Calcium in PDB 5xop: Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant

The structure of Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant, PDB code: 5xop was solved by S.Kumar, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.74 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.690, 101.359, 107.475, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25

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>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant (pdb code 5xop). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant, PDB code: 5xop:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:36.4 occ:1.00 OD1 A:ASP10 2.1 38.3 1.0 O A:HOH212 2.2 34.5 1.0 O A:ALA16 2.3 39.0 1.0 OD1 A:ASN12 2.4 36.4 1.0 OE1 A:GLU21 2.5 28.7 1.0 OE2 A:GLU21 2.5 27.3 1.0 OD1 A:ASP14 2.6 34.6 1.0 CD A:GLU21 2.8 30.4 1.0 CG A:ASP10 3.3 40.5 1.0 CG A:ASP14 3.3 39.7 1.0 CG A:ASN12 3.4 40.7 1.0 C A:ALA16 3.5 39.5 1.0 OD2 A:ASP14 3.5 36.8 1.0 ND2 A:ASN12 4.0 45.5 1.0 CA A:ASP10 4.1 35.7 1.0 OD2 A:ASP10 4.2 47.0 1.0 CB A:ASP10 4.2 38.9 1.0 N A:ASP14 4.2 46.2 1.0 N A:ALA16 4.3 41.2 1.0 CG A:GLU21 4.3 27.9 1.0 N A:ASN12 4.3 38.1 1.0 N A:VAL17 4.4 39.1 1.0 CA A:ALA16 4.4 36.9 1.0 CA A:VAL17 4.4 31.2 1.0 C A:ASP10 4.5 36.8 1.0 CB A:ASP14 4.5 45.3 1.0 CB A:ASN12 4.5 40.7 1.0 N A:SER18 4.6 29.2 1.0 N A:GLY13 4.6 47.9 1.0 CA A:ASN12 4.7 43.4 1.0 CA A:ASP14 4.8 44.3 1.0 CB A:ALA16 4.8 38.0 1.0 N A:VAL11 4.8 35.4 1.0 C A:ASN12 4.9 46.7 1.0 N A:GLY15 4.9 44.7 1.0 O A:ASP10 4.9 36.4 1.0 C A:ASP14 5.0 47.2 1.0

Calcium binding site 2 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:28.5 occ:1.00 OD1 A:ASP50 2.2 35.5 1.0 O A:PHE52 2.3 24.5 1.0 O A:HOH214 2.3 37.3 1.0 OD1 A:ASP46 2.3 33.7 1.0 OD1 A:ASP48 2.4 32.7 1.0 OE2 A:GLU57 2.5 28.4 1.0 OE1 A:GLU57 2.7 30.7 1.0 CD A:GLU57 3.0 30.8 1.0 CG A:ASP50 3.1 38.5 1.0 CG A:ASP48 3.3 39.0 1.0 CG A:ASP46 3.4 34.2 1.0 C A:PHE52 3.5 25.7 1.0 OD2 A:ASP50 3.6 41.9 1.0 OD2 A:ASP48 3.7 41.9 1.0 OD2 A:ASP46 4.1 36.6 1.0 N A:ASP50 4.1 38.7 1.0 N A:PHE52 4.3 29.1 1.0 CA A:ASP46 4.3 31.9 1.0 CB A:ASP46 4.3 33.4 1.0 CB A:ASP50 4.3 36.3 1.0 N A:ASP48 4.4 41.3 1.0 CA A:PHE52 4.4 29.4 1.0 CA A:ILE53 4.4 23.2 1.0 N A:ASP54 4.4 24.7 1.0 CG A:GLU57 4.4 30.8 1.0 N A:ILE53 4.5 22.9 1.0 C A:ASP46 4.5 36.3 1.0 N A:GLY49 4.5 41.7 1.0 CB A:ASP48 4.5 45.3 1.0 OD2 A:ASP54 4.6 35.0 1.0 CA A:ASP50 4.6 31.4 1.0 N A:LYS47 4.7 39.5 1.0 CA A:ASP48 4.8 44.2 1.0 N A:GLY51 4.8 32.6 1.0 C A:ASP48 4.8 45.5 1.0 CB A:PHE52 4.8 30.6 1.0 O A:HOH205 4.9 39.5 1.0 C A:ILE53 4.9 25.9 1.0 C A:ASP50 4.9 36.0 1.0 CG A:ASP54 4.9 31.6 1.0 O A:ASP46 5.0 33.0 1.0

