Zinc in PDB 5fgw: Structure of SDA1 Nuclease with Bound Zinc Ion

The structure of Structure of SDA1 Nuclease with Bound Zinc Ion, PDB code: 5fgw was solved by A.F.Moon, J.M.Krahn, L.Xun, M.J.Cuneo, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.13 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.104, 66.538, 83.536, 108.72, 90.01, 92.36
R / Rfree (%)	21.5 / 26

The structure of Structure of SDA1 Nuclease with Bound Zinc Ion also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Zinc atom in the Structure of SDA1 Nuclease with Bound Zinc Ion (pdb code 5fgw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 27 binding sites of Zinc where determined in the Structure of SDA1 Nuclease with Bound Zinc Ion, PDB code: 5fgw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.4 occ:1.00 O B:HOH430 1.9 26.3 1.0 O A:SER294 2.0 20.8 1.0 O B:HOH436 2.0 16.3 1.0 O B:HOH431 2.0 24.6 1.0 OD1 B:ASN211 2.0 22.0 1.0 OXT A:SER294 2.2 21.9 1.0 C A:SER294 2.5 24.1 1.0 CG B:ASN211 3.2 23.9 1.0 ND2 B:ASN211 3.8 15.4 1.0 N B:GLY188 3.9 17.6 1.0 CA A:SER294 4.0 29.7 1.0 OE2 B:GLU225 4.1 16.8 1.0 O B:ASN211 4.1 22.4 1.0 OE1 B:GLU225 4.1 25.2 1.0 OG B:SER187 4.2 20.1 1.0 O B:GLY188 4.3 16.8 1.0 CB B:ASN211 4.4 24.0 1.0 CB B:MET221 4.5 18.3 1.0 CA B:ASN211 4.5 24.9 1.0 CD B:GLU225 4.5 25.0 1.0 CA B:SER187 4.5 17.1 1.0 C B:SER187 4.6 16.0 1.0 CA B:GLY188 4.6 16.7 1.0 C B:ASN211 4.6 21.8 1.0 N A:SER294 4.8 32.2 1.0 CB A:SER294 4.8 21.9 1.0 C B:GLY188 4.9 21.9 1.0 CB B:SER187 4.9 22.8 1.0 CG B:MET221 4.9 16.0 1.0 OG A:SER294 4.9 26.5 1.0

Zinc binding site 2 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.8 occ:1.00 OD1 A:ASN211 2.0 23.5 1.0 O A:HOH441 2.0 22.9 1.0 O A:HOH436 2.1 18.2 1.0 O A:HOH426 2.2 18.2 1.0 CG A:ASN211 3.2 26.7 1.0 ND2 A:ASN211 3.8 18.9 1.0 OE2 A:GLU225 3.9 16.9 1.0 N A:GLY188 3.9 17.4 1.0 O A:ASN211 4.0 21.8 1.0 OE1 A:GLU225 4.2 26.1 1.0 OG A:SER187 4.2 19.9 1.0 CB A:ASN211 4.4 20.8 1.0 O A:GLY188 4.4 17.4 1.0 CB A:MET221 4.4 15.3 1.0 CD A:GLU225 4.5 21.9 1.0 CA A:ASN211 4.5 20.5 1.0 CA A:GLY188 4.6 18.8 1.0 CA A:SER187 4.6 17.7 1.0 C A:SER187 4.6 14.9 1.0 C A:ASN211 4.6 22.5 1.0 CG A:MET221 4.9 14.3 1.0 C A:GLY188 5.0 23.1 1.0 CB A:SER187 5.0 19.2 1.0

