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Calcium in PDB 7wn3: Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)

Calcium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) (pdb code 7wn3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units), PDB code: 7wn3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 7wn3

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Calcium binding site 1 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:107.1
occ:1.00
 OD2 A:ASP47 2.4 79.0 1.0
OD1 A:ASN166 2.5 81.8 1.0
OD1 A:ASN164 2.5 76.4 1.0
CB A:ASP172 2.9 83.0 1.0
O A:ASN164 2.9 76.4 1.0
O A:PHE168 3.0 84.2 1.0
CG A:ASP47 3.1 79.0 1.0
CB A:ASP47 3.1 79.0 1.0
OD2 A:ASP172 3.1 83.0 1.0
CG A:ASP172 3.4 83.0 1.0
CG A:ASN166 3.6 81.8 1.0
CG A:ASN164 3.7 76.4 1.0
C A:ASN164 3.9 76.4 1.0
C A:PHE168 4.1 84.2 1.0
CA A:ASP172 4.2 83.0 1.0
N A:ASN166 4.2 81.8 1.0
N A:ASP47 4.2 79.0 1.0
CA A:ASP47 4.2 79.0 1.0
OD1 A:ASP47 4.3 79.0 1.0
ND2 A:ASN166 4.3 81.8 1.0
N A:ASN164 4.4 76.4 1.0
CA A:ALA169 4.5 81.7 1.0
ND2 A:ASN164 4.5 76.4 1.0
OD1 A:ASP172 4.5 83.0 1.0
CA A:ASN164 4.5 76.4 1.0
O A:ASN166 4.7 81.8 1.0
N A:ASP172 4.7 83.0 1.0
OD1 A:ASP171 4.7 81.6 1.0
CB A:ASN164 4.7 76.4 1.0
N A:ALA169 4.7 81.7 1.0
CB A:ASN166 4.8 81.8 1.0
CA A:ASN166 4.8 81.8 1.0
O A:ASP47 4.8 79.0 1.0
C A:ASN166 4.9 81.8 1.0
N A:PHE165 4.9 81.6 1.0
C A:GLY163 5.0 71.2 1.0

Calcium binding site 2 out of 16 in 7wn3

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Calcium binding site 2 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:98.2
occ:1.00
 OD1 A:ASN528 2.4 104.4 1.0
OD1 A:ASP533 2.4 105.0 1.0
OD1 A:ASP534 2.4 100.6 1.0
OD2 A:ASP400 2.5 93.0 1.0
CG A:ASN528 3.0 104.4 1.0
O A:ASN530 3.1 89.8 1.0
CG A:ASP533 3.1 105.0 1.0
OD2 A:ASP533 3.1 105.0 1.0
ND2 A:ASN528 3.2 104.4 1.0
CB A:ASN526 3.2 115.4 1.0
ND2 A:ASN526 3.4 115.4 1.0
N A:ASN526 3.4 115.4 1.0
CG A:ASP534 3.6 100.6 1.0
CG A:ASN526 3.7 115.4 1.0
CG A:ASP400 3.8 93.0 1.0
CA A:ASN526 3.8 115.4 1.0
N A:TYR527 4.1 115.3 1.0
C A:ASN530 4.2 89.8 1.0
OD2 A:ASP534 4.3 100.6 1.0
N A:ASN528 4.3 104.4 1.0
N A:ASP534 4.3 100.6 1.0
CB A:ASN528 4.3 104.4 1.0
C A:ASN526 4.4 115.4 1.0
CA A:ASP534 4.4 100.6 1.0
OD1 A:ASP400 4.5 93.0 1.0
C A:GLY525 4.5 110.6 1.0
CB A:ASP533 4.5 105.0 1.0
CB A:ASP534 4.6 100.6 1.0
N A:ASN530 4.7 89.8 1.0
C A:ASP533 4.7 105.0 1.0
CA A:GLY525 4.7 110.6 1.0
CB A:ASN530 4.7 89.8 1.0
CB A:ASP400 4.8 93.0 1.0
CA A:ASN530 4.8 89.8 1.0
OD1 A:ASN526 4.8 115.4 1.0
CA A:ASN528 4.8 104.4 1.0