Calcium binding site 3 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:27.2 occ:1.00 O B:ALA16 2.2 28.5 1.0 OD1 B:ASP10 2.4 30.6 1.0 OD1 B:ASN12 2.4 33.0 1.0 O B:HOH214 2.4 28.3 1.0 OD1 B:ASP14 2.4 30.7 1.0 OE1 B:GLU21 2.5 24.7 1.0 OE2 B:GLU21 2.5 29.4 1.0 CD B:GLU21 2.8 29.2 1.0 CG B:ASP14 3.3 33.8 1.0 C B:ALA16 3.4 28.8 1.0 CG B:ASP10 3.5 32.4 1.0 CG B:ASN12 3.5 34.5 1.0 OD2 B:ASP14 3.7 31.6 1.0 ND2 B:ASN12 4.0 30.7 1.0 N B:ALA16 4.2 29.5 1.0 CA B:ASP10 4.2 27.4 1.0 N B:ASP14 4.2 31.9 1.0 CB B:ASP10 4.3 28.3 1.0 OD2 B:ASP10 4.3 29.6 1.0 CG B:GLU21 4.3 29.3 1.0 N B:VAL17 4.3 24.9 1.0 CA B:VAL17 4.4 26.4 1.0 O B:HOH225 4.4 34.9 1.0 O B:HOH206 4.4 34.0 1.0 CA B:ALA16 4.4 28.6 1.0 N B:ASN12 4.4 31.2 1.0 C B:ASP10 4.5 31.7 1.0 CB B:ASP14 4.6 32.3 1.0 N B:SER18 4.6 24.2 1.0 N B:GLY13 4.6 38.7 1.0 CB B:ASN12 4.7 38.2 1.0 N B:VAL11 4.8 33.2 1.0 CA B:ASP14 4.8 30.7 1.0 CB B:ALA16 4.9 30.8 1.0 CA B:ASN12 4.9 37.6 1.0 C B:ASN12 4.9 37.5 1.0 N B:GLY15 4.9 30.8 1.0 C B:VAL17 5.0 23.2 1.0 O B:ASP10 5.0 30.9 1.0

Calcium binding site 4 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:29.7 occ:1.00 OD1 B:ASP46 2.2 31.8 1.0 OD1 B:ASP50 2.4 33.2 1.0 O B:PHE52 2.4 32.6 1.0 O B:HOH218 2.4 35.7 1.0 OD1 B:ASP48 2.4 29.3 1.0 OE1 B:GLU57 2.5 32.6 1.0 OE2 B:GLU57 2.6 31.9 1.0 CD B:GLU57 2.9 32.6 1.0 CG B:ASP50 3.2 30.1 1.0 CG B:ASP48 3.4 29.3 1.0 CG B:ASP46 3.4 32.7 1.0 C B:PHE52 3.5 34.4 1.0 OD2 B:ASP50 3.6 26.2 1.0 OD2 B:ASP48 3.8 29.2 1.0 N B:ASP50 4.1 30.6 1.0 CA B:ASP46 4.2 27.3 1.0 N B:ASP48 4.2 30.3 1.0 OD2 B:ASP46 4.2 30.9 1.0 N B:PHE52 4.2 30.9 1.0 CB B:ASP46 4.3 28.1 1.0 CB B:ASP50 4.3 30.5 1.0 N B:ILE53 4.4 28.7 1.0 CA B:PHE52 4.4 31.7 1.0 CG B:GLU57 4.4 35.2 1.0 CA B:ILE53 4.4 26.2 1.0 C B:ASP46 4.4 27.1 1.0 OD2 B:ASP54 4.4 38.2 1.0 N B:GLY49 4.5 33.3 1.0 N B:ASP54 4.5 38.1 1.0 CB B:ASP48 4.5 29.5 1.0 CA B:ASP48 4.7 30.4 1.0 N B:LYS47 4.7 30.6 1.0 CA B:ASP50 4.7 31.1 1.0 N B:GLY51 4.8 31.9 1.0 C B:ASP48 4.8 35.8 1.0 CB B:PHE52 4.8 38.5 1.0 C B:ILE53 4.9 33.3 1.0 O B:HOH207 4.9 36.3 1.0 CG B:ASP54 4.9 33.6 1.0 CA B:CA103 5.0 27.6 1.0 O B:ASP46 5.0 26.9 1.0 C B:ASP50 5.0 32.4 1.0

Calcium binding site 5 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:27.6 occ:1.00 O B:HOH223 2.3 25.2 1.0 OD2 B:ASP48 2.3 29.2 1.0 OD2 B:ASP50 2.3 26.2 1.0 O B:HOH222 2.4 31.7 1.0 CG B:ASP50 3.4 30.1 1.0 CG B:ASP48 3.4 29.3 1.0 CB B:ASP50 3.8 30.5 1.0 OD1 B:ASP48 3.9 29.3 1.0 O B:HOH218 4.0 35.7 1.0 O B:HOH221 4.0 48.5 1.0 OD1 B:ASP50 4.4 33.2 1.0 CB B:ASP48 4.5 29.5 1.0 O B:HOH212 4.8 43.9 1.0 CA B:CA102 5.0 29.7 1.0

Calcium binding site 6 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:41.7 occ:1.00 O C:HOH209 1.9 38.9 1.0 OD1 C:ASP10 2.1 47.8 1.0 O C:ALA16 2.3 44.4 1.0 OD1 C:ASN12 2.3 49.1 1.0 OE1 C:GLU21 2.5 33.5 1.0 OE2 C:GLU21 2.6 45.3 1.0 OD1 C:ASP14 2.6 42.9 1.0 CD C:GLU21 2.9 37.5 1.0 CG C:ASP10 3.3 43.5 1.0 CG C:ASP14 3.3 48.9 1.0 CG C:ASN12 3.4 55.1 1.0 C C:ALA16 3.4 35.2 1.0 OD2 C:ASP14 3.5 44.6 1.0 ND2 C:ASN12 3.7 52.5 1.0 OD2 C:ASP10 4.0 57.1 1.0 N C:VAL17 4.2 38.4 1.0 CB C:ASP10 4.2 47.7 1.0 N C:ALA16 4.3 38.1 1.0 CA C:ASP10 4.3 48.6 1.0 CA C:VAL17 4.3 34.5 1.0 CA C:ALA16 4.4 32.8 1.0 CG C:GLU21 4.4 39.6 1.0 N C:ASP14 4.4 54.0 1.0 N C:SER18 4.5 30.8 1.0 N C:ASN12 4.6 60.2 1.0 CB C:ASP14 4.6 47.8 1.0 CB C:ASN12 4.7 57.7 1.0 C C:ASP10 4.7 59.7 1.0 N C:VAL11 4.8 56.3 1.0 N C:GLY13 4.8 58.0 1.0 CB C:ALA16 4.8 31.5 1.0 CA C:ASP14 4.9 48.0 1.0 CA C:ASN12 4.9 57.5 1.0 C C:VAL17 4.9 34.3 1.0 C C:ASN12 4.9 53.1 1.0 N C:GLY15 5.0 42.2 1.0

