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Calcium in PDB 1bu3: Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A.

Protein crystallography data

The structure of Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A., PDB code: 1bu3 was solved by R.C.Richardson, D.J.Nelson, W.E.Royer, D.J.Harrington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.710, 80.730, 42.160, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A. (pdb code 1bu3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A., PDB code: 1bu3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1bu3

Go back to Calcium Binding Sites List in 1bu3
Calcium binding site 1 out of 2 in the Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca109

b:16.1
occ:1.00
OD1 A:ASP53 2.3 17.3 1.0
O A:PHE57 2.3 16.6 1.0
OD1 A:ASP51 2.4 16.4 1.0
OE1 A:GLU59 2.4 18.1 1.0
OG A:SER55 2.4 15.6 1.0
OE1 A:GLU62 2.6 17.4 1.0
OE2 A:GLU62 2.6 16.9 1.0
CD A:GLU62 2.9 21.2 1.0
CG A:ASP53 3.3 18.2 1.0
CD A:GLU59 3.4 19.2 1.0
CG A:ASP51 3.5 16.4 1.0
CB A:SER55 3.6 15.9 1.0
C A:PHE57 3.6 17.0 1.0
OE2 A:GLU59 3.6 19.3 1.0
OD2 A:ASP53 3.7 21.0 1.0
N A:SER55 3.9 15.3 1.0
O A:HOH123 4.1 24.4 1.0
CA A:ASP51 4.1 16.9 1.0
CB A:ASP51 4.3 15.6 1.0
CA A:SER55 4.3 14.4 1.0
N A:PHE57 4.3 16.8 1.0
N A:GLU59 4.4 16.3 1.0
N A:ASP53 4.4 16.9 1.0
CG A:GLU62 4.4 18.4 1.0
CA A:ILE58 4.4 15.3 1.0
OD2 A:ASP51 4.4 14.6 1.0
N A:ILE58 4.4 16.8 1.0
C A:ASP51 4.5 16.9 1.0
CA A:PHE57 4.5 15.4 1.0
O A:HOH142 4.5 32.4 1.0
CB A:ASP53 4.6 15.1 1.0
N A:LYS54 4.6 20.7 1.0
N A:GLY56 4.7 13.2 1.0
N A:GLN52 4.7 17.8 1.0
CG A:GLU59 4.8 23.0 1.0
C A:SER55 4.8 12.2 1.0
CA A:ASP53 4.8 16.3 1.0
C A:ASP53 4.8 19.0 1.0
O A:ASP51 4.9 16.4 1.0
C A:ILE58 4.9 16.3 1.0

Calcium binding site 2 out of 2 in 1bu3

Go back to Calcium Binding Sites List in 1bu3
Calcium binding site 2 out of 2 in the Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Refined Crystal Structure of Calcium-Bound Silver Hake (Pi 4.2) Parvalbumin at 1.65 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca110

b:21.8
occ:1.00
O A:HOH130 2.3 26.1 1.0
O A:ALA96 2.3 21.5 1.0
OD2 A:ASP90 2.5 19.8 1.0
OD1 A:ASP94 2.5 25.6 1.0
OE1 A:GLU101 2.5 19.8 1.0
OD1 A:ASP92 2.5 29.1 1.0
OE2 A:GLU101 2.7 21.3 1.0
CD A:GLU101 2.9 19.5 1.0
CG A:ASP94 3.3 26.8 1.0
CG A:ASP92 3.3 30.1 1.0
C A:ALA96 3.5 20.9 1.0
CG A:ASP90 3.5 19.9 1.0
OD2 A:ASP92 3.6 31.7 1.0
OD2 A:ASP94 3.7 27.3 1.0
CA A:ASP90 4.1 23.1 1.0
N A:ASP94 4.2 27.7 1.0
CB A:ASP90 4.3 22.1 1.0
N A:ALA96 4.3 22.4 1.0
CA A:ILE97 4.3 19.4 1.0
N A:ILE97 4.3 19.6 1.0
N A:ASP92 4.3 27.6 1.0
CB A:ASP94 4.4 27.1 1.0
N A:GLY98 4.4 16.2 1.0
OD1 A:ASP90 4.4 22.1 1.0
CG A:GLU101 4.4 16.7 1.0
CA A:ALA96 4.5 20.8 1.0
C A:ASP90 4.5 24.1 1.0
CB A:ASP92 4.6 29.1 1.0
N A:SER91 4.7 24.4 1.0
CA A:ASP92 4.7 29.2 1.0
N A:GLY93 4.7 29.2 1.0
CA A:ASP94 4.7 26.9 1.0
C A:ASP92 4.7 30.5 1.0
C A:ILE97 4.9 18.8 1.0
N A:GLY95 4.9 23.7 1.0

Reference:

R.C.Richardson, N.M.King, D.J.Harrington, H.Sun, W.E.Royer, D.J.Nelson. X-Ray Crystal Structure and Molecular Dynamics Simulations of Silver Hake Parvalbumin (Isoform B). Protein Sci. V. 9 73 2000.
ISSN: ISSN 0961-8368
PubMed: 10739249
Page generated: Thu Jul 11 06:34:14 2024

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