Atomistry » Calcium » PDB 1b85-1bjj » 1bjf
Atomistry »
  Calcium »
    PDB 1b85-1bjj »
      1bjf »

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

Protein crystallography data

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

Calcium Binding Sites:

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 1bjf

Go back to Calcium Binding Sites List in 1bjf
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 1bjf

Go back to Calcium Binding Sites List in 1bjf
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 1bjf

Go back to Calcium Binding Sites List in 1bjf
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 1bjf

Go back to Calcium Binding Sites List in 1bjf
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 1bjf

Go back to Calcium Binding Sites List in 1bjf
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 1bjf

Go back to Calcium Binding Sites List in 1bjf
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

Reference:

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
Page generated: Sat Dec 12 02:49:48 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy