Calcium in PDB 6ij2: Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form

The structure of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form, PDB code: 6ij2 was solved by M.Yadav, K.Pal, U.Sen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.51 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.483, 42.711, 158.470, 90.00, 94.94, 90.00
R / Rfree (%)	18.2 / 22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form (pdb code 6ij2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form, PDB code: 6ij2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


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 A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:29.7 occ:1.00 O A:HOH729 2.3 27.8 1.0 OD1 A:ASP158 2.3 28.4 1.0 OP3 E:G503 2.3 44.1 1.0 OE2 A:GLU215 2.3 33.2 1.0 O A:ASP158 2.4 33.6 1.0 OD1 A:ASP159 2.5 40.3 1.0 OE1 A:GLU215 2.5 31.1 1.0 CD A:GLU215 2.7 32.9 1.0 C A:ASP158 3.2 29.0 1.0 CG A:ASP158 3.2 30.8 1.0 CG A:ASP159 3.6 42.3 1.0 P E:G503 3.6 45.1 1.0 O A:HOH738 3.8 27.3 1.0 CA A:ASP159 3.9 25.3 1.0 N A:ASP159 4.0 26.8 1.0 CA A:ASP158 4.0 27.1 1.0 OP2 E:G503 4.0 47.4 1.0 CB A:ASP158 4.0 31.2 1.0 OD2 A:ASP158 4.0 33.1 1.0 OP1 E:G503 4.2 44.6 1.0 CB A:ASP159 4.3 30.1 1.0 CG A:GLU215 4.3 31.6 1.0 CA A:CA602 4.3 26.5 1.0 O A:HOH779 4.4 26.2 1.0 CA A:CA604 4.5 84.3 1.0 OD2 A:ASP159 4.6 47.5 1.0 CB A:LYS179 4.7 24.0 1.0 O5' E:G503 4.7 45.0 1.0 CE A:LYS179 4.8 34.8 1.0

Calcium binding site 2 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


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 A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:26.5 occ:1.00 OE2 A:GLU128 2.3 29.7 1.0 O A:HOH738 2.3 27.3 1.0 OD1 A:ASN95 2.4 40.2 1.0 OE2 A:GLU45 2.4 27.9 1.0 OP1 E:G503 2.4 44.6 1.0 OD2 A:ASP158 2.4 33.1 1.0 OD1 A:ASP158 2.7 28.4 1.0 CG A:ASP158 2.9 30.8 1.0 CD A:GLU45 3.4 33.1 1.0 CG A:ASN95 3.4 37.4 1.0 CD A:GLU128 3.5 30.1 1.0 P E:G503 3.6 45.1 1.0 OP3 E:G503 3.6 44.1 1.0 OE1 A:GLU45 3.8 30.3 1.0 ND2 A:ASN95 3.8 31.7 1.0 O2' E:G504 4.2 47.5 1.0 NZ A:LYS179 4.2 26.9 1.0 OE1 A:GLU128 4.2 29.4 1.0 CB A:GLU128 4.3 31.0 1.0 CA A:CA601 4.3 29.7 1.0 CE A:LYS179 4.3 34.8 1.0 CB A:ASP158 4.3 31.2 1.0 OE1 A:GLU215 4.3 31.1 1.0 OP2 E:G503 4.5 47.4 1.0 CG A:GLU128 4.5 28.8 1.0 O A:HOH723 4.5 36.8 1.0 CG A:GLU45 4.6 28.9 1.0 O5' E:G503 4.7 45.0 1.0 CA A:CA604 4.7 84.3 1.0 CB A:ASN95 4.7 33.0 1.0 C5' E:G503 4.8 44.1 1.0