Calcium binding site 3 out of 16 in 7wn3

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Calcium binding site 3 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1302

b:50.0
occ:1.00
 O F:ILE1002 2.3 47.0 1.0
OD1 F:ASP1006 2.3 42.2 1.0
OD1 F:ASN998 2.4 45.1 1.0
OD1 F:ASN1005 2.4 44.6 1.0
OD2 F:ASP879 2.5 54.7 1.0
OD1 F:ASP1000 2.7 50.4 1.0
CG F:ASP1006 3.0 42.2 1.0
CG F:ASN998 3.2 45.1 1.0
OD2 F:ASP1006 3.4 42.2 1.0
CG F:ASP1000 3.5 50.4 1.0
ND2 F:ASN998 3.5 45.1 1.0
CG F:ASN1005 3.5 44.6 1.0
C F:ILE1002 3.5 47.0 1.0
OD2 F:ASP1000 3.6 50.4 1.0
C F:ASN1005 3.7 44.6 1.0
O F:ASN1005 3.7 44.6 1.0
CG F:ASP879 3.7 54.7 1.0
N F:ASP1006 3.7 42.2 1.0
CB F:ASP1006 4.1 42.2 1.0
CA F:ASP1006 4.1 42.2 1.0
N F:ASN998 4.3 45.1 1.0
CA F:ASN1005 4.3 44.6 1.0
CB F:ASP879 4.4 54.7 1.0
ND2 F:ASN1005 4.4 44.6 1.0
N F:GLN1003 4.4 48.8 1.0
N F:ASN1005 4.4 44.6 1.0
CB F:ASN998 4.5 45.1 1.0
CA F:GLN1003 4.5 48.8 1.0
CB F:ASN1005 4.5 44.6 1.0
N F:PHE999 4.5 49.7 1.0
CA F:ILE1002 4.5 47.0 1.0
N F:ASP1000 4.5 50.4 1.0
N F:ILE1002 4.6 47.0 1.0
OD1 F:ASP879 4.7 54.7 1.0
C F:GLN1003 4.7 48.8 1.0
CB F:ILE1002 4.7 47.0 1.0
CB F:ASP1000 4.7 50.4 1.0
CA F:ASN998 4.8 45.1 1.0
O F:GLN1003 4.9 48.8 1.0
C F:ASN998 5.0 45.1 1.0

Calcium binding site 4 out of 16 in 7wn3

Go back to Calcium Binding Sites List in 7wn3
Calcium binding site 4 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:

Calcium binding site 5 out of 16 in 7wn3

Go back to Calcium Binding Sites List in 7wn3
Calcium binding site 5 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:121.7
occ:1.00
 OD2 B:ASP47 2.4 92.9 1.0
OD1 B:ASN166 2.5 90.2 1.0
OD1 B:ASN164 2.5 88.6 1.0
CB B:ASP172 2.9 95.4 1.0
O B:ASN164 2.9 88.6 1.0
O B:PHE168 3.0 93.7 1.0
CG B:ASP47 3.1 92.9 1.0
CB B:ASP47 3.1 92.9 1.0
OD2 B:ASP172 3.1 95.4 1.0
CG B:ASP172 3.4 95.4 1.0
CG B:ASN166 3.6 90.2 1.0
CG B:ASN164 3.7 88.6 1.0
C B:ASN164 3.9 88.6 1.0
C B:PHE168 4.1 93.7 1.0
CA B:ASP172 4.2 95.4 1.0
N B:ASN166 4.2 90.2 1.0
N B:ASP47 4.2 92.9 1.0
CA B:ASP47 4.2 92.9 1.0
OD1 B:ASP47 4.3 92.9 1.0
ND2 B:ASN166 4.3 90.2 1.0
N B:ASN164 4.4 88.6 1.0
CA B:ALA169 4.5 93.1 1.0
ND2 B:ASN164 4.5 88.6 1.0
OD1 B:ASP172 4.5 95.4 1.0
CA B:ASN164 4.5 88.6 1.0
O B:ASN166 4.7 90.2 1.0
N B:ASP172 4.7 95.4 1.0
OD1 B:ASP171 4.7 96.8 1.0
CB B:ASN164 4.7 88.6 1.0
N B:ALA169 4.7 93.1 1.0
CB B:ASN166 4.8 90.2 1.0
CA B:ASN166 4.8 90.2 1.0
O B:ASP47 4.8 92.9 1.0
C B:ASN166 4.9 90.2 1.0
N B:PHE165 4.9 90.1 1.0
C B:GLY163 5.0 83.2 1.0

Calcium binding site 6 out of 16 in 7wn3

Go back to Calcium Binding Sites List in 7wn3
Calcium binding site 6 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:34.9
occ:1.00
 OD1 B:ASN528 2.4 42.8 1.0
OD1 B:ASP533 2.4 51.9 1.0
OD1 B:ASP534 2.4 46.5 1.0
OD2 B:ASP400 2.5 38.3 1.0
CG B:ASN528 3.0 42.8 1.0
O B:ASN530 3.1 51.2 1.0
CG B:ASP533 3.1 51.9 1.0
OD2 B:ASP533 3.1 51.9 1.0
ND2 B:ASN528 3.2 42.8 1.0
CB B:ASN526 3.2 45.0 1.0
ND2 B:ASN526 3.4 45.0 1.0
N B:ASN526 3.4 45.0 1.0
CG B:ASP534 3.6 46.5 1.0
CG B:ASN526 3.7 45.0 1.0
CG B:ASP400 3.8 38.3 1.0
CA B:ASN526 3.8 45.0 1.0
N B:TYR527 4.1 41.8 1.0
C B:ASN530 4.2 51.2 1.0
OD2 B:ASP534 4.3 46.5 1.0
N B:ASN528 4.3 42.8 1.0
N B:ASP534 4.3 46.5 1.0
CB B:ASN528 4.3 42.8 1.0
C B:ASN526 4.4 45.0 1.0
CA B:ASP534 4.4 46.5 1.0
OD1 B:ASP400 4.5 38.3 1.0
C B:GLY525 4.5 39.2 1.0
CB B:ASP533 4.5 51.9 1.0
CB B:ASP534 4.6 46.5 1.0
N B:ASN530 4.7 51.2 1.0
C B:ASP533 4.7 51.9 1.0
CA B:GLY525 4.7 39.2 1.0
CB B:ASN530 4.7 51.2 1.0
CB B:ASP400 4.8 38.3 1.0
CA B:ASN530 4.8 51.2 1.0
OD1 B:ASN526 4.8 45.0 1.0
CA B:ASN528 4.8 42.8 1.0

Calcium binding site 7 out of 16 in 7wn3

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Calcium binding site 7 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1302

b:71.5
occ:1.00
 O H:ILE1002 2.3 62.5 1.0
OD1 H:ASP1006 2.3 58.0 1.0
OD1 H:ASN998 2.4 61.6 1.0
OD1 H:ASN1005 2.4 60.9 1.0
OD2 H:ASP879 2.5 51.0 1.0
OD1 H:ASP1000 2.7 60.8 1.0
CG H:ASP1006 3.0 58.0 1.0
CG H:ASN998 3.2 61.6 1.0
OD2 H:ASP1006 3.4 58.0 1.0
CG H:ASP1000 3.5 60.8 1.0
ND2 H:ASN998 3.5 61.6 1.0
CG H:ASN1005 3.5 60.9 1.0
C H:ILE1002 3.5 62.5 1.0
OD2 H:ASP1000 3.6 60.8 1.0
C H:ASN1005 3.7 60.9 1.0
O H:ASN1005 3.7 60.9 1.0
CG H:ASP879 3.7 51.0 1.0
N H:ASP1006 3.7 58.0 1.0
CB H:ASP1006 4.1 58.0 1.0
CA H:ASP1006 4.1 58.0 1.0
N H:ASN998 4.3 61.6 1.0
CA H:ASN1005 4.3 60.9 1.0
CB H:ASP879 4.4 51.0 1.0
ND2 H:ASN1005 4.4 60.9 1.0
N H:GLN1003 4.4 56.1 1.0
N H:ASN1005 4.4 60.9 1.0
CB H:ASN998 4.5 61.6 1.0
CA H:GLN1003 4.5 56.1 1.0
CB H:ASN1005 4.5 60.9 1.0
N H:PHE999 4.5 65.0 1.0
CA H:ILE1002 4.5 62.5 1.0
N H:ASP1000 4.5 60.8 1.0
N H:ILE1002 4.6 62.5 1.0
OD1 H:ASP879 4.7 51.0 1.0
C H:GLN1003 4.7 56.1 1.0
CB H:ILE1002 4.7 62.5 1.0
CB H:ASP1000 4.7 60.8 1.0
CA H:ASN998 4.8 61.6 1.0
O H:GLN1003 4.9 56.1 1.0
C H:ASN998 5.0 61.6 1.0

Calcium binding site 8 out of 16 in 7wn3

Go back to Calcium Binding Sites List in 7wn3
Calcium binding site 8 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


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 Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:

