Zinc in PDB 5j7k: Loop Grafting Onto A Highly Stable FN3 Scaffold

The structure of Loop Grafting Onto A Highly Stable FN3 Scaffold, PDB code: 5j7k was solved by B.T.Porebski, N.Drinkwater, S.Mcgowan, A.M.Buckle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.22 / 2.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.220, 71.230, 126.141, 90.00, 90.43, 90.00
R / Rfree (%)	25.9 / 28.5

The binding sites of Zinc atom in the Loop Grafting Onto A Highly Stable FN3 Scaffold (pdb code 5j7k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Loop Grafting Onto A Highly Stable FN3 Scaffold, PDB code: 5j7k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Loop Grafting Onto A Highly Stable FN3 Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Loop Grafting Onto A Highly Stable FN3 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:0.6 occ:1.00 OE2 B:GLU65 2.3 82.0 1.0 O B:HOH202 2.6 45.9 1.0 CE1 G:HIS96 3.0 39.4 1.0 CD B:GLU65 3.5 64.3 1.0 NE2 G:HIS94 3.6 29.0 1.0 NE2 G:HIS96 3.8 35.4 1.0 ND1 G:HIS96 4.1 58.0 1.0 CE1 G:HIS94 4.1 52.8 1.0 CG B:GLU65 4.3 69.3 1.0 OE1 B:GLU65 4.4 54.5 1.0 OG1 B:THR91 4.7 40.4 1.0 CD2 G:HIS94 4.8 40.6 1.0

Zinc binding site 2 out of 7 in the Loop Grafting Onto A Highly Stable FN3 Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Loop Grafting Onto A Highly Stable FN3 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:0.8 occ:1.00 CE1 C:HIS94 3.0 37.7 1.0 OE2 A:GLU65 3.9 40.1 1.0 NE2 C:HIS94 3.9 37.5 1.0 ND1 C:HIS94 4.0 81.6 1.0 CD A:GLU65 4.6 51.3 1.0 OG A:SER89 4.9 39.2 1.0 NE2 C:HIS96 4.9 60.4 1.0 CD2 C:HIS96 5.0 59.8 1.0

Zinc binding site 3 out of 7 in the Loop Grafting Onto A Highly Stable FN3 Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Loop Grafting Onto A Highly Stable FN3 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:48.9 occ:1.00 OE2 D:GLU65 1.7 51.7 1.0 CD D:GLU65 2.3 33.2 1.0 OE1 D:GLU65 2.5 37.8 1.0 O D:HOH206 2.5 39.0 1.0 CG D:GLU65 3.7 29.8 1.0 CB D:GLU65 4.7 32.2 1.0

Zinc binding site 4 out of 7 in the Loop Grafting Onto A Highly Stable FN3 Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Loop Grafting Onto A Highly Stable FN3 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:0.1 occ:1.00 CE1 F:HIS53 2.2 75.3 1.0 NE2 F:HIS53 2.7 51.3 1.0 NE2 B:HIS53 2.7 50.2 1.0 ND1 F:HIS53 3.2 58.8 1.0 CD2 B:HIS53 3.3 56.9 1.0 CA B:LEU51 3.6 69.5 1.0 O B:ASP50 3.8 70.5 1.0 CD2 F:HIS53 3.8 45.5 1.0 N F:GLY24 3.9 50.5 1.0 CE1 B:HIS53 3.9 41.2 1.0 CB B:LEU51 4.0 69.9 1.0 CG F:HIS53 4.1 55.4 1.0 N B:LEU51 4.3 72.2 1.0 C B:ASP50 4.4 79.0 1.0 C B:LEU51 4.5 72.8 1.0 CA F:GLY24 4.6 53.1 1.0 CG B:HIS53 4.6 43.1 1.0 O B:LEU51 4.6 68.1 1.0 CA F:ARG23 4.7 47.0 1.0 CA B:GLY24 4.7 61.7 1.0 O B:GLY24 4.8 70.5 1.0 C B:GLY24 4.8 66.1 1.0 C F:ARG23 4.8 51.8 1.0 ND1 B:HIS53 4.8 53.5 1.0

Zinc binding site 5 out of 7 in the Loop Grafting Onto A Highly Stable FN3 Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Loop Grafting Onto A Highly Stable FN3 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn101 b:59.0 occ:1.00 O G:HOH201 2.5 22.6 1.0 OE1 G:GLU65 3.8 36.8 1.0 CD G:GLU65 4.3 40.4 1.0 OE2 G:GLU65 4.4 41.6 1.0 NE2 B:HIS94 4.8 50.5 1.0

Zinc binding site 6 out of 7 in the Loop Grafting Onto A Highly Stable FN3 Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Loop Grafting Onto A Highly Stable FN3 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:0.8 occ:1.00 CE1 A:HIS94 2.1 93.6 1.0 ND1 A:HIS94 3.0 77.4 1.0 NE2 A:HIS94 3.2 99.7 1.0 NE2 A:HIS95 3.5 64.4 1.0 CE1 A:HIS95 4.0 55.2 1.0 OE2 C:GLU65 4.1 66.7 1.0 CD2 A:HIS95 4.2 80.3 1.0 CG A:HIS94 4.2 66.5 1.0 O A:HOH203 4.3 27.6 1.0 CD2 A:HIS94 4.3 77.0 1.0 ND1 A:HIS95 4.9 60.3 1.0 CG A:HIS95 5.0 69.2 1.0 CD C:GLU65 5.0 58.2 1.0

Zinc binding site 7 out of 7 in the Loop Grafting Onto A Highly Stable FN3 Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Loop Grafting Onto A Highly Stable FN3 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn102 b:0.4 occ:1.00 OE1 H:GLU65 2.3 0.1 1.0 O H:HOH203 2.8 61.9 1.0 CD H:GLU65 3.3 0.1 1.0 CE1 E:HIS94 3.6 27.7 1.0 OE2 H:GLU65 3.7 92.0 1.0 ND1 E:HIS94 4.3 51.8 1.0 NE2 E:HIS94 4.5 28.7 1.0 CG H:GLU65 4.6 98.7 1.0 OG1 H:THR91 4.7 57.1 1.0 OG H:SER89 4.9 0.7 1.0

B.T.Porebski, P.J.Conroy, N.Drinkwater, P.Schofield, R.Vazquez-Lombardi, M.R.Hunter, D.E.Hoke, D.Christ, S.Mcgowan, A.M.Buckle. Circumventing the Stability-Function Trade-Off in An Engineered FN3 Domain. Protein Eng.Des.Sel. 2016.
ISSN: ESSN 1741-0134
PubMed: 27578887
DOI: 10.1093/PROTEIN/GZW046