Calcium in PDB 7jof: Calcium-Bound C2A Domain From Human Dysferlin

Protein crystallography data

The structure of Calcium-Bound C2A Domain From Human Dysferlin, PDB code: 7jof was solved by R.Tadayon, Y.Wang, L.Santamaria, P.Mercier, C.Forristal, G.S.Shaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.52, 54.78, 57.34, 116.8, 103.47, 92.92
R / Rfree (%) 24.1 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Calcium-Bound C2A Domain From Human Dysferlin (pdb code 7jof). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Calcium-Bound C2A Domain From Human Dysferlin, PDB code: 7jof:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7jof

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Calcium binding site 1 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:9.2
occ:1.00
 O A:HIS72 2.4 8.1 1.0
O A:HOH307 2.5 19.3 1.0
OD2 A:ASP18 2.6 9.9 1.0
OD2 A:ASP21 2.6 4.4 1.0
OD2 A:ASP71 2.6 7.0 1.0
OD1 A:ASP71 2.7 7.5 1.0
OE1 A:GLU73 2.8 12.8 1.0
CG A:ASP71 3.0 12.2 1.0
C A:HIS72 3.5 13.7 1.0
CG A:ASP18 3.5 8.1 1.0
CG A:ASP21 3.6 9.6 1.0
CD A:GLU73 3.9 12.7 1.0
OD1 A:ASP18 3.9 6.6 1.0
CA A:GLU73 4.0 14.3 1.0
CB A:ASP21 4.0 11.2 1.0
N A:GLU73 4.2 15.6 1.0
NH2 A:ARG79 4.2 7.2 1.0
CA A:CA202 4.4 9.5 1.0
C A:ASP71 4.5 11.0 1.0
CB A:ASP71 4.5 5.8 1.0
N A:HIS72 4.5 8.2 1.0
CA A:HIS72 4.6 11.5 1.0
O A:ASP71 4.6 8.2 1.0
N A:ASP21 4.6 6.2 1.0
N A:THR74 4.7 30.0 1.0
OE2 A:GLU73 4.7 14.7 1.0
CB A:ASP18 4.7 6.7 1.0
NE A:ARG79 4.7 3.8 1.0
OD1 A:ASP21 4.7 7.5 1.0
CB A:GLU73 4.7 11.8 1.0
OG1 A:THR74 4.9 30.0 1.0
C A:GLU73 4.9 24.1 1.0
CG A:GLU73 4.9 13.3 1.0
CA A:ASP21 5.0 13.2 1.0
CZ A:ARG79 5.0 9.9 1.0

Calcium binding site 2 out of 8 in 7jof

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Calcium binding site 2 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:9.5
occ:1.00
 OD1 A:ASP18 2.3 6.6 1.0
OD1 A:ASN40 2.6 8.0 1.0
O A:ILE19 2.6 4.8 1.0
OD2 A:ASP21 2.6 4.4 1.0
O A:HOH324 2.7 19.3 1.0
OD1 A:ASP21 2.7 7.5 1.0
CG A:ASP21 3.0 9.6 1.0
CG A:ASP18 3.2 8.1 1.0
OD2 A:ASP18 3.6 9.9 1.0
CG A:ASN40 3.7 4.7 1.0
C A:ILE19 3.7 5.6 1.0
N A:ILE19 3.8 4.9 1.0
O A:HOH307 4.1 19.3 1.0
CA A:ILE19 4.2 4.1 1.0
O A:HOH333 4.3 19.3 1.0
N A:ASN40 4.4 8.9 1.0
CB A:ILE19 4.4 10.7 1.0
ND2 A:ASN40 4.4 2.8 1.0
CA A:ASN40 4.4 4.1 1.0
O A:HOH376 4.4 19.3 1.0
CA A:CA201 4.4 9.2 1.0
CB A:ASP21 4.5 11.2 1.0
O A:HOH359 4.5 19.3 1.0
CB A:ASP18 4.6 6.7 1.0
O A:HOH342 4.6 19.3 1.0
C A:ASP18 4.6 15.8 1.0
CB A:ASN40 4.7 7.2 1.0
N A:ASP21 4.7 6.2 1.0
C A:SER20 4.7 6.2 1.0
CA A:ASP18 4.8 9.8 1.0
N A:SER20 4.8 2.2 1.0
O A:SER20 4.9 7.0 1.0