Calcium binding site 7 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca102 b:48.1 occ:1.00 OD1 C:ASP46 2.1 51.7 1.0 O C:HOH211 2.2 79.6 1.0 OD1 C:ASP50 2.3 47.5 1.0 OD1 C:ASP48 2.3 60.2 1.0 OE1 C:GLU57 2.4 41.3 1.0 O C:PHE52 2.4 45.6 1.0 OE2 C:GLU57 2.6 40.1 1.0 CD C:GLU57 2.8 48.4 1.0 CG C:ASP46 3.3 47.8 1.0 CG C:ASP50 3.3 56.6 1.0 CG C:ASP48 3.3 61.4 1.0 C C:PHE52 3.6 48.0 1.0 OD2 C:ASP48 3.7 61.7 1.0 OD2 C:ASP50 3.8 49.6 1.0 OD2 C:ASP46 4.1 44.0 1.0 OD2 C:ASP54 4.1 47.7 1.0 CA C:ASP46 4.2 47.1 1.0 CB C:ASP46 4.2 44.8 1.0 N C:ASP50 4.2 45.9 1.0 N C:PHE52 4.2 42.6 1.0 CG C:GLU57 4.3 46.2 1.0 CA C:ILE53 4.4 42.6 1.0 N C:ASP54 4.4 44.1 1.0 N C:ILE53 4.4 36.2 1.0 CA C:PHE52 4.4 44.3 1.0 C C:ASP46 4.4 43.0 1.0 CB C:ASP50 4.4 46.7 1.0 N C:ASP48 4.5 56.4 1.0 CB C:ASP48 4.6 53.1 1.0 N C:GLY49 4.6 55.3 1.0 N C:LYS47 4.7 46.6 1.0 CA C:ASP50 4.8 49.4 1.0 C C:ASP48 4.8 58.1 1.0 CA C:ASP48 4.8 53.3 1.0 C C:ILE53 4.9 41.9 1.0 CB C:PHE52 4.9 51.9 1.0 N C:GLY51 4.9 48.8 1.0 CG C:ASP54 4.9 43.6 1.0 O C:ASP46 5.0 45.0 1.0

Calcium binding site 8 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:28.1 occ:1.00 O D:ALA16 2.1 29.2 1.0 O D:HOH224 2.2 28.4 1.0 OD1 D:ASP10 2.3 33.8 1.0 OD1 D:ASN12 2.4 34.1 1.0 OE1 D:GLU21 2.4 26.4 1.0 OE2 D:GLU21 2.5 23.9 1.0 OD1 D:ASP14 2.5 32.5 1.0 CD D:GLU21 2.8 25.2 1.0 CG D:ASN12 3.3 34.7 1.0 CG D:ASP14 3.3 33.9 1.0 C D:ALA16 3.4 36.7 1.0 CG D:ASP10 3.4 34.7 1.0 OD2 D:ASP14 3.7 32.9 1.0 ND2 D:ASN12 3.9 38.0 1.0 CA D:ASP10 4.2 26.1 1.0 N D:ASP14 4.2 37.2 1.0 N D:ALA16 4.2 38.5 1.0 OD2 D:ASP10 4.2 35.0 1.0 CB D:ASP10 4.2 31.6 1.0 CA D:ALA16 4.3 35.7 1.0 N D:VAL17 4.4 33.2 1.0 CG D:GLU21 4.4 27.1 1.0 N D:ASN12 4.4 28.5 1.0 CA D:VAL17 4.4 30.4 1.0 C D:ASP10 4.5 30.3 1.0 CB D:ASP14 4.5 34.6 1.0 CB D:ASN12 4.5 31.8 1.0 N D:SER18 4.5 28.2 1.0 O D:HOH214 4.6 37.2 1.0 N D:GLY13 4.6 36.9 1.0 CA D:ASP14 4.7 34.1 1.0 CB D:ALA16 4.7 38.3 1.0 N D:VAL11 4.8 27.1 1.0 O D:HOH215 4.8 34.2 1.0 CA D:ASN12 4.8 31.9 1.0 N D:GLY15 4.9 35.5 1.0 C D:ASN12 4.9 37.6 1.0 O D:ASP10 5.0 29.8 1.0 OG D:SER18 5.0 29.0 1.0 C D:VAL17 5.0 27.1 1.0

Calcium binding site 9 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:25.7 occ:1.00 OD1 D:ASP46 2.2 28.9 1.0 O D:HOH221 2.2 33.9 1.0 O D:PHE52 2.3 21.9 1.0 OD1 D:ASP48 2.4 33.3 1.0 OD1 D:ASP50 2.4 27.9 1.0 OE1 D:GLU57 2.4 24.8 1.0 OE2 D:GLU57 2.6 29.5 1.0 CD D:GLU57 2.8 30.4 1.0 CG D:ASP46 3.3 26.9 1.0 CG D:ASP48 3.3 40.9 1.0 CG D:ASP50 3.3 33.6 1.0 C D:PHE52 3.5 26.0 1.0 OD2 D:ASP48 3.7 45.4 1.0 OD2 D:ASP50 3.8 28.9 1.0 OD2 D:ASP46 4.1 29.6 1.0 CB D:ASP46 4.1 25.6 1.0 N D:ASP48 4.2 36.7 1.0 CA D:ASP46 4.2 27.2 1.0 N D:PHE52 4.2 28.3 1.0 N D:ASP50 4.2 35.0 1.0 N D:ASP54 4.4 23.1 1.0 CG D:GLU57 4.4 28.5 1.0 N D:ILE53 4.4 21.6 1.0 OD2 D:ASP54 4.4 30.9 1.0 CA D:ILE53 4.4 20.1 1.0 CB D:ASP48 4.4 36.3 1.0 CA D:PHE52 4.4 25.2 1.0 CB D:ASP50 4.5 35.0 1.0 C D:ASP46 4.5 35.0 1.0 N D:GLY49 4.5 39.8 1.0 CA D:ASP48 4.6 38.5 1.0 N D:LYS47 4.7 37.1 1.0 C D:ASP48 4.7 44.4 1.0 CA D:ASP50 4.8 33.1 1.0 O D:HOH208 4.8 42.6 1.0 C D:ILE53 4.8 21.0 1.0 CG D:ASP54 4.8 26.0 1.0 O D:ASP46 4.8 32.9 1.0 O D:HOH204 4.9 39.9 1.0 CB D:PHE52 4.9 26.7 1.0 N D:GLY51 4.9 27.1 1.0

Calcium binding site 10 out of 13 in the Crystal Structure of N-Terminal Domain EHCABP1 Ef-2 Mutant


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 N-Terminal Domain EHCABP1 Ef-2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca101 b:26.0 occ:1.00 O E:ALA16 2.3 25.0 1.0 O E:HOH224 2.3 27.6 1.0 OD1 E:ASN12 2.3 34.8 1.0 OD1 E:ASP10 2.3 28.0 1.0 OD1 E:ASP14 2.4 27.5 1.0 OE1 E:GLU21 2.5 25.4 1.0 OE2 E:GLU21 2.5 24.1 1.0 CD E:GLU21 2.8 25.5 1.0 CG E:ASP14 3.3 39.4 1.0 CG E:ASP10 3.4 32.7 1.0 C E:ALA16 3.4 26.3 1.0 CG E:ASN12 3.5 40.2 1.0 OD2 E:ASP14 3.7 35.5 1.0 CA E:ASP10 4.0 24.3 1.0 ND2 E:ASN12 4.1 41.2 1.0 CB E:ASP10 4.1 27.1 1.0 OD2 E:ASP10 4.2 27.9 1.0 N E:ALA16 4.3 26.5 1.0 N E:ASN12 4.3 38.2 1.0 N E:VAL17 4.3 24.2 1.0 CA E:ALA16 4.3 27.2 1.0 CG E:GLU21 4.4 25.2 1.0 N E:VAL11 4.4 29.9 1.0 N E:ASP14 4.4 36.5 1.0 C E:ASP10 4.4 28.9 1.0 CA E:VAL17 4.4 24.4 1.0 O E:HOH219 4.5 31.8 1.0 CB E:ASP14 4.6 36.8 1.0 N E:GLY13 4.6 40.0 1.0 N E:SER18 4.7 22.6 1.0 CB E:ALA16 4.7 30.3 1.0 CB E:ASN12 4.7 41.7 1.0 CA E:ASN12 4.8 39.5 1.0 CA E:ASP14 4.9 36.1 1.0 C E:ASN12 5.0 42.7 1.0

S.Kumar, N.Padhan, N.Alam, S.Gourinath. Crystal Structure of Calcium Binding Protein-1 From Entamoeba Histolytica: A Novel Arrangement of Ef Hand Motifs. Proteins V. 68 990 2007.
ISSN: ESSN 1097-0134
PubMed: 17554780
DOI: 10.1002/PROT.21455