Zinc in PDB 3fc3: Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I, PDB code: 3fc3 was solved by M.Sokolowska, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.71 / 1.75
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.089, 90.089, 334.254, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 20.5

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I (pdb code 3fc3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I, PDB code: 3fc3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I


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 Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.1 occ:0.90 SG A:CYS68 2.3 18.6 1.0 SG A:CYS100 2.3 24.1 1.0 SG A:CYS97 2.4 19.7 1.0 SG A:CYS71 2.4 20.9 1.0 CB A:CYS68 3.1 19.3 1.0 CB A:CYS100 3.3 23.8 1.0 CB A:CYS71 3.4 19.1 1.0 CB A:CYS97 3.5 19.5 1.0 N A:CYS71 3.7 19.0 1.0 N A:CYS97 3.9 19.8 1.0 O A:HOH288 3.9 34.5 1.0 CA A:CYS71 4.2 19.0 1.0 N A:CYS100 4.2 22.6 1.0 CA A:CYS97 4.3 19.5 1.0 O A:HOH369 4.3 36.9 1.0 CA A:CYS100 4.3 23.0 1.0 CA A:CYS68 4.6 18.7 1.0 NZ A:LYS75 4.7 24.7 1.0 CB A:ILE70 4.7 18.6 1.0 CE A:LYS75 4.8 24.2 1.0 O A:CYS97 4.8 19.9 1.0 C A:ILE70 4.8 19.6 1.0 C A:CYS97 4.9 19.6 1.0 N A:ILE70 5.0 18.6 1.0 C A:CYS71 5.0 18.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I


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 Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.8 occ:0.90 SG A:CYS130 2.3 20.5 1.0 SG A:CYS164 2.3 20.4 1.0 SG A:CYS161 2.3 19.4 1.0 SG A:CYS133 2.4 20.6 1.0 CB A:CYS130 3.1 20.3 1.0 CB A:CYS133 3.3 20.8 1.0 CB A:CYS164 3.3 20.0 1.0 CB A:CYS161 3.5 19.0 1.0 N A:CYS133 3.7 21.7 1.0 N A:CYS161 4.0 19.2 1.0 CA A:CYS133 4.1 20.9 1.0 O A:HOH490 4.1 23.0 1.0 O A:HOH481 4.2 22.4 1.0 N A:CYS164 4.2 18.4 1.0 CA A:CYS161 4.3 18.3 1.0 CA A:CYS164 4.3 19.3 1.0 CA A:CYS130 4.6 20.7 1.0 NZ A:LYS135 4.7 20.3 1.0 CB A:ILE132 4.7 24.4 1.0 O A:CYS161 4.7 18.3 1.0 C A:CYS161 4.8 18.4 1.0 C A:ILE132 4.9 23.0 1.0 C A:CYS133 5.0 20.8 1.0 N A:ILE132 5.0 23.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I


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 Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:19.3 occ:0.80 SG B:CYS100 2.3 23.0 1.0 SG B:CYS68 2.3 18.2 1.0 SG B:CYS97 2.4 19.9 1.0 SG B:CYS71 2.4 20.1 1.0 CB B:CYS68 3.2 18.3 1.0 CB B:CYS100 3.2 23.6 1.0 CB B:CYS71 3.4 18.4 1.0 CB B:CYS97 3.6 19.0 1.0 N B:CYS71 3.7 18.6 1.0 N B:CYS97 3.9 18.9 1.0 O B:HOH251 4.0 33.0 1.0 CA B:CYS71 4.1 18.2 1.0 N B:CYS100 4.2 22.2 1.0 O B:HOH247 4.3 38.6 1.0 CA B:CYS100 4.3 22.9 1.0 CA B:CYS97 4.3 19.2 1.0 NZ B:LYS75 4.5 24.8 1.0 CA B:CYS68 4.6 18.3 1.0 CB B:ILE70 4.7 19.9 1.0 CE B:LYS75 4.8 24.0 1.0 O B:CYS97 4.8 20.9 1.0 C B:ILE70 4.8 19.8 1.0 C B:CYS97 4.9 19.9 1.0 N B:ILE70 5.0 19.1 1.0 C B:CYS71 5.0 17.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I


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 Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:17.4 occ:0.90 SG B:CYS161 2.3 19.2 1.0 SG B:CYS164 2.3 19.6 1.0 SG B:CYS130 2.3 19.0 1.0 SG B:CYS133 2.4 20.4 1.0 CB B:CYS130 3.1 18.9 1.0 CB B:CYS164 3.2 19.7 1.0 CB B:CYS133 3.4 19.6 1.0 CB B:CYS161 3.5 19.6 1.0 N B:CYS133 3.7 20.6 1.0 N B:CYS161 4.0 19.2 1.0 O B:HOH443 4.0 21.0 1.0 CA B:CYS133 4.1 19.9 1.0 N B:CYS164 4.2 19.1 1.0 O B:HOH473 4.2 21.4 1.0 CA B:CYS164 4.3 19.2 1.0 CA B:CYS161 4.3 18.9 1.0 CA B:CYS130 4.6 19.2 1.0 CB B:ILE132 4.6 21.6 1.0 NZ B:LYS135 4.7 23.1 1.0 O B:CYS161 4.8 18.4 1.0 C B:ILE132 4.8 21.3 1.0 C B:CYS161 4.9 18.8 1.0 N B:ILE132 4.9 21.4 1.0 C B:CYS133 5.0 19.4 1.0

M.Sokolowska, H.Czapinska, M.Bochtler. Crystal Structure of the Beta Beta Alpha-Me Type II Restriction Endonuclease HPY99I with Target Dna. Nucleic Acids Res. V. 37 3799 2009.
ISSN: ISSN 0305-1048
PubMed: 19380375
DOI: 10.1093/NAR/GKP228