.0 HE1 B:TYR37 3.8 22.8 1.0 HH B:TYR37 3.8 26.9 1.0 HH B:TYR88 3.9 29.8 1.0 HE2 B:TYR88 4.0 24.6 1.0 CH3 B:ACT202 4.0 38.7 1.0 H3 B:ACT202 4.0 46.5 1.0 H2 B:ACT202 4.1 46.5 1.0 CD1 D:LEU99 4.2 25.3 1.0 HD13 D:LEU99 4.3 30.4 1.0 OH B:TYR88 4.4 24.8 1.0 NE2 B:HIS39 4.4 31.8 1.0 H1 B:ACT205 4.4 54.5 1.0 CD2 B:HIS39 4.4 26.0 1.0 CH3 B:ACT204 4.4 31.4 1.0 CE2 B:TYR88 4.5 20.4 1.0 CD2 D:LEU99 4.6 22.7 1.0 OH B:TYR37 4.7 22.4 1.0 HB3 B:PRO45 4.7 20.6 1.0 HD22 D:LEU99 4.7 27.3 1.0 CE1 B:TYR37 4.7 18.9 1.0 CZ B:TYR88 4.7 21.5 1.0 H2 B:ACT204 4.7 37.7 1.0 HD12 D:LEU99 4.8 30.4 1.0 H3 B:ACT204 4.9 37.7 1.0 CG D:LEU99 5.0 20.5 1.0 H1 B:ACT204 5.0 37.7 1.0 H1 B:ACT202 5.0 46.5 1.0

Zinc binding site 3 out of 7 in the Immunoglobulin Light Chain Variable Domain Al-T05


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Immunoglobulin Light Chain Variable Domain Al-T05 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:57.2 occ:1.00 O B:ACT205 2.0 50.1 1.0 OXT B:ACT205 2.3 54.6 1.0 OD2 B:ASP86 2.4 25.8 1.0 C B:ACT205 2.5 51.8 1.0 CG B:ASP86 3.2 24.1 1.0 OD1 B:ASP86 3.3 22.3 1.0 O B:HOH385 3.5 42.6 1.0 CH3 B:ACT205 3.9 45.4 1.0 H1 B:ACT202 4.0 46.5 1.0 O B:ACT202 4.2 30.6 1.0 H2 B:ACT205 4.2 54.5 1.0 H1 B:ACT205 4.3 54.5 1.0 H2 B:ACT202 4.4 46.5 1.0 CB B:ASP86 4.5 18.4 1.0 CH3 B:ACT202 4.5 38.7 1.0 C B:ACT202 4.6 48.6 1.0 H3 B:ACT205 4.6 54.5 1.0 HB3 B:ASP86 4.7 22.1 1.0 HH B:TYR88 4.7 29.8 1.0 HB2 B:LYS106 4.7 20.1 1.0 HB2 B:ASP86 4.7 22.1 1.0 HG2 B:PRO41 4.8 34.1 1.0 HG3 B:PRO41 5.0 34.1 1.0 OH B:TYR88 5.0 24.8 1.0

Zinc binding site 4 out of 7 in the Immunoglobulin Light Chain Variable Domain Al-T05


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Immunoglobulin Light Chain Variable Domain Al-T05 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:57.0 occ:1.00 OXT C:ACT205 1.9 36.9 1.0 O C:ACT202 2.1 14.3 1.0 O C:ACT205 2.2 21.3 1.0 ND1 C:HIS39 2.3 32.9 1.0 C C:ACT205 2.3 28.6 1.0 O C:ACT203 2.4 41.8 1.0 CG C:HIS39 3.0 26.0 1.0 HB3 C:HIS39 3.1 23.5 1.0 CE1 C:HIS39 3.2 38.1 1.0 HB2 C:HIS39 3.2 23.5 1.0 CB C:HIS39 3.3 19.6 1.0 C C:ACT202 3.3 38.7 1.0 C C:ACT203 3.4 42.8 1.0 HE1 C:HIS39 3.4 45.8 1.0 CH3 C:ACT205 3.8 35.4 1.0 OXT C:ACT203 3.8 39.8 1.0 HE1 C:TYR37 3.8 20.0 1.0 HD21 A:LEU99 3.8 30.2 1.0 HD11 A:LEU99 3.8 36.3 1.0 HH C:TYR37 3.9 25.1 1.0 OXT C:ACT202 3.9 35.3 1.0 H2 C:ACT205 4.0 42.5 1.0 H1 C:ACT202 4.1 49.0 1.0 CD2 C:HIS39 4.1 28.1 1.0 NE2 C:HIS39 4.1 23.1 1.0 HE2 C:TYR88 4.3 25.6 1.0 H1 C:ACT205 4.3 42.5 1.0 CH3 C:ACT202 4.3 40.8 1.0 HH C:TYR88 4.3 34.8 1.0 H3 C:ACT205 4.4 42.5 1.0 HB3 C:PRO45 4.5 24.6 1.0 HD22 A:LEU99 4.5 30.2 1.0 HD13 A:LEU99 4.5 36.3 1.0 HG3 C:PRO45 4.5 28.4 1.0 CD2 A:LEU99 4.6 25.1 1.0 CD1 A:LEU99 4.6 30.2 1.0 O C:HOH301 4.6 34.1 1.0 CH3 C:ACT203 4.6 41.3 1.0 H3 C:ACT203 4.6 49.6 1.0 CE1 C:TYR37 4.7 16.7 1.0 OH C:TYR37 4.7 20.9 1.0 CE2 C:TYR88 4.8 21.3 1.0 OH C:TYR88 4.8 29.0 1.0 HG A:SER35 4.8 24.2 0.4 CA C:HIS39 4.8 18.3 1.0 HD2 C:HIS39 4.9 33.8 1.0 HE2 C:HIS39 4.9 27.8 1.0 H3 C:ACT202 5.0 49.0 1.0

Zinc binding site 5 out of 7 in the Immunoglobulin Light Chain Variable Domain Al-T05


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Immunoglobulin Light Chain Variable Domain Al-T05 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn204 b:49.2 occ:1.00 OD2 C:ASP86 2.5 29.3 1.0 O C:HOH413 2.5 48.9 1.0 CG C:ASP86 3.1 24.2 1.0 OD1 C:ASP86 3.3 26.0 1.0 O C:HOH404 3.3 41.0 1.0 H2 C:ACT202 3.5 49.0 1.0 OXT C:ACT202 4.0 35.3 1.0 CH3 C:ACT202 4.3 40.8 1.0 HH C:TYR88 4.4 34.8 1.0 C C:ACT202 4.4 38.7 1.0 CB C:ASP86 4.4 22.1 1.0 HB3 C:ASP86 4.5 26.6 1.0 H3 C:ACT202 4.6 49.0 1.0 OH C:TYR88 4.7 29.0 1.0 HB2 C:ASP86 4.7 26.6 1.0 HG2 C:PRO41 4.7 27.8 1.0 HB2 C:LYS106 4.7 28.0 1.0 O C:HOH345 4.8 26.5 1.0 HG3 C:PRO41 4.9 27.8 1.0

Zinc binding site 6 out of 7 in the Immunoglobulin Light Chain Variable Domain Al-T05


