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Calcium in PDB 8ghf: Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles

Other elements in 8ghf:

The structure of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles (pdb code 8ghf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles, PDB code: 8ghf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8ghf

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Calcium binding site 1 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:30.4
occ:1.00
 O A:ARG514 2.4 34.6 1.0
O A:SER533 2.4 37.1 1.0
O A:SER600 2.4 48.7 1.0
OE1 A:GLU535 2.5 41.0 1.0
OE2 A:GLU535 2.5 40.6 1.0
OD2 A:ASP367 2.6 48.0 1.0
CD A:GLU535 2.8 39.5 1.0
C A:SER533 3.6 31.7 1.0
C A:SER600 3.6 48.1 1.0
C A:ARG514 3.6 36.8 1.0
CG A:ASP367 3.7 46.3 1.0
OH A:TYR537 4.2 45.9 1.0
CA A:SER600 4.3 43.7 1.0
CG A:GLU535 4.3 33.0 1.0
CA A:SER533 4.3 32.1 1.0
N A:ARG514 4.4 26.9 1.0
CB A:ASP367 4.4 40.8 1.0
N A:SER515 4.5 45.4 1.0
CA A:SER515 4.5 45.1 1.0
N A:ASN534 4.6 35.4 1.0
CB A:SER533 4.6 37.2 1.0
CA A:ARG514 4.6 30.6 1.0
OD1 A:ASP367 4.7 50.0 1.0
N A:ASP601 4.7 54.0 1.0
CA A:ASN534 4.8 31.4 1.0
N A:GLU535 4.9 37.4 1.0
C A:ASN534 4.9 38.5 1.0
CB A:SER600 4.9 45.6 1.0
CA A:ASP601 4.9 53.1 1.0
CB A:GLU535 5.0 28.7 1.0

Calcium binding site 2 out of 8 in 8ghf

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1503

b:42.8
occ:1.00
 O A:ASP892 2.4 57.5 1.0
OD2 A:ASP897 2.4 79.3 1.0
OD1 A:ASP897 2.4 84.0 1.0
O A:GLN889 2.4 42.6 1.0
OD2 A:ASP895 2.7 76.9 1.0
CG A:ASP897 2.7 80.0 1.0
OD1 B:ASN449 3.2 38.9 1.0
CG A:ASP895 3.4 78.3 1.0
OD1 A:ASP895 3.4 80.0 1.0
C A:ASP892 3.5 57.8 1.0
C A:GLN889 3.5 34.9 1.0
CA A:GLN889 4.0 33.5 1.0
CG B:ASN449 4.2 33.3 1.0
CB A:ASP897 4.3 80.4 1.0
N A:ASP892 4.3 49.5 1.0
CA A:ASP892 4.3 50.8 1.0
N A:GLN893 4.4 53.3 1.0
ND2 B:ASN449 4.5 29.9 1.0
CB A:ASP892 4.6 52.0 1.0
CA A:GLN893 4.6 49.3 1.0
CB A:GLN889 4.6 32.3 1.0
N A:PHE890 4.6 27.3 1.0
CB A:ASP895 4.7 75.1 1.0
C A:GLN893 4.8 52.9 1.0
O A:ASP895 4.8 78.4 1.0
N A:ASP895 4.8 75.2 1.0
O A:VAL888 5.0 36.7 1.0
C A:ASP895 5.0 78.0 1.0

Calcium binding site 3 out of 8 in 8ghf

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1502

b:30.8
occ:1.00
 O B:SER533 2.4 36.8 1.0
O B:ARG514 2.4 35.5 1.0
O B:SER600 2.4 47.8 1.0
OE1 B:GLU535 2.5 41.4 1.0
OE2 B:GLU535 2.5 40.9 1.0
OD2 B:ASP367 2.7 49.0 1.0
CD B:GLU535 2.8 39.9 1.0
C B:SER533 3.6 31.6 1.0
C B:SER600 3.6 47.7 1.0
C B:ARG514 3.6 36.5 1.0
CG B:ASP367 3.8 47.6 1.0
CA B:SER533 4.3 32.4 1.0
CG B:GLU535 4.3 33.5 1.0
CA B:SER600 4.3 43.2 1.0
OH B:TYR537 4.3 46.6 1.0
N B:ARG514 4.4 27.1 1.0
CB B:ASP367 4.4 41.7 1.0
CA B:SER515 4.4 45.8 1.0
N B:SER515 4.5 46.1 1.0
CB B:SER533 4.6 37.7 1.0
N B:ASN534 4.6 35.7 1.0
CA B:ARG514 4.6 30.5 1.0
N B:ASP601 4.7 53.5 1.0
OD1 B:ASP367 4.8 51.0 1.0
CA B:ASN534 4.8 31.5 1.0
N B:GLU535 4.9 37.9 1.0
C B:ASN534 4.9 38.5 1.0
CB B:SER600 4.9 45.0 1.0
CA B:ASP601 4.9 52.7 1.0
CB B:GLU535 5.0 29.1 1.0

