Zinc in PDB 4k6t: Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385

The structure of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385, PDB code: 4k6t was solved by T.Stehle, J.Bauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.26 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.940, 67.180, 121.430, 90.00, 96.81, 90.00
R / Rfree (%)	16 / 20

The structure of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 (pdb code 4k6t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385, PDB code: 4k6t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:24.9 occ:1.00 OXT A:ACT405 2.0 22.2 1.0 OE2 A:GLU351 2.0 23.6 1.0 OXT B:ACT406 2.0 23.8 1.0 C B:ACT406 2.7 24.8 1.0 O B:ACT406 2.7 29.8 1.0 CD A:GLU351 2.8 25.8 1.0 C A:ACT405 2.9 41.0 1.0 OE1 A:GLU351 2.9 23.0 1.0 O A:ACT405 3.2 15.5 1.0 O A:HOH586 3.5 23.2 1.0 CH3 B:ACT406 4.2 35.0 1.0 NZ B:LYS300 4.2 58.8 1.0 CG A:GLU351 4.2 20.8 1.0 CE1 B:TYR302 4.3 22.5 1.0 CH3 A:ACT405 4.3 32.0 1.0 CE1 A:HIS231 4.5 18.1 1.0 OH B:TYR302 4.5 23.0 1.0 CZ B:TYR302 4.8 23.1 1.0 ZN A:ZN403 4.9 24.0 1.0

Zinc binding site 2 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:24.0 occ:1.00 O A:ACT405 1.8 15.5 1.0 OXT A:ACT406 2.0 18.9 1.0 NE2 A:HIS231 2.1 19.0 1.0 O A:ACT406 2.5 22.9 1.0 C A:ACT406 2.5 21.6 1.0 C A:ACT405 2.9 41.0 1.0 CD2 A:HIS231 3.1 19.9 1.0 CE1 A:HIS231 3.1 18.1 1.0 CH3 A:ACT405 3.5 32.0 1.0 OXT A:ACT405 4.0 22.2 1.0 O A:HOH618 4.0 24.9 1.0 CH3 A:ACT406 4.0 27.4 1.0 ND1 A:HIS231 4.2 18.8 1.0 CG A:HIS231 4.3 19.0 1.0 O A:HOH639 4.4 34.5 1.0 CD1 A:ILE232 4.5 23.5 1.0 CG1 A:ILE232 4.7 28.2 1.0 ZN A:ZN402 4.9 24.9 1.0

Zinc binding site 3 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:68.8 occ:1.00 OD2 A:ASP318 2.2 37.0 1.0 CG A:ASP318 3.1 23.8 1.0 OD1 A:ASP318 3.3 26.4 1.0 O A:HOH631 4.3 38.8 1.0 CB A:ASP318 4.5 21.7 1.0 O A:HOH544 4.9 30.9 1.0

Zinc binding site 4 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:40.5 occ:1.00 OE2 B:GLU351 1.9 32.6 1.0 NE2 B:HIS231 2.1 25.2 1.0 OXT B:ACT407 2.3 40.6 1.0 O B:HOH600 2.5 26.7 1.0 CD B:GLU351 2.9 29.7 1.0 CD2 B:HIS231 3.0 21.7 1.0 C B:ACT407 3.1 31.7 1.0 CE1 B:HIS231 3.1 24.5 1.0 O C:HOH566 3.2 32.4 1.0 CG B:GLU351 3.3 27.0 1.0 O B:ACT407 3.5 24.7 1.0 OE1 B:GLU351 4.0 37.0 1.0 CH3 B:ACT407 4.0 34.2 1.0 O B:VAL225 4.1 21.4 1.0 CG B:HIS231 4.1 22.8 1.0 ND1 B:HIS231 4.2 25.8 1.0 CE C:LYS300 4.2 46.8 1.0 CA B:VAL226 4.6 25.9 1.0 CD1 B:ILE232 4.6 28.5 1.0 O B:VAL226 4.6 27.3 1.0 CB B:GLU351 4.7 24.8 1.0 NZ C:LYS300 4.8 47.0 1.0 CD C:LYS300 4.8 41.7 1.0 C B:VAL226 4.9 25.6 1.0

Zinc binding site 5 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:71.9 occ:1.00 OD1 B:ASP258 2.5 44.1 1.0 OD2 B:ASP258 2.7 35.9 1.0 CG B:ASP258 2.9 38.0 1.0 CB B:ASP258 4.4 31.9 1.0 O B:HOH610 4.4 36.7 1.0 CE B:LYS264 4.5 38.6 1.0

