Atomistry » Calcium » PDB 6zqx-7apy » 6zyh
Atomistry »
  Calcium »
    PDB 6zqx-7apy »
      6zyh »

Calcium in PDB 6zyh: Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium

Enzymatic activity of Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium

All present enzymatic activity of Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium:
3.6.4.10;

Protein crystallography data

The structure of Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium, PDB code: 6zyh was solved by Y.Yan, S.Preissler, D.Ron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.13 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.359, 51.862, 93.082, 78.07, 86.72, 62.28
R / Rfree (%) 20.9 / 22.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium (pdb code 6zyh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium, PDB code: 6zyh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6zyh

Go back to Calcium Binding Sites List in 6zyh
Calcium binding site 1 out of 4 in the Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium


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 GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:23.5
occ:1.00
 O A:HIS252 2.3 24.6 1.0
O A:HOH651 2.4 23.6 1.0
O B:GLY315 2.4 29.6 1.0
O B:HOH689 2.4 23.2 1.0
O A:HOH681 2.5 27.3 1.0
O B:HOH604 2.5 28.3 1.0
OD1 A:ASP257 2.6 23.9 1.0
OD2 A:ASP257 2.7 23.4 1.0
CG A:ASP257 3.0 23.5 1.0
C B:GLY315 3.4 29.7 1.0
C A:HIS252 3.5 25.0 1.0
CA B:GLY315 3.8 29.9 1.0
CA A:HIS252 4.2 25.9 1.0
CB A:HIS252 4.2 27.0 1.0
N A:LEU253 4.4 24.9 1.0
CB A:ASP257 4.5 23.4 1.0
O A:HOH701 4.5 32.8 1.0
OG B:SER311 4.5 31.2 1.0
OD1 B:ASP317 4.6 30.5 1.0
N B:GLU316 4.6 30.3 1.0
CA A:LEU253 4.6 24.7 1.0
OE1 A:GLU256 4.7 25.5 0.5
OD2 B:ASP317 4.7 32.3 1.0
O A:GLY228 4.8 24.0 1.0
N A:GLY254 5.0 24.0 1.0
CG B:ASP317 5.0 30.9 1.0

Calcium binding site 2 out of 4 in 6zyh

Go back to Calcium Binding Sites List in 6zyh
Calcium binding site 2 out of 4 in the Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium


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 GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:26.1
occ:1.00
 O A:HOH605 2.3 30.8 1.0
O1B A:ADP501 2.3 24.2 1.0
O1A A:ADP501 2.3 23.1 1.0
O A:HOH689 2.4 28.9 1.0
O A:HOH652 2.4 29.4 1.0
O A:HOH642 2.4 28.8 1.0
O A:HOH674 2.5 36.8 1.0
PB A:ADP501 3.4 24.3 1.0
PA A:ADP501 3.4 23.9 1.0
O3A A:ADP501 3.5 24.2 1.0
O A:HOH654 3.8 30.7 1.0
O3B A:ADP501 3.9 24.6 1.0
OD2 A:ASP34 4.2 30.0 1.0
O A:HOH618 4.2 30.3 1.0
O A:HOH609 4.2 34.1 1.0
OD1 A:ASP224 4.3 30.7 1.0
O2A A:ADP501 4.4 23.9 1.0
CA A:GLY363 4.4 24.3 1.0
O5' A:ADP501 4.6 23.4 1.0
O2B A:ADP501 4.7 24.9 1.0
O A:HOH648 4.7 41.1 1.0
O A:HOH658 4.7 26.4 1.0
CA A:GLY226 4.8 21.6 1.0
OD1 A:ASP34 4.8 28.7 1.0
CG A:ASP34 4.9 29.6 1.0

Calcium binding site 3 out of 4 in 6zyh

Go back to Calcium Binding Sites List in 6zyh
Calcium binding site 3 out of 4 in the Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium


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 GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:25.4
occ:1.00
 O2A B:ADP501 2.3 23.6 1.0
O2B B:ADP501 2.3 23.8 1.0
O B:HOH643 2.3 26.4 1.0
O B:HOH702 2.4 30.5 1.0
O B:HOH613 2.4 33.7 1.0
O B:HOH695 2.4 31.6 1.0
O B:HOH663 2.4 32.8 1.0
PB B:ADP501 3.4 24.0 1.0
PA B:ADP501 3.4 24.6 1.0
O3A B:ADP501 3.5 23.9 1.0
O B:HOH667 3.9 34.5 1.0
O3B B:ADP501 4.0 23.1 1.0
O B:HOH632 4.1 29.7 1.0
OD2 B:ASP34 4.1 30.0 1.0
O B:HOH606 4.2 36.4 1.0
CA B:GLY363 4.3 24.6 1.0
OD1 B:ASP224 4.3 32.3 1.0
O1A B:ADP501 4.4 23.6 1.0
O B:HOH653 4.6 31.5 1.0
O5' B:ADP501 4.6 23.7 1.0
O1B B:ADP501 4.7 24.5 1.0
CA B:GLY226 4.8 21.8 1.0
O B:HOH624 4.8 32.7 1.0
OD1 B:ASP34 4.8 28.8 1.0
CG B:ASP34 4.9 28.9 1.0

Calcium binding site 4 out of 4 in 6zyh

Go back to Calcium Binding Sites List in 6zyh
Calcium binding site 4 out of 4 in the Crystal Structure of GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium


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 GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:24.1
occ:1.00
 O B:HIS252 2.3 25.4 1.0
O B:HOH669 2.4 25.6 1.0
O B:HOH704 2.5 30.6 1.0
OD1 B:ASP257 2.5 23.2 1.0
OD2 B:ASP257 2.7 22.1 1.0
CG B:ASP257 2.9 22.5 1.0
C B:HIS252 3.4 25.7 1.0
CA B:HIS252 4.2 26.8 1.0
CB B:HIS252 4.2 27.4 1.0
CB B:ASP257 4.4 22.3 1.0
N B:LEU253 4.4 25.3 1.0
CA B:LEU253 4.6 24.8 1.0
O B:HOH712 4.6 36.5 1.0
O B:GLY228 4.9 23.4 1.0
OE1 B:GLU256 4.9 26.4 0.6

Reference:

S.Preissler, C.Rato, Y.Yan, L.A.Perera, A.Czako, D.Ron. Calcium Depletion Challenges Endoplasmic Reticulum Proteostasis By Destabilising Bip-Substrate Complexes. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 33295873
DOI: 10.7554/ELIFE.62601
Page generated: Thu Jul 18 22:48:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy