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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

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