Zinc binding site 3 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:48.2 occ:1.00 NE2 A:HIS51 2.1 36.1 1.0 ND1 A:HIS56 2.1 43.6 1.0 O A:HOH493 2.3 41.7 1.0 O A:HOH487 2.3 32.6 1.0 O A:HOH454 2.8 42.0 1.0 CD2 A:HIS51 2.8 30.7 1.0 CG A:HIS56 3.0 32.3 1.0 CE1 A:HIS56 3.1 37.1 1.0 CE1 A:HIS51 3.2 38.4 1.0 CB A:HIS56 3.3 32.7 1.0 CA A:HIS56 3.6 29.9 1.0 CG A:HIS51 4.0 33.1 1.0 CD2 A:HIS56 4.1 35.6 1.0 NE2 A:HIS56 4.1 32.5 1.0 ND1 A:HIS51 4.2 34.0 1.0 N A:VAL57 4.2 35.7 1.0 C A:HIS56 4.3 28.7 1.0 O A:VAL57 4.7 36.9 1.0 O A:TYR55 4.9 29.4 1.0 N A:HIS56 4.9 23.4 1.0

Zinc binding site 4 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:57.4 occ:1.00 O A:HOH423 2.2 30.3 1.0 O A:HOH419 2.3 29.4 0.7 O A:HOH464 2.4 28.2 0.7 O A:HOH401 2.9 40.3 1.0 OG A:SER120 3.1 34.8 1.0 OE1 A:GLU125 3.6 53.5 1.0 OD1 A:ASP192 3.6 33.6 1.0 CB A:SER120 3.7 25.3 1.0 CA A:SER120 3.9 22.2 1.0 O A:GLY196 4.1 22.2 1.0 O A:TYR123 4.3 46.3 1.0 O A:ASP192 4.4 26.4 1.0 CD A:GLU125 4.5 57.3 1.0 CG A:ASP192 4.6 40.8 1.0 CG A:GLU125 4.7 41.1 1.0 O A:SER120 4.8 35.1 1.0 N A:SER120 4.9 27.4 1.0 C A:SER120 4.9 27.6 1.0 C A:GLY195 5.0 21.8 1.0 N A:GLU125 5.0 38.1 1.0

Zinc binding site 5 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:67.8 occ:0.70 O A:HOH435 2.3 30.4 1.0 O A:HOH495 2.4 51.1 1.0 OE2 A:GLU125 2.4 56.8 1.0 O A:HOH485 2.5 39.4 1.0 O A:HOH409 2.7 46.6 1.0 CD A:GLU125 3.3 57.3 1.0 OE1 A:GLU125 3.9 53.5 1.0 OE2 A:GLU128 3.9 22.2 1.0 CG A:GLU125 4.3 41.1 1.0 O A:HOH488 4.5 46.8 0.8 CG A:ARG197 4.5 23.0 1.0 CD A:ARG197 4.6 18.1 1.0 NE A:ARG197 4.7 20.0 1.0 CB A:GLU125 4.8 35.5 1.0 CD A:PRO198 4.9 18.7 1.0 CD A:GLU128 5.0 25.6 1.0

Zinc binding site 6 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:25.3 occ:0.44 ZN A:ZN306 0.0 25.3 0.4 ND1 A:HIS95 1.5 25.4 0.3 CE1 A:HIS95 1.7 28.1 0.3 CG A:HIS95 1.8 23.6 0.3 ND1 A:HIS95 1.9 26.9 0.7 NE2 A:HIS95 2.1 25.5 0.3 CD2 A:HIS95 2.2 26.5 0.3 CG A:HIS95 2.8 21.1 0.7 ZN A:ZN306 2.9 32.9 0.6 CB A:HIS95 3.0 22.3 0.3 CE1 A:HIS95 3.0 26.3 0.7 CB A:HIS95 3.1 22.4 0.7 CD2 A:HIS95 4.0 21.2 0.7 CA A:HIS95 4.0 20.7 0.3 NE2 A:HIS95 4.0 27.5 0.7 CA A:HIS95 4.1 20.6 0.7 OH A:TYR109 4.1 28.0 1.0 O A:HOH427 4.6 29.2 1.0 CZ A:TYR109 4.7 33.5 1.0 C A:HIS95 4.7 21.4 0.3 C A:HIS95 5.0 22.4 0.7