Calcium binding site 3 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


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 A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:57.1 occ:1.00 O A:SER162 2.2 35.3 1.0 O A:TYR164 2.2 41.5 1.0 O A:HOH756 2.4 34.5 1.0 O A:ASP159 2.4 29.1 1.0 O A:HOH743 2.5 33.9 1.0 C A:TYR164 3.3 43.7 1.0 C A:SER162 3.4 36.1 1.0 N A:TYR164 3.5 39.6 1.0 C A:ASP159 3.5 27.8 1.0 CA A:TYR164 3.9 41.2 1.0 N A:SER162 4.0 27.0 1.0 CB A:ASP159 4.0 30.1 1.0 OE2 A:GLU131 4.0 46.5 1.0 C A:GLY163 4.0 37.8 1.0 N A:GLY166 4.1 31.2 1.0 O D:HOH782 4.2 22.9 1.0 OE1 A:GLU131 4.3 45.8 1.0 CA A:GLY163 4.3 38.5 1.0 N A:PHE160 4.3 25.0 1.0 CA A:ASP159 4.3 25.3 1.0 N A:GLY163 4.3 33.4 1.0 CA A:PHE160 4.4 25.9 1.0 CA A:SER162 4.4 32.5 1.0 O A:HOH764 4.4 33.5 1.0 N A:GLY161 4.4 26.8 1.0 N A:SER165 4.4 36.6 1.0 C A:SER165 4.5 38.9 1.0 CA A:GLY166 4.5 34.3 1.0 CB A:TYR164 4.6 40.1 1.0 CD A:GLU131 4.6 51.3 1.0 O A:HOH712 4.6 38.5 1.0 CB D:SER165 4.7 36.0 1.0 OG A:SER162 4.7 44.9 1.0 C A:PHE160 4.7 26.4 1.0 CA A:SER165 4.8 30.6 1.0 O A:GLY163 4.8 39.5 1.0

Calcium binding site 4 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:84.3 occ:1.00 O E:HOH604 2.4 69.4 1.0 OD2 A:ASP159 2.5 47.5 1.0 OP2 E:G503 2.7 47.4 1.0 OG1 A:THR130 2.8 39.3 1.0 OD1 A:ASP159 2.8 40.3 1.0 CG A:ASP159 3.0 42.3 1.0 OD2 A:ASP158 3.2 33.1 1.0 CG A:ASP158 3.6 30.8 1.0 P E:G503 3.6 45.1 1.0 OP1 E:G503 3.8 44.6 1.0 CB A:THR130 3.8 46.1 1.0 CG2 A:THR130 3.9 46.4 1.0 O A:HOH723 3.9 36.8 1.0 OP3 E:G503 4.0 44.1 1.0 O2' E:G504 4.0 47.5 1.0 O3' E:G504 4.1 50.7 1.0 CB A:ASP158 4.2 31.2 1.0 OD1 A:ASP158 4.2 28.4 1.0 CA A:CA601 4.5 29.7 1.0 CB A:ASP159 4.5 30.1 1.0 O A:HOH712 4.7 38.5 1.0 CA A:CA602 4.7 26.5 1.0 O A:HOH729 4.8 27.8 1.0 OD1 A:ASN95 4.9 40.2 1.0

Calcium binding site 5 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:23.8 occ:1.00 O B:HOH731 2.3 27.0 1.0 OP3 F:G503 2.3 27.3 1.0 O B:ASP158 2.3 26.9 1.0 OE2 B:GLU215 2.4 26.1 1.0 OD1 B:ASP158 2.4 26.1 1.0 OD1 B:ASP159 2.5 32.6 1.0 OE1 B:GLU215 2.5 28.5 1.0 CD B:GLU215 2.8 26.9 1.0 C B:ASP158 3.2 26.0 1.0 CG B:ASP158 3.3 23.3 1.0 P F:G503 3.6 27.8 1.0 CG B:ASP159 3.6 40.4 1.0 O B:HOH711 3.7 23.6 1.0 O F:HOH603 3.8 37.5 1.0 CA B:ASP159 3.9 22.0 1.0 OP2 F:G503 4.0 33.5 1.0 N B:ASP159 4.0 24.5 1.0 OD2 B:ASP158 4.0 26.5 1.0 CA B:ASP158 4.1 22.2 1.0 CB B:ASP158 4.1 24.3 1.0 OP1 F:G503 4.1 27.6 1.0 O F:HOH601 4.2 34.6 1.0 O B:HOH761 4.2 24.6 1.0 CA B:CA602 4.3 23.2 1.0 CG B:GLU215 4.3 23.6 1.0 CB B:ASP159 4.3 25.7 1.0 CA B:CA604 4.4 74.7 1.0 OD2 B:ASP159 4.6 34.9 1.0 O5' F:G503 4.6 35.7 1.0 CB B:LYS179 4.7 20.1 1.0 OD1 B:ASP181 4.9 28.5 1.0

