Calcium in PDB 1bjf: Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms

The structure of Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms, PDB code: 1bjf was solved by S.Vijay-Kumar, V.D.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.680, 93.350, 50.625, 90.00, 98.29, 90.00
R / Rfree (%)	21.8 / 30.8

The binding sites of Calcium atom in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms (pdb code 1bjf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms, PDB code: 1bjf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms


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 Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:16.9 occ:1.00 OD1 A:ASN75 2.0 30.6 1.0 OE1 A:GLU84 2.3 13.7 1.0 OD1 A:ASP73 2.3 10.2 1.0 OD1 A:ASP77 2.4 24.1 1.0 O A:HOH505 2.4 39.8 1.0 OE2 A:GLU84 2.4 10.9 1.0 O A:THR79 2.5 10.2 1.0 CD A:GLU84 2.7 7.4 1.0 CG A:ASN75 2.7 24.4 1.0 ND2 A:ASN75 2.8 24.4 1.0 CG A:ASP77 3.1 28.2 1.0 OD2 A:ASP77 3.4 30.5 1.0 CG A:ASP73 3.5 9.5 1.0 C A:THR79 3.6 10.0 1.0 N A:ASN75 4.1 18.3 1.0 CB A:ASN75 4.1 21.8 1.0 CG A:GLU84 4.2 3.7 1.0 N A:ASP77 4.2 24.0 1.0 CB A:ASP77 4.3 26.1 1.0 O A:HOH663 4.3 33.6 1.0 OD2 A:ASP73 4.3 17.1 1.0 N A:GLY76 4.4 21.8 1.0 CA A:ASP73 4.4 8.5 1.0 CA A:ILE80 4.4 11.8 1.0 N A:THR79 4.4 7.5 1.0 CB A:ASP73 4.4 5.3 1.0 C A:ASP73 4.5 13.7 1.0 OG1 A:THR79 4.5 19.6 1.0 N A:ILE80 4.5 14.3 1.0 N A:ALA74 4.5 15.3 1.0 OD2 A:ASP81 4.5 11.4 1.0 CA A:ASN75 4.6 17.0 1.0 CA A:THR79 4.6 9.3 1.0 N A:ASP81 4.7 12.6 1.0 CA A:ASP77 4.8 25.0 1.0 C A:ASN75 4.9 18.8 1.0 CG A:ASP81 4.9 15.7 1.0 N A:GLY78 4.9 21.7 1.0 O A:ASP73 5.0 12.4 1.0 CB A:GLU84 5.0 3.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms


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 Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:24.6 occ:1.00 OD1 A:ASN113 2.1 15.8 1.0 OD1 A:ASP111 2.2 25.1 1.0 OE2 A:GLU120 2.4 22.3 1.0 O A:HOH587 2.5 68.2 1.0 O A:TYR115 2.5 19.2 1.0 OE1 A:GLU120 2.6 30.2 1.0 OD1 A:ASP109 2.6 26.9 1.0 CD A:GLU120 2.8 20.0 1.0 CG A:ASP111 3.1 24.2 1.0 CG A:ASN113 3.2 20.3 1.0 OD2 A:ASP111 3.4 22.9 1.0 C A:TYR115 3.6 17.6 1.0 CG A:ASP109 3.8 13.3 1.0 ND2 A:ASN113 3.9 20.7 1.0 N A:ASP111 4.1 15.8 1.0 CB A:ASN113 4.2 18.0 1.0 N A:ASN113 4.2 18.5 1.0 CG A:GLU120 4.3 14.2 1.0 N A:TYR115 4.3 16.8 1.0 CB A:ASP111 4.4 24.7 1.0 CA A:ASP109 4.4 12.2 1.0 CA A:TYR115 4.5 13.0 1.0 CA A:ASP111 4.6 21.6 1.0 N A:LEU110 4.6 14.2 1.0 N A:ILE116 4.6 13.4 1.0 N A:GLY112 4.6 26.0 1.0 OG A:SER117 4.6 35.0 1.0 C A:ASP109 4.6 13.0 1.0 OD2 A:ASP109 4.6 24.0 1.0 C A:ASP111 4.7 25.1 1.0 CA A:ILE116 4.7 12.2 1.0 CA A:ASN113 4.7 17.3 1.0 CB A:ASP109 4.7 10.9 1.0 CB A:TYR115 4.7 17.4 1.0 N A:SER117 4.8 12.9 1.0 N A:GLY114 5.0 18.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms


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 Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:22.5 occ:1.00 OD1 A:ASP161 2.0 12.6 1.0 OD1 A:ASN159 2.3 20.0 1.0 O A:HOH513 2.3 7.4 1.0 OE1 A:GLU168 2.3 8.8 1.0 O A:LYS163 2.4 21.5 1.0 OD1 A:ASP157 2.4 25.9 1.0 OE2 A:GLU168 2.7 19.3 1.0 CD A:GLU168 2.9 12.6 1.0 CG A:ASP161 3.0 14.6 1.0 CG A:ASN159 3.4 18.3 1.0 OD2 A:ASP161 3.5 17.2 1.0 CG A:ASP157 3.5 23.1 1.0 C A:LYS163 3.6 16.7 1.0 CA A:ASP157 3.8 22.6 1.0 ND2 A:ASN159 4.1 23.7 1.0 C A:ASP157 4.1 22.6 1.0 CB A:ASP157 4.2 18.2 1.0 N A:ASN159 4.2 21.2 1.0 N A:ASP161 4.3 21.7 1.0 CB A:ASP161 4.3 15.1 1.0 N A:LYS163 4.4 23.0 1.0 CG A:GLU168 4.4 16.5 1.0 N A:THR158 4.5 24.0 1.0 CA A:LYS163 4.5 20.3 1.0 OD2 A:ASP157 4.5 28.2 1.0 N A:LEU164 4.5 12.6 1.0 CA A:LEU164 4.5 11.1 1.0 N A:SER165 4.6 16.8 1.0 CB A:ASN159 4.6 19.9 1.0 O A:ASP157 4.6 15.8 1.0 N A:ARG160 4.7 20.6 1.0 CA A:ASP161 4.7 20.4 1.0 CA A:ASN159 4.8 17.3 1.0 CB A:LYS163 4.8 14.9 1.0 C A:ASN159 4.9 20.3 1.0 N A:ASP157 4.9 17.7 1.0 C A:ASP161 5.0 20.1 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms


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 Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca406 b:17.4 occ:1.00 OD1 B:ASN75 2.0 18.4 1.0 OD1 B:ASP73 2.2 6.4 1.0 OE1 B:GLU84 2.2 3.3 1.0 OE2 B:GLU84 2.3 16.5 1.0 O B:HOH506 2.4 50.5 1.0 OD1 B:ASP77 2.5 21.8 1.0 O B:THR79 2.5 3.9 1.0 CD B:GLU84 2.6 12.1 1.0 CG B:ASN75 2.6 19.8 1.0 ND2 B:ASN75 2.7 24.7 1.0 CG B:ASP77 3.1 24.1 1.0 CG B:ASP73 3.4 10.3 1.0 OD2 B:ASP77 3.4 32.2 1.0 C B:THR79 3.7 5.3 1.0 N B:ASN75 4.0 13.7 1.0 CB B:ASN75 4.0 12.1 1.0 CG B:GLU84 4.1 7.2 1.0 N B:ASP77 4.2 16.5 1.0 OD2 B:ASP73 4.2 13.3 1.0 N B:GLY76 4.3 10.1 1.0 CB B:ASP77 4.3 17.7 1.0 CA B:ASP73 4.3 8.8 1.0 C B:ASP73 4.4 6.4 1.0 CB B:ASP73 4.4 7.2 1.0 N B:THR79 4.4 10.4 1.0 N B:ALA74 4.5 11.8 1.0 OG1 B:THR79 4.5 3.9 1.0 CA B:ILE80 4.5 12.4 1.0 CA B:ASN75 4.5 10.3 1.0 N B:ILE80 4.5 5.4 1.0 OD2 B:ASP81 4.5 29.3 1.0 CA B:THR79 4.6 8.8 1.0 CA B:ASP77 4.7 15.2 1.0 N B:ASP81 4.7 19.6 1.0 C B:ASN75 4.8 7.7 1.0 O B:ASP73 4.8 6.3 1.0 CG B:ASP81 4.9 26.2 1.0 N B:GLY78 4.9 15.7 1.0 CB B:GLU84 4.9 9.3 1.0 C B:ALA74 5.0 12.4 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms


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 Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca407 b:16.5 occ:1.00 O B:HOH616 2.2 36.2 1.0 OD1 B:ASN113 2.2 5.8 1.0 OD1 B:ASP111 2.2 19.1 1.0 OE2 B:GLU120 2.3 23.6 1.0 O B:TYR115 2.4 16.0 1.0 OE1 B:GLU120 2.5 19.4 1.0 OD1 B:ASP109 2.5 16.2 1.0 CD B:GLU120 2.7 16.1 1.0 CG B:ASP111 3.1 19.1 1.0 CG B:ASN113 3.2 9.2 1.0 OD2 B:ASP111 3.4 21.2 1.0 C B:TYR115 3.6 15.8 1.0 CG B:ASP109 3.8 10.8 1.0 ND2 B:ASN113 3.9 9.4 1.0 N B:ASP111 4.1 19.0 1.0 CG B:GLU120 4.2 17.3 1.0 CB B:ASN113 4.2 3.3 1.0 N B:ASN113 4.2 11.7 1.0 N B:TYR115 4.3 20.1 1.0 CA B:ASP109 4.4 10.2 1.0 CB B:ASP111 4.4 22.3 1.0 CA B:TYR115 4.4 13.9 1.0 N B:LEU110 4.5 16.8 1.0 N B:ILE116 4.5 17.4 1.0 C B:ASP109 4.5 12.8 1.0 OD2 B:ASP109 4.6 20.2 1.0 N B:GLY112 4.6 21.8 1.0 CA B:ILE116 4.6 15.4 1.0 CA B:ASP111 4.6 18.5 1.0 CB B:ASP109 4.7 4.6 1.0 CA B:ASN113 4.7 10.2 1.0 CB B:TYR115 4.7 10.9 1.0 N B:SER117 4.7 15.6 1.0 C B:ASP111 4.8 22.1 1.0 N B:GLY114 5.0 11.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms


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 Recombinant Bovine Neurocalcin Delta at 2.4 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca408 b:34.8 occ:1.00 OD1 B:ASP161 2.1 38.7 1.0 OE1 B:GLU168 2.3 19.0 1.0 O B:LYS163 2.3 19.0 1.0 OD1 B:ASN159 2.3 49.6 1.0 O B:HOH507 2.4 17.4 1.0 OD1 B:ASP157 2.5 31.1 1.0 OE2 B:GLU168 2.8 20.9 1.0 CD B:GLU168 2.9 16.6 1.0 CG B:ASP161 3.1 34.6 1.0 OD2 B:ASP161 3.5 38.5 1.0 C B:LYS163 3.5 14.1 1.0 CG B:ASN159 3.5 46.0 1.0 CG B:ASP157 3.6 28.2 1.0 CA B:ASP157 3.8 27.9 1.0 C B:ASP157 4.2 27.2 1.0 N B:ASN159 4.2 31.2 1.0 CB B:ASP157 4.3 24.5 1.0 ND2 B:ASN159 4.3 51.3 1.0 N B:ASP161 4.3 33.7 1.0 N B:LYS163 4.3 21.6 1.0 CB B:ASP161 4.4 29.7 1.0 CG B:GLU168 4.4 12.9 1.0 CA B:LYS163 4.4 15.3 1.0 N B:LEU164 4.4 10.9 1.0 N B:THR158 4.4 30.7 1.0 CA B:LEU164 4.5 12.5 1.0 N B:SER165 4.6 13.9 1.0 OD2 B:ASP157 4.6 27.6 1.0 N B:ARG160 4.6 27.2 1.0 CB B:ASN159 4.6 35.0 1.0 O B:ASP157 4.7 28.7 1.0 CA B:ASP161 4.8 28.9 1.0 CA B:ASN159 4.8 29.9 1.0 CB B:LYS163 4.8 20.0 1.0 C B:ASN159 4.9 27.4 1.0 C B:LEU164 5.0 14.0 1.0 N B:ASP157 5.0 28.3 1.0

S.Vijay-Kumar, V.D.Kumar. Crystal Structure of Recombinant Bovine Neurocalcin. Nat.Struct.Biol. V. 6 80 1999.
ISSN: ISSN 1072-8368
PubMed: 9886296
DOI: 10.1038/4956