Zinc in PDB 8oq9: Crystal Structure of the Titin Domain FN3-56

All present enzymatic activity of Crystal Structure of the Titin Domain FN3-56:
2.7.11.1;

The structure of Crystal Structure of the Titin Domain FN3-56, PDB code: 8oq9 was solved by M.Rees, M.Gautel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.69 / 1.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.53, 89.63, 97.11, 90, 90, 90
R / Rfree (%)	16.4 / 19.2

The structure of Crystal Structure of the Titin Domain FN3-56 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Titin Domain FN3-56 (pdb code 8oq9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Titin Domain FN3-56, PDB code: 8oq9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Titin Domain FN3-56


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 Titin Domain FN3-56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:12.6 occ:0.81 OE1 A:GLU83 1.8 18.7 1.0 OD1 C:ASP62 1.9 14.3 1.0 NE2 A:HIS41 2.1 15.3 1.0 CL C:CL202 2.2 20.9 1.0 CG C:ASP62 2.7 15.8 1.0 CD A:GLU83 2.8 18.5 1.0 OD2 C:ASP62 2.9 18.6 1.0 OE2 A:GLU83 3.1 16.8 1.0 CE1 A:HIS41 3.1 20.0 1.0 CD2 A:HIS41 3.1 13.3 1.0 HE1 A:HIS41 3.3 24.0 1.0 HD2 A:HIS41 3.3 16.0 1.0 H C:LEU63 3.6 16.7 1.0 HG2 A:PRO59 3.6 15.5 1.0 HD12 A:ILE88 3.7 22.8 1.0 HG3 A:PRO59 3.9 15.5 1.0 HG2 C:ARG64 4.0 22.9 1.0 HB3 A:GLU83 4.1 22.1 1.0 HB A:ILE88 4.1 16.7 1.0 CG A:GLU83 4.1 19.7 1.0 HD3 C:ARG64 4.1 26.6 1.0 CB C:ASP62 4.2 15.4 1.0 CG A:PRO59 4.2 12.9 1.0 ND1 A:HIS41 4.2 18.5 1.0 CG A:HIS41 4.3 14.9 1.0 O C:HOH403 4.3 33.5 1.0 HA C:ASP62 4.3 18.6 1.0 HB2 C:LEU63 4.4 16.1 1.0 N C:LEU63 4.4 13.9 1.0 HG2 A:GLU83 4.4 23.7 1.0 HB3 C:ASP62 4.5 18.5 1.0 CB A:GLU83 4.5 18.4 1.0 HB2 A:GLU83 4.5 22.1 1.0 O C:HOH394 4.6 29.7 1.0 CD1 A:ILE88 4.6 19.0 1.0 HD2 C:ARG64 4.7 26.6 1.0 HG13 A:ILE88 4.7 20.8 1.0 CA C:ASP62 4.7 15.5 1.0 CD C:ARG64 4.7 22.2 1.0 HB2 C:ASP62 4.8 18.5 1.0 CG C:ARG64 4.8 19.1 1.0 HG C:LEU63 4.8 16.8 1.0 HG3 A:GLU83 4.8 23.7 1.0 CB A:ILE88 5.0 13.9 1.0 HB3 A:PRO59 5.0 17.4 1.0 HD1 A:HIS41 5.0 22.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Titin Domain FN3-56


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 Titin Domain FN3-56 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:31.7 occ:0.63 HE1 B:HIS41 1.5 36.2 1.0 CE1 B:HIS41 2.0 30.1 1.0 HE2 B:HIS41 2.0 48.5 1.0 NE2 B:HIS41 2.2 40.4 1.0 OE2 B:GLU83 2.2 40.4 1.0 CL B:CL204 2.3 38.2 0.8 HD11 B:ILE88 2.8 39.2 1.0 CD B:GLU83 3.0 36.0 1.0 HG3 B:PRO59 3.0 36.2 1.0 ND1 B:HIS41 3.2 35.4 1.0 OE1 B:GLU83 3.3 47.9 1.0 HD13 B:ILE88 3.5 39.2 1.0 CD1 B:ILE88 3.5 32.6 1.0 CD2 B:HIS41 3.5 31.5 1.0 HG2 B:PRO59 3.7 36.2 1.0 HG12 B:ILE88 3.8 34.9 1.0 CG B:PRO59 3.8 30.1 1.0 CG B:HIS41 4.0 25.6 1.0 CG1 B:ILE88 4.2 29.1 1.0 HD2 B:HIS41 4.2 37.8 1.0 O B:HOH411 4.2 38.0 1.0 HB3 B:PRO59 4.2 29.1 1.0 HD12 B:ILE88 4.3 39.2 1.0 CG B:GLU83 4.3 31.0 1.0 HG13 B:ILE88 4.4 34.9 1.0 HG2 B:GLU83 4.4 37.2 1.0 ZN B:ZN203 4.6 33.7 0.6 CB B:PRO59 4.6 24.3 1.0 HB3 B:GLU83 4.7 29.8 1.0 HD3 B:PRO59 4.8 32.3 1.0 O B:HOH376 4.9 18.5 0.5 CD B:PRO59 5.0 26.9 1.0 CB B:GLU83 5.0 24.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Titin Domain FN3-56