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Immunoglobulin Light Chain Variable Domain Al-T05 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:63.1 occ:1.00 OXT D:ACT202 1.9 46.1 1.0 O D:ACT202 2.0 21.9 1.0 OXT D:ACT203 2.3 25.0 1.0 C D:ACT202 2.3 26.0 1.0 O D:HOH328 2.3 39.5 1.0 ND1 D:HIS39 2.4 32.2 1.0 O D:ACT203 2.4 32.1 1.0 C D:ACT203 2.7 33.7 1.0 HB3 D:HIS39 3.0 32.4 1.0 CG D:HIS39 3.3 29.1 1.0 CE1 D:HIS39 3.3 36.1 1.0 O D:HOH323 3.5 44.2 1.0 CB D:HIS39 3.5 27.0 1.0 HE1 D:HIS39 3.5 43.4 1.0 HD21 B:LEU99 3.6 34.6 1.0 HB2 D:HIS39 3.6 32.4 1.0 CH3 D:ACT202 3.8 20.5 1.0 HD11 B:LEU99 3.8 29.9 1.0 HH D:TYR37 4.0 23.8 1.0 HE2 D:TYR88 4.0 24.9 1.0 HE1 D:TYR37 4.0 28.4 1.0 H2 D:ACT202 4.1 24.6 1.0 OH D:TYR88 4.2 29.0 1.0 CH3 D:ACT203 4.2 32.4 1.0 H1 D:ACT202 4.2 24.6 1.0 H3 D:ACT202 4.4 24.6 1.0 CD2 D:HIS39 4.4 24.8 1.0 NE2 D:HIS39 4.4 36.5 1.0 CD2 B:LEU99 4.5 28.8 1.0 HD22 B:LEU99 4.5 34.6 1.0 CE2 D:TYR88 4.5 20.7 1.0 CD1 B:LEU99 4.6 24.9 1.0 HD13 B:LEU99 4.6 29.9 1.0 HG3 D:PRO45 4.7 34.2 1.0 CZ D:TYR88 4.7 20.7 1.0 HH D:TYR88 4.7 34.8 1.0 H3 D:ACT203 4.7 38.9 1.0 H2 D:ACT203 4.7 38.9 1.0 H1 D:ACT203 4.7 38.9 1.0 OH D:TYR37 4.8 19.8 1.0 CE1 D:TYR37 4.9 23.7 1.0 CA D:HIS39 5.0 16.1 1.0

Zinc binding site 7 out of 7 in the Immunoglobulin Light Chain Variable Domain Al-T05


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Immunoglobulin Light Chain Variable Domain Al-T05 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn204 b:47.2 occ:0.45 OD1 D:ASP51 2.0 32.1 1.0 O B:HOH351 2.0 18.9 1.0 O D:HOH364 2.1 32.0 1.0 CG D:ASP51 2.8 34.2 1.0 OD2 D:ASP51 2.9 31.8 1.0 H B:GLY42 3.0 29.7 1.0 O D:HOH367 3.1 30.9 1.0 HE2 B:HIS39 3.2 38.2 1.0 HE1 B:HIS39 3.4 46.8 1.0 HD2 D:TYR33 3.4 58.3 1.0 HD1 D:TYR50 3.5 26.2 1.0 NE2 B:HIS39 3.8 31.8 1.0 N B:GLY42 3.8 24.8 1.0 CD2 D:TYR33 3.8 48.6 1.0 CE1 B:HIS39 3.9 39.0 1.0 HA B:PRO41 3.9 27.6 1.0 HA2 B:GLY42 4.1 31.1 1.0 O D:HOH319 4.1 28.9 1.0 CB D:ASP51 4.2 28.4 1.0 HE2 D:TYR33 4.2 56.8 1.0 CE2 D:TYR33 4.3 47.3 1.0 HA D:ASP51 4.4 23.8 1.0 H D:ASP51 4.4 20.9 1.0 CD1 D:TYR50 4.4 21.8 1.0 CA B:GLY42 4.4 25.9 1.0 H B:THR43 4.5 34.9 1.0 HB2 D:TYR33 4.5 38.1 1.0 HB3 D:TYR33 4.5 38.1 1.0 CG D:TYR33 4.6 32.2 1.0 HE1 D:TYR50 4.6 23.7 1.0 HB3 D:ASP51 4.7 34.0 1.0 CA D:ASP51 4.7 19.8 1.0 HB2 D:ASP51 4.7 34.0 1.0 HB2 D:TYR50 4.7 24.8 1.0 CA B:PRO41 4.7 23.0 1.0 N D:ASP51 4.7 17.4 1.0 C B:PRO41 4.8 21.9 1.0 CB D:TYR33 4.8 31.7 1.0 O B:THR43 4.8 23.6 1.0 HB3 B:PRO41 4.9 34.5 1.0 N B:THR43 4.9 29.1 1.0 C B:GLY42 4.9 26.2 1.0 CE1 D:TYR50 5.0 19.7 1.0

L.M.Blancas-Mejia, P.Misra, M.Ramirez-Alvarado. Differences in Protein Concentration Dependence For Nucleation and Elongation in Light Chain Amyloid Formation. Biochemistry V. 56 757 2017.
ISSN: ISSN 1520-4995
PubMed: 28074646
DOI: 10.1021/ACS.BIOCHEM.6B01043