Zinc binding site 7 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:32.9 occ:0.56 ZN A:ZN306 0.0 32.9 0.6 NE2 A:HIS95 2.2 25.5 0.3 O A:HOH492 2.4 30.5 1.0 CE1 A:HIS95 2.5 28.1 0.3 ZN A:ZN306 2.9 25.3 0.4 CE1 A:HIS95 3.1 26.3 0.7 ND1 A:HIS95 3.2 26.9 0.7 CD2 A:HIS95 3.4 26.5 0.3 ND1 A:HIS95 3.6 25.4 0.3 CG A:HIS95 4.1 23.6 0.3 NE2 A:HIS95 4.4 27.5 0.7 OH A:TYR109 4.5 28.0 1.0 CG A:HIS95 4.6 21.1 0.7

Zinc binding site 8 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:46.6 occ:1.00 O A:HOH490 2.0 35.4 1.0 ND1 A:HIS231 2.2 37.7 1.0 O A:HOH497 2.3 32.4 1.0 O A:HOH486 2.3 41.8 0.9 CG A:HIS231 3.1 31.6 1.0 CE1 A:HIS231 3.2 39.8 1.0 CB A:HIS231 3.3 31.1 1.0 CA A:HIS231 4.0 32.1 1.0 CD2 A:HIS231 4.2 30.8 1.0 NE2 A:HIS231 4.2 35.9 1.0 N A:HIS231 4.8 30.0 1.0 ND2 A:ASN235 4.9 35.0 1.0 CB A:PHE268 4.9 39.2 1.0 CG1 A:ILE269 4.9 32.5 1.0 CD1 A:ILE269 5.0 27.5 1.0

Zinc binding site 9 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:61.5 occ:1.00 O A:HOH496 2.0 33.0 0.7 NE2 A:HIS239 2.1 35.0 1.0 O A:HOH489 2.3 41.9 1.0 CE1 A:HIS239 2.9 33.1 1.0 CD2 A:HIS239 3.2 31.6 1.0 CB A:SER265 3.6 32.4 1.0 OH A:TYR241 3.7 46.5 1.0 ND1 A:HIS239 4.1 33.7 1.0 CE1 A:TYR241 4.1 40.5 1.0 CG A:HIS239 4.2 27.0 1.0 CZ A:TYR241 4.3 39.5 1.0 CA A:SER265 4.6 33.8 1.0 OG A:SER265 4.6 29.4 1.0

Zinc binding site 10 out of 27 in the Structure of SDA1 Nuclease with Bound Zinc Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of SDA1 Nuclease with Bound Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:44.0 occ:1.00 O B:HOH490 2.0 37.4 1.0 ND1 B:HIS56 2.0 40.3 1.0 NE2 B:HIS51 2.2 32.7 1.0 OXT B:ACT310 2.4 39.1 1.0 CD2 B:HIS51 2.8 37.1 1.0 CG B:HIS56 3.0 33.5 1.0 CE1 B:HIS56 3.0 37.4 1.0 O B:ACT310 3.0 40.8 1.0 C B:ACT310 3.1 50.0 1.0 CB B:HIS56 3.3 29.0 1.0 CE1 B:HIS51 3.3 31.9 1.0 CA B:HIS56 3.7 29.9 1.0 CG B:HIS51 4.1 30.9 1.0 NE2 B:HIS56 4.1 38.1 1.0 CD2 B:HIS56 4.1 38.2 1.0 ND1 B:HIS51 4.3 30.0 1.0 N B:VAL57 4.3 30.0 1.0 C B:HIS56 4.4 33.3 1.0 CH3 B:ACT310 4.6 59.9 1.0 O B:VAL57 4.7 43.2 1.0 O B:TYR55 4.8 27.3 1.0 N B:HIS56 5.0 28.0 1.0

A.F.Moon, J.M.Krahn, X.Lu, M.J.Cuneo, L.C.Pedersen. Structural Characterization of the Virulence Factor SDA1 Nuclease From Streptococcus Pyogenes. Nucleic Acids Res. V. 44 3946 2016.
ISSN: ESSN 1362-4962
PubMed: 26969731
DOI: 10.1093/NAR/GKW143