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 Titin Domain FN3-56 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:23.4 occ:0.55 O B:HOH328 1.8 41.3 1.0 OD2 C:ASP32 1.8 28.1 1.0 OE1 B:GLU36 1.9 29.8 1.0 CL B:CL205 2.2 49.4 1.0 CG C:ASP32 2.8 21.7 1.0 CD B:GLU36 2.8 29.8 1.0 HH22 C:ARG28 2.9 36.3 1.0 OE2 B:GLU36 3.1 27.8 1.0 OD1 C:ASP32 3.1 20.1 1.0 HH12 C:ARG28 3.7 31.1 1.0 NH2 C:ARG28 3.7 30.2 1.0 O C:HOH398 3.8 41.8 1.0 CB C:ASP32 4.1 16.3 1.0 HH21 C:ARG28 4.2 36.3 1.0 CG B:GLU36 4.2 27.3 1.0 O B:HOH386 4.2 27.8 1.0 HB3 C:ASP32 4.2 19.6 1.0 HG2 B:GLU36 4.4 32.8 1.0 HB2 C:ASP32 4.4 19.6 1.0 NH1 C:ARG28 4.4 25.9 1.0 HB3 B:GLU36 4.4 24.7 1.0 O C:HOH347 4.5 21.9 1.0 CZ C:ARG28 4.5 21.1 1.0 O C:HOH414 4.6 33.7 1.0 HA2 C:GLY34 4.7 27.2 1.0 O C:SER35 4.7 20.9 1.0 H C:GLY34 4.7 24.2 1.0 O A:HOH408 4.8 29.8 1.0 HG3 B:GLU36 4.8 32.8 1.0 CB B:GLU36 4.9 20.6 1.0 H C:ASP32 4.9 22.1 1.0 HA C:GLU36 5.0 20.9 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Titin Domain FN3-56


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 Titin Domain FN3-56 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:33.7 occ:0.63 O B:HOH412 2.1 21.7 1.0 ND1 B:HIS41 2.2 35.4 1.0 O B:HOH411 2.4 38.0 1.0 O B:HOH408 2.4 35.2 1.0 CE1 B:HIS41 2.9 30.1 1.0 HB3 B:HIS41 3.0 19.1 1.0 CG B:HIS41 3.0 25.6 1.0 HE1 B:HIS41 3.1 36.2 1.0 HD2 B:ARG54 3.1 54.6 1.0 CB B:HIS41 3.4 15.9 1.0 HA B:HIS41 3.6 19.6 1.0 HD3 B:ARG54 3.6 54.6 1.0 CD B:ARG54 3.8 45.5 1.0 NE2 B:HIS41 3.9 40.4 1.0 HG3 B:PRO59 3.9 36.2 1.0 CD2 B:HIS41 3.9 31.5 1.0 CA B:HIS41 4.1 16.3 1.0 HG2 B:ARG54 4.2 41.8 1.0 HB2 B:HIS41 4.3 19.1 1.0 HD3 B:PRO59 4.5 32.3 1.0 HE2 B:HIS41 4.6 48.5 1.0 ZN B:ZN201 4.6 31.7 0.6 HA B:PRO59 4.6 21.9 1.0 H B:VAL42 4.6 15.7 1.0 CG B:ARG54 4.6 34.9 1.0 HB3 B:PRO59 4.6 29.1 1.0 CG B:PRO59 4.7 30.1 1.0 HD2 B:HIS41 4.7 37.8 1.0 N B:PRO59 4.8 21.7 1.0 HD13 B:ILE88 4.9 39.2 1.0 CD B:PRO59 4.9 26.9 1.0 NE B:ARG54 4.9 46.0 1.0 C B:HIS41 5.0 15.4 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Titin Domain FN3-56


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 Titin Domain FN3-56 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:14.2 occ:1.00 OE2 C:GLU83 2.0 12.7 0.6 NE2 C:HIS41 2.1 11.6 1.0 OE1 C:GLU83 2.2 12.0 0.4 CD C:GLU83 2.6 12.8 0.6 OE1 C:GLU83 2.6 13.3 0.6 OE2 C:GLU83 2.8 11.5 0.4 CD C:GLU83 2.8 13.8 0.4 CD2 C:HIS41 3.0 11.2 1.0 HD2 C:HIS41 3.1 13.4 1.0 CE1 C:HIS41 3.1 16.5 1.0 HG3 C:PRO59 3.1 23.9 1.0 HE1 C:HIS41 3.4 19.8 1.0 O C:HOH307 4.0 16.3 1.0 CG C:GLU83 4.0 13.3 0.6 HD12 C:ILE88 4.1 17.7 1.0 CG C:PRO59 4.1 19.9 1.0 CG C:HIS41 4.2 10.2 1.0 ND1 C:HIS41 4.2 14.6 1.0 HG3 C:GLU83 4.3 15.9 0.6 CG C:GLU83 4.3 16.2 0.4 HB3 C:PRO59 4.3 23.1 1.0 HG2 C:GLU83 4.3 15.9 0.6 HH12 C:ARG54 4.4 16.2 1.0 HG2 C:PRO59 4.5 23.9 1.0 HG2 C:GLU83 4.5 19.5 0.4 HD3 C:PRO59 4.6 20.1 1.0 HB3 C:GLU83 4.7 18.1 0.4 CB C:PRO59 4.8 19.2 1.0 HG3 C:GLU83 4.9 19.5 0.4 HB C:ILE88 4.9 16.2 1.0 CD C:PRO59 4.9 16.7 1.0 HD1 C:HIS41 5.0 17.5 1.0 NH1 C:ARG54 5.0 13.5 1.0

M.Rees, R.Nikoopour, A.Alexandrovich, M.Pfuhl, L.R.Lopes, M.M.Akhtar, P.Syrris, P.Elliott, G.Carr-White, M.Gautel. Structure Determination and Analysis of Titin A-Band Fibronectin Type III Domains Provides Insights For Disease-Linked Variants and Protein Oligomerisation. J.Struct.Biol. 08009 2023.
ISSN: ESSN 1095-8657
PubMed: 37549721
DOI: 10.1016/J.JSB.2023.108009