Calcium binding site 6 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:23.2 occ:1.00 OE2 B:GLU128 2.3 26.3 1.0 OD1 B:ASN95 2.4 28.3 1.0 OE2 B:GLU45 2.4 23.7 1.0 O B:HOH711 2.4 23.6 1.0 OD2 B:ASP158 2.4 26.5 1.0 OP1 F:G503 2.4 27.6 1.0 OD1 B:ASP158 2.7 26.1 1.0 CG B:ASP158 2.8 23.3 1.0 CD B:GLU45 3.4 24.6 1.0 CG B:ASN95 3.4 24.7 1.0 CD B:GLU128 3.6 25.5 1.0 P F:G503 3.6 27.8 1.0 OP3 F:G503 3.6 27.3 1.0 ND2 B:ASN95 3.8 25.6 1.0 OE1 B:GLU45 3.8 26.4 1.0 O2' F:G504 4.1 31.1 1.0 NZ B:LYS179 4.1 20.8 1.0 OE1 B:GLU128 4.3 25.5 1.0 CA B:CA601 4.3 23.8 1.0 CB B:ASP158 4.3 24.3 1.0 OE1 B:GLU215 4.3 28.5 1.0 CB B:GLU128 4.4 22.9 1.0 CA B:CA604 4.4 74.7 1.0 O B:HOH729 4.4 33.9 1.0 O F:HOH602 4.5 61.3 1.0 OP2 F:G503 4.5 33.5 1.0 CG B:GLU128 4.6 21.9 1.0 CG B:GLU45 4.6 23.9 1.0 O5' F:G503 4.7 35.7 1.0 C5' F:G503 4.8 30.2 1.0 CB B:ASN95 4.8 23.7 1.0 CD B:LYS179 5.0 25.2 1.0

Calcium binding site 7 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:41.3 occ:1.00 O B:TYR164 2.2 27.9 1.0 O B:SER162 2.3 27.1 1.0 O B:HOH818 2.4 29.3 1.0 O B:ASP159 2.4 23.7 1.0 O B:HOH763 2.5 27.2 1.0 C B:TYR164 3.3 31.9 1.0 N B:TYR164 3.4 30.3 1.0 C B:SER162 3.5 29.1 1.0 C B:ASP159 3.5 26.2 1.0 CA B:TYR164 3.9 31.8 1.0 N B:GLY166 4.0 22.6 1.0 C B:GLY163 4.0 28.3 1.0 O C:HOH792 4.1 18.7 1.0 N B:SER162 4.1 22.5 1.0 CB B:ASP159 4.1 25.7 1.0 OE1 B:GLU131 4.1 32.2 1.0 OE2 B:GLU131 4.3 35.6 1.0 CA B:GLY163 4.3 27.0 1.0 N B:PHE160 4.4 19.8 1.0 N B:GLY163 4.4 27.3 1.0 CA B:PHE160 4.4 22.4 1.0 N B:SER165 4.4 32.0 1.0 CA B:ASP159 4.4 22.0 1.0 N B:GLY161 4.4 20.8 1.0 O B:HOH776 4.4 27.5 1.0 C B:SER165 4.4 29.5 1.0 CA B:SER162 4.5 27.8 1.0 CA B:GLY166 4.5 27.4 1.0 CD B:GLU131 4.5 39.1 1.0 O B:HOH728 4.6 36.6 1.0 CB B:TYR164 4.6 32.2 1.0 CB C:SER165 4.6 29.7 1.0 CA B:SER165 4.7 28.1 1.0 C B:PHE160 4.8 17.9 1.0 O B:GLY163 4.8 33.9 1.0 OG B:SER162 4.9 49.0 1.0

