Calcium in PDB 7edb: ECOT38I Restriction Endonuclease Complexed with Dna

The structure of ECOT38I Restriction Endonuclease Complexed with Dna, PDB code: 7edb was solved by K.Kita, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 2.39
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	156.291, 156.291, 173.049, 90, 90, 120
R / Rfree (%)	16.2 / 19.7

The structure of ECOT38I Restriction Endonuclease Complexed with Dna also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the ECOT38I Restriction Endonuclease Complexed with Dna (pdb code 7edb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the ECOT38I Restriction Endonuclease Complexed with Dna, PDB code: 7edb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the ECOT38I Restriction Endonuclease Complexed with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of ECOT38I Restriction Endonuclease Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:31.1 occ:1.00 OP1 F:DC9 2.2 33.4 1.0 O A:VAL246 2.3 34.5 1.0 OD2 A:ASP231 2.3 33.3 1.0 OE1 A:GLU245 2.3 35.8 1.0 O F:HOH215 2.3 31.0 1.0 O A:HOH614 2.4 31.1 1.0 CG A:ASP231 3.0 32.9 1.0 OD1 A:ASP231 3.1 34.4 1.0 CD A:GLU245 3.2 37.3 1.0 C A:VAL246 3.4 31.2 1.0 P F:DC9 3.5 32.4 1.0 N A:VAL246 3.7 31.8 1.0 OE2 A:GLU245 3.8 38.1 1.0 CA F:CA101 3.9 38.3 1.0 O A:HOH574 4.0 37.0 1.0 CA A:VAL246 4.1 30.5 1.0 O5' F:DC9 4.1 30.6 1.0 C5' F:DC9 4.2 28.6 1.0 OP2 F:DC9 4.2 33.3 1.0 CG A:GLU245 4.3 33.3 1.0 NZ A:LYS247 4.4 36.8 1.0 CB A:ASP231 4.4 30.4 1.0 CB A:VAL246 4.5 30.4 1.0 N A:LYS247 4.5 31.7 1.0 CD A:LYS247 4.6 41.4 1.0 O A:HOH530 4.6 30.8 1.0 C A:GLU245 4.7 31.4 1.0 O3' F:DT8 4.7 30.4 1.0 O A:HOH599 4.7 44.1 1.0 OP2 F:DT10 4.7 32.1 1.0 CA A:LYS247 4.8 33.5 1.0 O A:HOH561 4.8 43.1 1.0 O A:HOH559 4.9 34.5 1.0 CE A:LYS247 4.9 35.7 1.0 CA A:GLU245 4.9 30.5 1.0

Calcium binding site 2 out of 4 in the ECOT38I Restriction Endonuclease Complexed with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of ECOT38I Restriction Endonuclease Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:68.8 occ:1.00 O A:ASP122 2.5 40.1 1.0 C A:ASP122 3.6 37.3 1.0 CA A:ASP122 4.0 38.1 1.0 CB A:ASP122 4.0 44.3 1.0 CD A:PRO124 4.6 39.6 1.0 N A:ASN123 4.8 33.2 1.0 CE B:MET117 4.8 33.4 1.0 N A:PRO124 4.9 38.4 1.0

Calcium binding site 3 out of 4 in the ECOT38I Restriction Endonuclease Complexed with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of ECOT38I Restriction Endonuclease Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:75.8 occ:1.00 O B:HOH523 2.5 46.8 1.0 O B:HOH584 2.7 55.9 1.0 OD1 B:ASN175 2.8 86.9 1.0 O B:HOH606 2.9 55.8 1.0 CB B:ASN172 2.9 62.7 0.4 O B:SER173 2.9 59.7 1.0 CB B:ASN172 3.1 62.6 0.6 CG B:ASN172 3.5 61.5 0.4 ND2 B:ASN172 3.6 62.9 0.4 ND2 B:ASN172 3.8 57.6 0.6 CG B:ASN172 4.0 55.9 0.6 CG B:ASN175 4.0 83.9 1.0 C B:SER173 4.1 60.1 1.0 CA B:ASN172 4.1 64.3 0.4 C B:ASN172 4.2 59.0 1.0 O B:HOH548 4.2 54.9 1.0 CA B:ASN172 4.2 64.3 0.6 N B:SER173 4.3 55.4 1.0 O B:HOH616 4.3 49.4 1.0 OD1 B:ASN172 4.4 60.7 0.4 N B:ASN175 4.6 76.0 1.0 O B:ASN172 4.7 55.0 1.0 ND2 B:ASN175 4.7 86.4 1.0 CA B:SER173 4.8 56.1 1.0 C B:ILE174 4.9 67.5 1.0 CA B:ASN175 5.0 80.2 1.0

Calcium binding site 4 out of 4 in the ECOT38I Restriction Endonuclease Complexed with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of ECOT38I Restriction Endonuclease Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca101 b:38.3 occ:1.00 O A:HOH561 2.3 43.1 1.0 OD1 A:ASP231 2.4 34.4 1.0 O A:HOH503 2.4 36.9 1.0 O A:HOH559 2.5 34.5 1.0 O A:HOH599 2.5 44.1 1.0 OP1 F:DC9 2.5 33.4 1.0 O3' F:DT8 2.6 30.4 1.0 P F:DC9 3.2 32.4 1.0 CG A:ASP231 3.5 32.9 1.0 C3' F:DT8 3.9 29.1 1.0 CA A:CA401 3.9 31.1 1.0 O A:HOH556 3.9 44.9 1.0 O A:HOH574 4.1 37.0 1.0 C4' F:DT8 4.1 32.2 1.0 OE2 A:GLU245 4.1 38.1 1.0 OE1 A:GLU228 4.1 48.4 1.0 OD2 A:ASP231 4.2 33.3 1.0 OP2 F:DC9 4.2 33.3 1.0 O A:HOH510 4.3 41.4 1.0 O5' F:DC9 4.4 30.6 1.0 OE1 A:GLU245 4.4 35.8 1.0 C5' F:DC9 4.5 28.6 1.0 CA A:ASP231 4.5 33.4 1.0 O A:GLN221 4.6 34.5 1.0 N A:ASP231 4.6 34.2 1.0 C2' F:DT8 4.6 32.9 1.0 CB A:ASP231 4.6 30.4 1.0 CD A:GLU245 4.7 37.3 1.0 C5' F:DT8 4.8 29.5 1.0 O A:VAL219 4.8 31.7 1.0 C A:LEU230 4.9 34.5 1.0 O A:HOH614 4.9 31.1 1.0 NZ A:LYS262 5.0 40.3 1.0 O F:HOH223 5.0 36.0 1.0

K.Kita, B.Mikami. Structural Analysis of ECOT38I Restriction Endonuclease To Be Published.