Calcium in PDB 4abt: Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna

All present enzymatic activity of Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna:
3.1.21.4;

The structure of Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna, PDB code: 4abt was solved by E.N.Manakova, S.Grazulis, M.Zaremba, G.Tamulaitiene, D.Golovenko, V.Siksnys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.95 / 2.22
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.899, 90.081, 92.711, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 23.5

The binding sites of Calcium atom in the Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna (pdb code 4abt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna, PDB code: 4abt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1287 b:28.1 occ:1.00 O A:HOH2088 2.3 18.0 1.0 OD2 A:ASP140 2.4 17.8 1.0 OP1 E:DC5 2.6 23.9 1.0 O A:HOH2087 2.6 18.2 1.0 O A:CYS186 2.6 13.0 1.0 O A:HOH2045 2.8 15.3 1.0 CG A:ASP140 3.2 20.1 1.0 OD1 A:ASP140 3.2 23.6 1.0 P E:DC5 3.7 16.8 1.0 C A:CYS186 3.8 13.2 1.0 O5' E:DC5 3.9 17.9 1.0 N A:CYS186 3.9 13.4 1.0 C5' E:DC5 4.1 14.5 1.0 NZ A:LYS187 4.2 15.5 1.0 O A:HOH2066 4.4 37.6 1.0 CA A:CYS186 4.4 12.1 1.0 OP2 E:DC5 4.5 18.2 1.0 CB A:SER185 4.5 14.4 0.5 CB A:ASP140 4.6 19.9 1.0 O A:HOH2067 4.6 40.3 1.0 OP2 E:DC6 4.6 9.2 1.0 CG A:LYS187 4.7 14.3 1.0 CE A:LYS187 4.7 11.6 1.0 C A:SER185 4.8 14.1 1.0 CB A:SER185 4.8 14.2 0.5 CB A:CYS186 4.8 11.3 1.0 N A:LYS187 4.8 14.2 1.0 CA A:SER185 4.9 14.6 0.5 CA A:SER185 4.9 14.5 0.5 OG A:SER185 4.9 13.8 0.5 O3' E:DG4 4.9 19.5 1.0 O A:HOH2042 5.0 12.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1287 b:14.8 occ:1.00 O B:HOH2074 2.3 14.3 1.0 OP1 G:DC5 2.3 12.5 1.0 OD2 B:ASP140 2.4 14.8 1.0 O B:CYS186 2.5 12.3 1.0 O B:HOH2041 2.5 14.8 1.0 O B:HOH2060 2.5 6.0 1.0 CG B:ASP140 3.2 19.8 1.0 OD1 B:ASP140 3.3 15.3 1.0 C B:CYS186 3.6 12.9 1.0 P G:DC5 3.6 14.7 1.0 N B:CYS186 3.8 14.0 1.0 O B:HOH2059 4.0 22.8 1.0 C5' G:DC5 4.1 10.5 1.0 O5' G:DC5 4.1 14.1 1.0 CA B:CYS186 4.2 13.4 1.0 OP2 G:DC5 4.2 15.0 1.0 NZ B:LYS187 4.4 13.2 1.0 CG B:LYS187 4.4 13.0 1.0 OP2 G:DC6 4.5 8.2 1.0 OE2 B:GLU70 4.5 24.6 1.0 CB B:ASP140 4.6 19.4 1.0 O B:HOH2040 4.6 14.0 1.0 CB B:CYS186 4.7 13.3 1.0 N B:LYS187 4.7 13.2 1.0 C B:SER185 4.7 15.1 1.0 O3' G:DG4 4.8 17.9 1.0 CE B:LYS187 4.8 10.6 1.0 CB B:SER185 4.9 16.2 1.0 CA B:SER185 4.9 15.7 1.0 O3' G:DC5 5.0 17.1 1.0 CA B:LYS187 5.0 13.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1000 b:30.0 occ:0.50 O E:HOH2006 2.4 14.9 1.0 O E:HOH2014 2.5 13.7 1.0 O E:HOH2005 2.8 14.5 1.0 O4' E:DG8 4.5 15.4 1.0 O A:HOH2009 4.6 15.4 1.0 N3 E:DG7 4.6 10.2 1.0 O E:HOH2009 4.7 16.6 1.0 N2 E:DG7 4.8 14.4 1.0 O E:HOH2013 4.8 22.8 1.0 C4' E:DG8 4.9 16.3 1.0 O4' E:DG7 5.0 12.2 1.0

E.N.Manakova, S.Grazulis, M.Zaremba, G.Tamulaitiene, D.Golovenko, V.Siksnys. Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved Dna To Be Published.