Calcium binding site 3 out of 8 in 7jof

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Calcium binding site 3 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:9.1
occ:1.00
 O B:ILE19 2.3 9.8 1.0
OD1 B:ASN40 2.4 12.0 1.0
OD1 B:ASP18 2.5 4.4 1.0
O B:HOH380 2.5 19.3 1.0
OD1 B:ASP21 2.5 2.7 1.0
O B:HOH352 2.6 19.3 1.0
OD2 B:ASP21 2.6 9.4 1.0
CG B:ASP21 2.9 8.1 1.0
C B:ILE19 3.4 6.4 1.0
CG B:ASP18 3.5 10.8 1.0
CG B:ASN40 3.6 10.3 1.0
N B:ILE19 3.7 4.0 1.0
OD2 B:ASP18 3.9 10.3 1.0
CA B:ILE19 4.0 12.1 1.0
CA B:ASN40 4.2 10.3 1.0
N B:ASN40 4.2 5.4 1.0
CB B:ILE19 4.3 4.9 1.0
CA B:CA202 4.3 7.2 1.0
CB B:ASP21 4.3 6.9 1.0
O B:HOH360 4.4 19.3 1.0
C B:SER20 4.4 4.7 1.0
N B:ASP21 4.5 5.8 1.0
CB B:ASN40 4.5 7.0 1.0
ND2 B:ASN40 4.5 8.7 1.0
N B:SER20 4.6 6.0 1.0
O B:SER20 4.6 5.3 1.0
C B:ASP18 4.6 8.1 1.0
CB B:ASP18 4.7 4.9 1.0
O B:HOH381 4.8 19.3 1.0
CA B:ASP18 4.9 6.5 1.0
CA B:ASP21 4.9 9.8 1.0
CA B:SER20 4.9 4.1 1.0

Calcium binding site 4 out of 8 in 7jof

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Calcium binding site 4 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:7.2
occ:1.00
 OD2 B:ASP21 2.3 9.4 1.0
OD2 B:ASP18 2.4 10.3 1.0
O B:HIS72 2.4 10.1 1.0
OD1 B:ASP71 2.5 11.0 1.0
OE2 B:GLU73 2.6 30.0 1.0
O B:HOH360 2.6 19.3 1.0
OD2 B:ASP71 2.7 23.4 1.0
CG B:ASP71 2.9 16.4 1.0
CG B:ASP18 3.3 10.8 1.0
CG B:ASP21 3.5 8.1 1.0
C B:HIS72 3.6 11.2 1.0
OD1 B:ASP18 3.6 4.4 1.0
CD B:GLU73 3.7 30.0 1.0
CB B:ASP21 4.0 6.9 1.0
CG B:GLU73 4.2 30.0 1.0
O B:HOH359 4.3 19.3 1.0
CA B:GLU73 4.3 30.0 1.0
NH2 B:ARG79 4.3 15.9 1.0
CA B:CA201 4.3 9.1 1.0
N B:HIS72 4.3 11.7 1.0
N B:GLU73 4.4 30.0 1.0
CB B:ASP71 4.4 10.2 1.0
N B:ASP21 4.4 5.8 1.0
C B:ASP71 4.4 13.3 1.0
OD1 B:ASP21 4.5 2.7 1.0
CA B:HIS72 4.6 13.5 1.0
O B:HOH361 4.6 19.3 1.0
CB B:ASP18 4.6 4.9 1.0
O B:HOH380 4.6 19.3 1.0
O B:ASP71 4.7 11.4 1.0
OE1 B:GLU73 4.8 30.0 1.0
O B:ILE19 4.8 9.8 1.0
CA B:ASP21 4.8 9.8 1.0
CB B:GLU73 4.9 30.0 1.0
CA B:ASP71 4.9 6.3 1.0
NE B:ARG79 4.9 16.4 1.0