Calcium binding site 4 out of 8 in 8ghf

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Calcium binding site 4 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1503

b:40.9
occ:1.00
 OD2 B:ASP897 2.4 76.2 1.0
O B:ASP892 2.4 57.3 1.0
O B:GLN889 2.4 42.2 1.0
OD1 B:ASP897 2.5 81.0 1.0
OD2 B:ASP895 2.7 73.8 1.0
CG B:ASP897 2.8 76.9 1.0
OD1 D:ASN449 3.1 39.1 1.0
CG B:ASP895 3.4 75.5 1.0
OD1 B:ASP895 3.5 77.4 1.0
C B:ASP892 3.5 57.5 1.0
C B:GLN889 3.6 34.8 1.0
CA B:GLN889 4.1 33.0 1.0
CG D:ASN449 4.1 33.6 1.0
CB B:ASP897 4.3 77.6 1.0
N B:ASP892 4.3 49.2 1.0
CA B:ASP892 4.4 50.6 1.0
N B:GLN893 4.4 52.4 1.0
ND2 D:ASN449 4.5 30.1 1.0
CA B:GLN893 4.5 48.3 1.0
CB B:GLN889 4.6 32.1 1.0
CB B:ASP892 4.6 51.9 1.0
N B:PHE890 4.7 27.8 1.0
C B:GLN893 4.7 52.1 1.0
CB B:ASP895 4.8 72.5 1.0
O B:ASP895 4.8 75.8 1.0
N B:ASP895 4.8 72.4 1.0
C B:ASP895 4.9 75.5 1.0

Calcium binding site 5 out of 8 in 8ghf

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Calcium binding site 5 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1505

b:30.3
occ:1.00
 O C:SER533 2.4 37.5 1.0
O C:ARG514 2.4 36.3 1.0
O C:SER600 2.5 48.6 1.0
OE2 C:GLU535 2.5 40.8 1.0
OE1 C:GLU535 2.5 40.8 1.0
OD2 C:ASP367 2.7 49.4 1.0
CD C:GLU535 2.8 39.6 1.0
C C:SER533 3.6 32.3 1.0
C C:SER600 3.6 48.0 1.0
C C:ARG514 3.6 36.9 1.0
CG C:ASP367 3.8 47.4 1.0
CA C:SER533 4.3 32.5 1.0
CA C:SER600 4.3 43.7 1.0
CG C:GLU535 4.3 33.3 1.0
OH C:TYR537 4.3 46.9 1.0
N C:ARG514 4.4 27.8 1.0
CA C:SER515 4.4 45.9 1.0
CB C:ASP367 4.4 41.1 1.0
N C:SER515 4.4 47.0 1.0
CB C:SER533 4.6 38.1 1.0
N C:ASN534 4.6 35.6 1.0
CA C:ARG514 4.6 30.3 1.0
N C:ASP601 4.7 53.9 1.0
OD1 C:ASP367 4.7 50.8 1.0
CA C:ASN534 4.8 31.5 1.0
N C:GLU535 4.9 37.8 1.0
C C:ASN534 4.9 38.6 1.0
CB C:SER600 4.9 45.3 1.0
CA C:ASP601 4.9 53.4 1.0

Calcium binding site 6 out of 8 in 8ghf

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Calcium binding site 6 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1506