Calcium binding site 9 out of 16 in 7wn3

Go back to Calcium Binding Sites List in 7wn3
Calcium binding site 9 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca801

b:74.1
occ:1.00
 OD2 E:ASP47 2.4 64.8 1.0
OD1 E:ASN166 2.5 67.6 1.0
OD1 E:ASN164 2.5 63.0 1.0
CB E:ASP172 2.9 68.0 1.0
O E:ASN164 2.9 63.0 1.0
O E:PHE168 3.0 66.6 1.0
CG E:ASP47 3.1 64.8 1.0
CB E:ASP47 3.1 64.8 1.0
OD2 E:ASP172 3.1 68.0 1.0
CG E:ASP172 3.4 68.0 1.0
CG E:ASN166 3.6 67.6 1.0
CG E:ASN164 3.7 63.0 1.0
C E:ASN164 3.9 63.0 1.0
C E:PHE168 4.1 66.6 1.0
CA E:ASP172 4.2 68.0 1.0
N E:ASN166 4.2 67.6 1.0
N E:ASP47 4.2 64.8 1.0
CA E:ASP47 4.2 64.8 1.0
OD1 E:ASP47 4.3 64.8 1.0
ND2 E:ASN166 4.3 67.6 1.0
N E:ASN164 4.4 63.0 1.0
CA E:ALA169 4.5 61.5 1.0
ND2 E:ASN164 4.5 63.0 1.0
OD1 E:ASP172 4.5 68.0 1.0
CA E:ASN164 4.5 63.0 1.0
O E:ASN166 4.7 67.6 1.0
N E:ASP172 4.7 68.0 1.0
OD1 E:ASP171 4.7 67.8 1.0
CB E:ASN164 4.7 63.0 1.0
N E:ALA169 4.7 61.5 1.0
CB E:ASN166 4.8 67.6 1.0
CA E:ASN166 4.8 67.6 1.0
O E:ASP47 4.8 64.8 1.0
C E:ASN166 4.9 67.6 1.0
N E:PHE165 4.9 68.5 1.0
C E:GLY163 5.0 58.5 1.0

Calcium binding site 10 out of 16 in 7wn3

Go back to Calcium Binding Sites List in 7wn3
Calcium binding site 10 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of Vwf D'D3 Dimer (2M Mutant) Complexed with D1D2 at 3.29 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca802

b:39.7
occ:1.00
 OD1 E:ASN528 2.4 50.3 1.0
OD1 E:ASP533 2.4 50.6 1.0
OD1 E:ASP534 2.4 46.1 1.0
OD2 E:ASP400 2.5 38.8 1.0
CG E:ASN528 3.0 50.3 1.0
O E:ASN530 3.1 50.0 1.0
CG E:ASP533 3.1 50.6 1.0
OD2 E:ASP533 3.1 50.6 1.0
ND2 E:ASN528 3.2 50.3 1.0
CB E:ASN526 3.2 49.7 1.0
ND2 E:ASN526 3.4 49.7 1.0
N E:ASN526 3.4 49.7 1.0
CG E:ASP534 3.6 46.1 1.0
CG E:ASN526 3.7 49.7 1.0
CG E:ASP400 3.8 38.8 1.0
CA E:ASN526 3.8 49.7 1.0
N E:TYR527 4.1 49.4 1.0
C E:ASN530 4.2 50.0 1.0
OD2 E:ASP534 4.3 46.1 1.0
N E:ASN528 4.3 50.3 1.0
N E:ASP534 4.3 46.1 1.0
CB E:ASN528 4.3 50.3 1.0
C E:ASN526 4.4 49.7 1.0
CA E:ASP534 4.4 46.1 1.0
OD1 E:ASP400 4.5 38.8 1.0
C E:GLY525 4.5 43.0 1.0
CB E:ASP533 4.5 50.6 1.0
CB E:ASP534 4.6 46.1 1.0
N E:ASN530 4.7 50.0 1.0
C E:ASP533 4.7 50.6 1.0
CA E:GLY525 4.7 43.0 1.0
CB E:ASN530 4.7 50.0 1.0
CB E:ASP400 4.8 38.8 1.0
CA E:ASN530 4.8 50.0 1.0
OD1 E:ASN526 4.8 49.7 1.0
CA E:ASN528 4.8 50.3 1.0

Reference:

Z.Shu, J.Zeng, L.Xia, H.Cai, A.Zhou. Structural Mechanism of Vwf D'D3 Dimer Formation. Cell Discov V. 8 14 2022.
ISSN: ESSN 2056-5968
PubMed: 35169124
DOI: 10.1038/S41421-022-00378-2
Page generated: Fri Jul 19 05:44:53 2024

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