Calcium binding site 5 out of 8 in 7jof

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Calcium binding site 5 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:10.0
occ:1.00
 OE1 C:GLU73 2.5 13.8 1.0
OD2 C:ASP18 2.6 10.1 1.0
OD2 C:ASP21 2.6 4.8 1.0
O C:HIS72 2.6 11.7 1.0
OD1 C:ASP71 2.6 4.8 1.0
OD2 C:ASP71 2.7 20.7 1.0
CG C:ASP71 3.0 11.4 1.0
CG C:ASP18 3.3 7.5 1.0
OD1 C:ASP18 3.5 10.4 1.0
CG C:ASP21 3.6 14.2 1.0
C C:HIS72 3.7 12.8 1.0
CD C:GLU73 3.7 19.4 1.0
CB C:ASP21 4.0 5.5 1.0
NH2 C:ARG79 4.3 32.3 1.0
CA C:CA202 4.3 9.8 1.0
CA C:GLU73 4.3 24.6 1.0
CG C:GLU73 4.4 13.7 1.0
CB C:ASP71 4.4 12.1 1.0
N C:GLU73 4.5 8.1 1.0
N C:ASP21 4.5 7.3 1.0
N C:HIS72 4.5 7.5 1.0
C C:ASP71 4.6 9.9 1.0
CB C:ASP18 4.6 11.5 1.0
O C:HOH366 4.7 19.3 1.0
OD1 C:ASP21 4.7 9.1 1.0
OE2 C:GLU73 4.7 6.4 1.0
CA C:HIS72 4.7 7.1 1.0
O C:ILE19 4.8 10.6 1.0
O C:HOH347 4.8 30.0 1.0
CA C:ASP21 4.8 9.6 1.0
O C:ASP71 4.9 8.2 1.0
CB C:GLU73 5.0 17.7 1.0
CA C:ASP71 5.0 7.8 1.0

Calcium binding site 6 out of 8 in 7jof

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Calcium binding site 6 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:9.8
occ:1.00
 O C:HOH366 2.6 19.3 1.0
O C:ILE19 2.6 10.6 1.0
OD1 C:ASN40 2.6 10.8 1.0
OD2 C:ASP21 2.6 4.8 1.0
OD1 C:ASP18 2.6 10.4 1.0
O C:HOH333 2.7 19.3 1.0
OD1 C:ASP21 2.7 9.1 1.0
CG C:ASP21 2.9 14.2 1.0
CG C:ASP18 3.5 7.5 1.0
C C:ILE19 3.6 10.8 1.0
CG C:ASN40 3.7 14.9 1.0
N C:ILE19 3.7 3.5 1.0
OD2 C:ASP18 3.8 10.1 1.0
CA C:ILE19 4.1 7.2 1.0
CA C:ASN40 4.3 6.1 1.0
CB C:ILE19 4.3 11.9 1.0
CA C:CA201 4.3 10.0 1.0
N C:ASN40 4.4 13.2 1.0
CB C:ASP21 4.4 5.5 1.0
ND2 C:ASN40 4.5 14.4 1.0
CB C:ASN40 4.6 10.4 1.0
C C:ASP18 4.6 10.3 1.0
N C:ASP21 4.6 7.3 1.0
C C:SER20 4.7 11.1 1.0
CB C:ASP18 4.7 11.5 1.0
O C:HOH348 4.8 19.3 1.0
N C:SER20 4.8 2.3 1.0
CA C:ASP18 4.9 7.8 1.0
O C:SER20 4.9 4.9 1.0
O C:HOH373 4.9 19.3 1.0
CA C:ASP21 5.0 9.6 1.0

Calcium binding site 7 out of 8 in 7jof

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Calcium binding site 7 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:8.9
occ:1.00
 OD1 D:ASP21 2.4 4.5 1.0
OD1 D:ASP18 2.6 6.6 1.0
OD1 D:ASN40 2.6 8.3 1.0
O D:ILE19 2.6 12.6 1.0
O D:HOH371 2.6 19.3 1.0
O D:HOH346 2.8 19.3 1.0
OD2 D:ASP21 3.0 5.7 1.0
CG D:ASP21 3.0 5.9 1.0
CG D:ASP18 3.4 8.1 1.0
N D:ILE19 3.6 5.4 1.0
C D:ILE19 3.7 7.9 1.0
CG D:ASN40 3.8 3.8 1.0
OD2 D:ASP18 3.8 10.6 1.0
O D:HOH330 4.1 19.3 1.0
CA D:ILE19 4.1 7.6 1.0
CA D:CA202 4.3 5.4 1.0
CA D:ASN40 4.4 8.6 1.0
C D:ASP18 4.5 6.9 1.0
CB D:ILE19 4.5 12.6 1.0
N D:ASN40 4.5 13.1 1.0
CB D:ASP21 4.5 5.2 1.0
CB D:ASP18 4.5 6.5 1.0
O C:HOH331 4.6 19.3 1.0
CB D:ASN40 4.6 9.2 1.0
CA D:ASP18 4.7 7.8 1.0
N D:ASP21 4.7 6.0 1.0
ND2 D:ASN40 4.7 9.6 1.0
N D:SER20 4.8 4.6 1.0
C D:SER20 4.8 9.8 1.0

Calcium binding site 8 out of 8 in 7jof

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Calcium binding site 8 out of 8 in the Calcium-Bound C2A Domain From Human Dysferlin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Calcium-Bound C2A Domain From Human Dysferlin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:5.4
occ:1.00
 OD2 D:ASP21 2.3 5.7 1.0
OE1 D:GLU73 2.6 10.6 1.0
O D:HIS72 2.6 7.9 1.0
OD2 D:ASP18 2.6 10.6 1.0
OD1 D:ASP71 2.6 4.8 1.0
OD2 D:ASP71 2.7 5.1 1.0
O D:HOH330 2.7 19.3 1.0
CG D:ASP71 3.0 12.8 1.0
CG D:ASP18 3.3 8.1 1.0
OD1 D:ASP18 3.4 6.6 1.0
CG D:ASP21 3.4 5.9 1.0
CD D:GLU73 3.6 12.6 1.0
C D:HIS72 3.7 10.0 1.0
CG D:GLU73 4.0 14.5 1.0
CB D:ASP21 4.0 5.2 1.0
CA D:GLU73 4.3 13.7 1.0
CA D:CA201 4.3 8.9 1.0
OD1 D:ASP21 4.4 4.5 1.0
N D:GLU73 4.4 7.8 1.0
N D:HIS72 4.4 6.1 1.0
CB D:ASP71 4.4 8.6 1.0
C D:ASP71 4.5 9.0 1.0
N D:ASP21 4.5 6.0 1.0
NH2 D:ARG79 4.5 3.5 1.0
CB D:ASP18 4.6 6.5 1.0
CA D:HIS72 4.7 9.7 1.0
O D:ASP71 4.7 4.9 1.0
OE2 D:GLU73 4.7 23.4 1.0
CB D:GLU73 4.8 13.7 1.0
CA D:ASP21 4.9 4.2 1.0
O D:HOH371 4.9 19.3 1.0
CA D:ASP71 4.9 5.9 1.0
O D:ILE19 5.0 12.6 1.0
NE D:ARG79 5.0 21.4 1.0

Reference:

Y.Wang, R.Tadayon, L.Santamaria, P.Mercier, C.J.Forristal, G.S.Shaw. Calcium Binds and Rigidifies the Dysferlin C2A Domain in A Tightly Coupled Manner. Biochem.J. V. 478 197 2021.
ISSN: ESSN 1470-8728
PubMed: 33449082
DOI: 10.1042/BCJ20200773
Page generated: Sat Jul 10 11:29:20 2021

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