b:43.0
occ:1.00
 O C:ASP892 2.4 57.9 1.0
OD2 C:ASP897 2.4 78.3 1.0
OD1 C:ASP897 2.4 83.0 1.0
O C:GLN889 2.4 43.2 1.0
OD2 C:ASP895 2.7 77.1 1.0
CG C:ASP897 2.7 78.9 1.0
OD1 A:ASN449 3.2 38.5 1.0
CG C:ASP895 3.4 78.4 1.0
OD1 C:ASP895 3.4 80.2 1.0
C C:ASP892 3.5 58.0 1.0
C C:GLN889 3.5 35.3 1.0
CA C:GLN889 4.0 33.6 1.0
CG A:ASN449 4.2 33.2 1.0
CB C:ASP897 4.3 79.2 1.0
N C:ASP892 4.3 49.9 1.0
CA C:ASP892 4.3 51.0 1.0
N C:GLN893 4.4 53.3 1.0
ND2 A:ASN449 4.5 29.8 1.0
CA C:GLN893 4.6 49.5 1.0
CB C:ASP892 4.6 52.7 1.0
CB C:GLN889 4.6 32.4 1.0
N C:PHE890 4.6 27.1 1.0
CB C:ASP895 4.7 75.0 1.0
C C:GLN893 4.8 52.8 1.0
O C:ASP895 4.8 78.3 1.0
N C:ASP895 4.8 74.9 1.0
O C:VAL888 4.9 36.8 1.0
C C:ASP895 5.0 77.9 1.0

Calcium binding site 7 out of 8 in 8ghf

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Calcium binding site 7 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1505

b:31.0
occ:1.00
 O D:SER533 2.4 37.6 1.0
O D:ARG514 2.4 36.8 1.0
O D:SER600 2.5 48.2 1.0
OE1 D:GLU535 2.5 42.0 1.0
OE2 D:GLU535 2.5 40.9 1.0
OD2 D:ASP367 2.7 49.2 1.0
CD D:GLU535 2.8 40.1 1.0
C D:SER533 3.6 32.6 1.0
C D:ARG514 3.6 37.2 1.0
C D:SER600 3.6 47.8 1.0
CG D:ASP367 3.8 47.4 1.0
CA D:SER533 4.3 33.1 1.0
CG D:GLU535 4.3 33.8 1.0
CA D:SER600 4.3 43.2 1.0
OH D:TYR537 4.3 46.8 1.0
N D:ARG514 4.4 27.9 1.0
CA D:SER515 4.4 45.9 1.0
CB D:ASP367 4.4 41.5 1.0
N D:SER515 4.4 46.5 1.0
CB D:SER533 4.6 38.1 1.0
N D:ASN534 4.6 36.2 1.0
CA D:ARG514 4.6 31.0 1.0
N D:ASP601 4.7 53.9 1.0
OD1 D:ASP367 4.7 50.9 1.0
CA D:ASN534 4.8 32.1 1.0
N D:GLU535 4.9 38.6 1.0
C D:ASN534 4.9 39.1 1.0
CB D:SER600 4.9 44.9 1.0
CA D:ASP601 4.9 53.2 1.0
CB D:GLU535 5.0 30.1 1.0

Calcium binding site 8 out of 8 in 8ghf

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Calcium binding site 8 out of 8 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1506

b:43.2
occ:1.00
 O D:ASP892 2.4 57.4 1.0
OD2 D:ASP897 2.4 78.5 1.0
OD1 D:ASP897 2.4 83.0 1.0
O D:GLN889 2.4 42.4 1.0
OD2 D:ASP895 2.7 75.9 1.0
CG D:ASP897 2.7 78.9 1.0
OD1 C:ASN449 3.2 38.4 1.0
CG D:ASP895 3.4 77.4 1.0
OD1 D:ASP895 3.4 79.4 1.0
C D:ASP892 3.5 57.5 1.0
C D:GLN889 3.5 34.5 1.0
CA D:GLN889 4.0 32.9 1.0
CG C:ASN449 4.2 33.2 1.0
CB D:ASP897 4.3 79.3 1.0
N D:ASP892 4.3 48.8 1.0
CA D:ASP892 4.3 50.3 1.0
N D:GLN893 4.4 52.5 1.0
ND2 C:ASN449 4.5 30.0 1.0
CA D:GLN893 4.6 48.5 1.0
CB D:ASP892 4.6 52.3 1.0
CB D:GLN889 4.6 32.1 1.0
N D:PHE890 4.6 26.8 1.0
CB D:ASP895 4.7 73.8 1.0
C D:GLN893 4.8 52.1 1.0
O D:ASP895 4.8 77.7 1.0
N D:ASP895 4.8 73.9 1.0
O D:VAL888 5.0 36.4 1.0
C D:ASP895 5.0 77.3 1.0

Reference:

X.Tao, C.Zhao, R.Mackinnon. Membrane Protein Isolation and Structure Determination in Cell-Derived Membrane Vesicles. Proc.Natl.Acad.Sci.Usa V. 120 25120 2023.
ISSN: ESSN 1091-6490
PubMed: 37098056
DOI: 10.1073/PNAS.2302325120
Page generated: Fri Jul 19 09:12:09 2024

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