Calcium binding site 8 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:74.7 occ:1.00 O F:HOH602 2.3 61.3 1.0 OD2 B:ASP159 2.6 34.9 1.0 OG1 B:THR130 2.7 31.2 1.0 OD2 B:ASP158 2.8 26.5 1.0 OD1 B:ASP159 2.8 32.6 1.0 OP2 F:G503 2.8 33.5 1.0 CG B:ASP159 3.0 40.4 1.0 CG B:ASP158 3.4 23.3 1.0 O B:HOH729 3.6 33.9 1.0 P F:G503 3.6 27.8 1.0 OP1 F:G503 3.7 27.6 1.0 CB B:THR130 3.8 36.5 1.0 O F:HOH601 3.9 34.6 1.0 CG2 B:THR130 3.9 35.5 1.0 OP3 F:G503 4.0 27.3 1.0 OD1 B:ASP158 4.0 26.1 1.0 O2' F:G504 4.0 31.1 1.0 CB B:ASP158 4.0 24.3 1.0 O3' F:G504 4.3 30.4 1.0 CA B:CA601 4.4 23.8 1.0 CA B:CA602 4.4 23.2 1.0 CB B:ASP159 4.5 25.7 1.0 OD1 B:ASN95 4.6 28.3 1.0 O B:HOH731 4.9 27.0 1.0 O B:HOH728 5.0 36.6 1.0

Calcium binding site 9 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:23.9 occ:1.00 OE2 C:GLU128 2.3 27.7 1.0 O C:HOH740 2.3 27.1 1.0 OE2 C:GLU45 2.4 25.9 1.0 OD1 C:ASN95 2.4 31.9 1.0 OP1 G:G503 2.4 33.5 1.0 OD2 C:ASP158 2.5 28.4 1.0 OD1 C:ASP158 2.7 24.6 1.0 CG C:ASP158 2.9 27.1 1.0 CD C:GLU45 3.4 29.1 1.0 CG C:ASN95 3.4 32.9 1.0 CD C:GLU128 3.5 27.6 1.0 P G:G503 3.6 33.6 1.0 OP3 G:G503 3.6 32.4 1.0 ND2 C:ASN95 3.8 26.7 1.0 OE1 C:GLU45 3.8 28.9 1.0 O2' G:G504 4.1 36.8 1.0 NZ C:LYS179 4.1 23.1 1.0 OE1 C:GLU128 4.2 26.3 1.0 CA C:CA602 4.3 26.9 1.0 CB C:GLU128 4.3 28.6 1.0 OE1 C:GLU215 4.3 28.6 1.0 CB C:ASP158 4.4 27.5 1.0 CG C:GLU128 4.5 30.2 1.0 OP2 G:G503 4.5 36.1 1.0 CA C:CA604 4.6 0.8 1.0 CG C:GLU45 4.6 23.7 1.0 O C:HOH734 4.7 33.9 1.0 O5' G:G503 4.7 35.7 1.0 O G:HOH605 4.7 76.2 1.0 C5' G:G503 4.8 35.2 1.0 CB C:ASN95 4.8 28.6 1.0 CD C:LYS179 4.9 20.2 1.0

Calcium binding site 10 out of 16 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca602 b:26.9 occ:1.00 O C:HOH728 2.3 27.3 1.0 O C:ASP158 2.4 29.4 1.0 OD1 C:ASP158 2.4 24.6 1.0 OP3 G:G503 2.4 32.4 1.0 OD1 C:ASP159 2.4 33.6 1.0 OE2 C:GLU215 2.4 31.2 1.0 OE1 C:GLU215 2.5 28.6 1.0 CD C:GLU215 2.8 34.9 1.0 C C:ASP158 3.2 27.3 1.0 CG C:ASP158 3.3 27.1 1.0 CG C:ASP159 3.6 34.7 1.0 P G:G503 3.7 33.6 1.0 O C:HOH740 3.8 27.1 1.0 O G:HOH602 3.9 39.9 1.0 CA C:ASP159 3.9 24.8 1.0 CA C:ASP158 4.0 25.6 1.0 N C:ASP159 4.0 21.7 1.0 CB C:ASP158 4.0 27.5 1.0 OD2 C:ASP158 4.1 28.4 1.0 OP2 G:G503 4.1 36.1 1.0 OP1 G:G503 4.2 33.5 1.0 CB C:ASP159 4.3 26.5 1.0 O G:HOH601 4.3 50.9 1.0 O C:HOH771 4.3 24.0 1.0 CA C:CA601 4.3 23.9 1.0 CG C:GLU215 4.3 26.4 1.0 CA C:CA604 4.5 0.8 1.0 OD2 C:ASP159 4.5 34.3 1.0 CB C:LYS179 4.7 20.7 1.0 O5' G:G503 4.7 35.7 1.0 OD1 C:ASP181 5.0 30.3 1.0

M.Yadav, K.Pal, U.Sen. Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - 5'-Pgpg Bound Form To Be Published.