Zinc in PDB 6ghc: Modification Dependent Ecokmcra Restriction Endonuclease

The structure of Modification Dependent Ecokmcra Restriction Endonuclease, PDB code: 6ghc was solved by H.Czapinska, M.Kowalska, E.Zagorskaite, E.Manakova, S.Xu, V.Siksnys, G.Sasnauskas, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.19 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.045, 90.383, 95.406, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 28.3

The binding sites of Zinc atom in the Modification Dependent Ecokmcra Restriction Endonuclease (pdb code 6ghc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Modification Dependent Ecokmcra Restriction Endonuclease, PDB code: 6ghc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.1 occ:1.00 SG A:CYS251 2.3 1.0 1.0 SG A:CYS248 2.4 0.8 1.0 SG A:CYS210 2.5 0.4 1.0 SG A:CYS207 2.9 0.1 1.0 CB A:CYS251 3.1 0.7 1.0 CB A:CYS207 3.2 0.8 1.0 CB A:CYS248 3.5 0.5 1.0 CB A:CYS210 3.5 1.0 1.0 N A:CYS248 3.8 0.3 1.0 ND2 A:ASN209 4.1 0.8 1.0 CA A:CYS248 4.2 0.8 1.0 N A:CYS251 4.2 0.5 1.0 N A:CYS210 4.3 0.9 1.0 CA A:CYS251 4.3 0.1 1.0 CA A:CYS210 4.4 0.3 1.0 O A:CYS210 4.5 0.1 1.0 O A:CYS248 4.6 0.4 1.0 C A:CYS210 4.7 0.2 1.0 CA A:CYS207 4.7 0.1 1.0 C A:CYS248 4.8 0.7 1.0 C A:LEU247 5.0 0.4 1.0

Zinc binding site 2 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:99.8 occ:0.53 ND1 A:HIS228 2.3 0.6 1.0 NE2 A:HIS252 2.3 0.8 1.0 NE2 A:HIS256 2.5 0.4 1.0 O A:HOH428 2.6 89.5 1.0 CE1 A:HIS256 3.2 0.2 1.0 CG A:HIS228 3.3 1.0 1.0 CD2 A:HIS252 3.3 0.0 1.0 CE1 A:HIS228 3.3 0.4 1.0 CE1 A:HIS252 3.3 0.5 1.0 O A:HOH417 3.4 0.8 1.0 CB A:HIS228 3.5 0.6 1.0 O A:HOH413 3.5 93.9 1.0 CD2 A:HIS256 3.6 0.3 1.0 CA A:HIS228 3.9 0.0 1.0 NE2 A:HIS228 4.4 0.1 1.0 ND1 A:HIS256 4.4 0.1 1.0 CD2 A:HIS228 4.4 0.2 1.0 ND1 A:HIS252 4.4 0.2 1.0 CG A:HIS252 4.5 0.9 1.0 N A:HIS229 4.5 0.4 1.0 CG A:HIS256 4.6 0.3 1.0 O A:VAL227 4.7 0.2 1.0 C A:HIS228 4.7 0.5 1.0

Zinc binding site 3 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.6 occ:1.00 SG B:CYS248 2.1 0.3 1.0 SG B:CYS210 2.3 0.8 1.0 SG B:CYS207 2.4 0.7 1.0 SG B:CYS251 2.8 0.0 1.0 CB B:CYS207 3.0 0.1 1.0 CB B:CYS248 3.3 0.5 1.0 CB B:CYS251 3.4 0.3 1.0 CB B:CYS210 3.6 0.9 1.0 N B:CYS248 3.8 0.0 1.0 CA B:CYS248 4.1 0.9 1.0 N B:CYS210 4.2 0.4 1.0 N B:CYS251 4.4 0.6 1.0 CA B:CYS210 4.4 0.8 1.0 O B:CYS210 4.5 0.9 1.0 CA B:CYS207 4.5 0.5 1.0 CA B:CYS251 4.5 0.5 1.0 O B:CYS248 4.6 0.1 1.0 C B:CYS248 4.7 0.7 1.0 C B:CYS210 4.8 0.5 1.0 C B:LEU247 5.0 0.5 1.0

Zinc binding site 4 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.8 occ:0.55 ND1 B:HIS228 2.2 0.3 1.0 NE2 B:HIS252 2.5 0.6 1.0 O B:HOH422 2.6 84.6 1.0 O B:HOH421 2.7 95.8 1.0 O B:HOH420 3.0 0.7 1.0 CE1 B:HIS228 3.0 0.6 1.0 NE2 B:HIS256 3.2 0.8 1.0 CG B:HIS228 3.3 0.3 1.0 CE1 B:HIS252 3.4 0.9 1.0 CD2 B:HIS252 3.6 0.8 1.0 CE1 B:HIS256 3.6 0.8 1.0 CA B:HIS228 3.7 1.0 1.0 CB B:HIS228 3.8 0.4 1.0 N B:HIS229 4.0 0.4 1.0 NE2 B:HIS228 4.2 0.5 1.0 CD2 B:HIS228 4.3 0.5 1.0 C B:HIS228 4.4 0.3 1.0 CD2 B:HIS256 4.4 0.8 1.0 ND1 B:HIS252 4.6 0.2 1.0 O B:VAL227 4.6 0.9 1.0 CG B:HIS252 4.7 0.6 1.0 O B:HIS229 4.7 0.7 1.0 ND1 B:HIS256 4.9 0.2 1.0 N B:HIS228 4.9 0.6 1.0

H.Czapinska, M.Kowalska, E.Zagorskaite, E.Manakova, A.Slyvka, S.Y.Xu, V.Siksnys, G.Sasnauskas, M.Bochtler. Activity and Structure of Ecokmcra. Nucleic Acids Res. V. 46 9829 2018.
ISSN: ESSN 1362-4962
PubMed: 30107581
DOI: 10.1093/NAR/GKY731