Zinc binding site 6 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:81.2 occ:1.00 OD2 B:ASP318 2.5 36.4 1.0 CG B:ASP318 3.3 23.1 1.0 OD1 B:ASP318 3.3 27.7 1.0 CB B:ASP318 4.7 22.3 1.0 O B:HOH554 4.7 35.5 1.0 NE2 B:GLN319 4.8 20.5 1.0 CD B:LYS316 5.0 22.5 0.5

Zinc binding site 7 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:37.0 occ:1.00 OE2 C:GLU351 1.8 40.6 1.0 NE2 C:HIS231 2.1 25.3 1.0 O C:HOH562 2.5 32.8 1.0 CD C:GLU351 2.7 35.7 1.0 O C:HOH561 2.8 32.8 1.0 CE1 C:HIS231 3.0 24.0 1.0 CD2 C:HIS231 3.0 23.1 1.0 CG C:GLU351 3.5 30.6 1.0 OE1 C:GLU351 3.6 30.5 1.0 CE A:LYS300 4.1 40.0 1.0 ND1 C:HIS231 4.1 25.8 1.0 CG C:HIS231 4.2 25.9 1.0 NZ A:LYS300 4.2 36.6 1.0 O C:VAL225 4.4 23.1 1.0 O C:VAL226 4.6 27.5 1.0 CA C:VAL226 4.8 25.7 1.0 CB C:GLU351 4.9 26.6 1.0 CD1 C:ILE232 5.0 33.8 1.0

Zinc binding site 8 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:22.0 occ:0.87 OE2 E:GLU351 1.8 25.5 1.0 OXT F:ACT404 2.0 26.0 1.0 NE2 E:HIS231 2.1 19.4 1.0 O E:HOH588 2.2 18.6 1.0 O F:HOH602 2.3 29.2 1.0 CD E:GLU351 2.9 26.9 1.0 CE1 E:HIS231 3.0 21.4 1.0 C F:ACT404 3.0 34.2 1.0 CD2 E:HIS231 3.1 19.0 1.0 O F:ACT404 3.3 25.3 1.0 CG E:GLU351 3.4 21.9 1.0 O E:HOH594 3.8 23.6 1.0 OE1 E:GLU351 4.0 24.5 1.0 O F:HOH566 4.1 49.0 1.0 O E:VAL225 4.1 20.2 1.0 ND1 E:HIS231 4.1 20.3 1.0 CG E:HIS231 4.2 19.6 1.0 CH3 F:ACT404 4.3 32.6 1.0 CA E:VAL226 4.5 22.4 1.0 CE F:LYS300 4.6 26.7 1.0 CD1 E:ILE232 4.7 25.7 1.0 CB E:GLU351 4.7 22.1 1.0 O E:VAL226 4.7 21.3 1.0 O F:HOH603 4.8 36.7 1.0 C E:VAL226 5.0 23.6 1.0 NZ F:LYS300 5.0 24.9 1.0

Zinc binding site 9 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:87.3 occ:1.00 OD2 E:ASP318 2.4 35.4 1.0 CG E:ASP318 3.2 29.8 1.0 OD1 E:ASP318 3.3 27.9 1.0 CB E:ASP318 4.6 25.6 1.0 CD E:LYS316 4.8 29.2 1.0 OE1 E:GLN319 5.0 24.9 1.0 O E:HOH519 5.0 33.6 1.0

Zinc binding site 10 out of 14 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:33.7 occ:1.00 OE1 F:GLU351 1.7 29.9 1.0 NE2 F:HIS231 2.2 23.1 1.0 O F:HOH621 2.2 31.7 1.0 CD F:GLU351 2.7 36.9 1.0 CE1 F:HIS231 3.1 23.8 1.0 CD2 F:HIS231 3.2 23.0 1.0 CG F:GLU351 3.4 31.7 1.0 OE2 F:GLU351 3.7 34.6 1.0 O F:HOH620 3.9 38.0 1.0 CE G:LYS300 4.1 40.0 1.0 O F:VAL225 4.2 22.1 1.0 ND1 F:HIS231 4.3 24.6 1.0 CG F:HIS231 4.3 24.2 1.0 NZ G:LYS300 4.3 35.1 1.0 O F:VAL226 4.6 24.6 1.0 CA F:VAL226 4.7 25.4 1.0 CB F:GLU351 4.8 26.5 1.0 CD1 F:ILE232 4.9 27.4 1.0 C F:VAL226 5.0 27.4 1.0 CD G:LYS300 5.0 39.5 1.0

R.Caraballo, M.Saleeb, J.Bauer, N.Chandra, R.J.Storm, L.Fraengsmyr, T.Stehle, N.Arnberg, M.Elofsson. Triazole Linker-Based Trivalent Sialic Acid Inhibitors of Adenovirus Type 37 Infection of Human Corneal Epithelial Cells To Be Published.