Calcium in PDB 8wv5: C-Reactive Protein, Decamer

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the C-Reactive Protein, Decamer (pdb code 8wv5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the C-Reactive Protein, Decamer, PDB code: 8wv5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in 8wv5

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Calcium binding site 1 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:139.5
occ:1.00
CG E:GLU147 2.3 126.0 1.0
OE1 E:GLU138 2.4 119.4 1.0
OE2 E:GLU147 2.4 126.0 1.0
OD2 E:ASP140 2.4 125.6 1.0
OE1 E:GLN150 2.4 115.5 1.0
CD E:GLU147 2.6 126.0 1.0
CG E:ASP140 3.3 125.6 1.0
CD E:GLN150 3.4 115.5 1.0
CD E:GLU138 3.5 119.4 1.0
CB E:GLU147 3.6 126.0 1.0
OD1 E:ASP140 3.6 125.6 1.0
OE1 E:GLU147 3.7 126.0 1.0
OE2 E:GLU138 3.9 119.4 1.0
NE2 E:GLN150 4.1 115.5 1.0
O E:GLU138 4.4 119.4 1.0
CG E:GLN150 4.5 115.5 1.0
CB E:ASP140 4.7 125.6 1.0
CG E:GLU138 4.7 119.4 1.0
CA E:GLU147 4.8 126.0 1.0
CA E:CA302 5.0 132.2 1.0

Calcium binding site 2 out of 20 in 8wv5

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Calcium binding site 2 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:132.2
occ:1.00
ND2 E:ASN61 2.2 127.0 1.0
OD1 E:ASP140 2.4 125.6 1.0
OD2 E:ASP60 2.4 129.3 1.0
OE2 E:GLU138 2.4 119.4 1.0
OD1 E:ASN61 2.4 127.0 1.0
CG E:ASN61 2.6 127.0 1.0
CG E:ASP60 3.4 129.3 1.0
CG E:ASP140 3.5 125.6 1.0
CD E:GLU138 3.6 119.4 1.0
O E:GLN139 3.7 121.0 1.0
CA E:ASP140 3.9 125.6 1.0
CB E:ASN61 4.1 127.0 1.0
OD1 E:ASP60 4.1 129.3 1.0
O E:ASP60 4.1 129.3 1.0
OE1 E:GLU138 4.2 119.4 1.0
CB E:ASP140 4.3 125.6 1.0
CB E:ASP60 4.3 129.3 1.0
OD2 E:ASP140 4.3 125.6 1.0
C E:ASP60 4.4 129.3 1.0
C E:GLN139 4.4 121.0 1.0
N E:ASP140 4.5 125.6 1.0
N E:ASN61 4.7 127.0 1.0
CG E:GLU138 4.7 119.4 1.0
CA E:ASN61 4.7 127.0 1.0
C E:ASP140 4.9 125.6 1.0
CA E:CA301 5.0 139.5 1.0

Calcium binding site 3 out of 20 in 8wv5

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Calcium binding site 3 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:127.2
occ:1.00
OE1 A:GLU138 2.4 111.5 1.0
OE2 A:GLU147 2.4 117.7 1.0
OD2 A:ASP140 2.4 114.9 1.0
OE1 A:GLN150 2.4 101.8 1.0
CD A:GLU147 2.7 117.7 1.0
CG A:GLU147 2.9 117.7 1.0
CG A:ASP140 3.4 114.9 1.0
CD A:GLN150 3.5 101.8 1.0
CD A:GLU138 3.5 111.5 1.0
OE1 A:GLU147 3.5 117.7 1.0
OD1 A:ASP140 3.8 114.9 1.0
CB A:GLU147 3.9 117.7 1.0
NE2 A:GLN150 4.0 101.8 1.0
OE2 A:GLU138 4.1 111.5 1.0
CG A:GLU138 4.5 111.5 1.0
O A:GLU138 4.5 111.5 1.0
CG A:GLN150 4.6 101.8 1.0
CB A:ASP140 4.7 114.9 1.0
CB A:GLU138 4.8 111.5 1.0

Calcium binding site 4 out of 20 in 8wv5

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Calcium binding site 4 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:132.5
occ:1.00
ND2 A:ASN61 2.3 112.5 1.0
OD1 A:ASP140 2.4 114.9 1.0
OD1 A:ASN61 2.4 112.5 1.0
OE2 A:GLU138 2.4 111.5 1.0
OD2 A:ASP60 2.5 118.6 1.0
CG A:ASP60 2.5 118.6 1.0
CG A:ASN61 2.6 112.5 1.0
OD1 A:ASP60 2.7 118.6 1.0
CB A:ASP60 3.3 118.6 1.0
CG A:ASP140 3.5 114.9 1.0
CD A:GLU138 3.6 111.5 1.0
CA A:ASP140 3.8 114.9 1.0
O A:GLN139 3.9 110.7 1.0
CB A:ASN61 4.0 112.5 1.0
C A:ASP60 4.1 118.6 1.0
OE1 A:GLU138 4.2 111.5 1.0
CB A:ASP140 4.2 114.9 1.0
N A:ASN61 4.3 112.5 1.0
O A:ASP60 4.3 118.6 1.0
CA A:ASP60 4.3 118.6 1.0
OD2 A:ASP140 4.5 114.9 1.0
C A:GLN139 4.5 110.7 1.0
N A:ASP140 4.5 114.9 1.0
CA A:ASN61 4.6 112.5 1.0
C A:ASP140 4.8 114.9 1.0
CG A:GLU138 4.8 111.5 1.0

Calcium binding site 5 out of 20 in 8wv5

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Calcium binding site 5 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:137.2
occ:1.00
OE1 B:GLU138 2.4 119.9 1.0
OE2 B:GLU147 2.4 127.1 1.0
OD2 B:ASP140 2.4 125.9 1.0
OE1 B:GLN150 2.4 119.1 1.0
CD B:GLU147 2.6 127.1 1.0
CG B:GLU147 2.7 127.1 1.0
CG B:ASP140 3.3 125.9 1.0
CD B:GLN150 3.4 119.1 1.0
CD B:GLU138 3.5 119.9 1.0
OE1 B:GLU147 3.5 127.1 1.0
OD1 B:ASP140 3.6 125.9 1.0
CB B:GLU147 3.6 127.1 1.0
OE2 B:GLU138 3.9 119.9 1.0
NE2 B:GLN150 4.0 119.1 1.0
O B:GLU138 4.3 119.9 1.0
CG B:GLN150 4.5 119.1 1.0
CB B:ASP140 4.6 125.9 1.0
CG B:GLU138 4.7 119.9 1.0
CA B:CA302 4.8 133.4 1.0
CA B:GLU147 4.9 127.1 1.0

Calcium binding site 6 out of 20 in 8wv5

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Calcium binding site 6 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:133.4
occ:1.00
ND2 B:ASN61 2.3 123.5 1.0
OD1 B:ASP140 2.4 125.9 1.0
OD2 B:ASP60 2.4 127.1 1.0
OD1 B:ASN61 2.4 123.5 1.0
OE2 B:GLU138 2.4 119.9 1.0
CG B:ASN61 2.6 123.5 1.0
CG B:ASP60 3.4 127.1 1.0
CG B:ASP140 3.5 125.9 1.0
CD B:GLU138 3.6 119.9 1.0
O B:GLN139 3.7 119.8 1.0
CA B:ASP140 3.9 125.9 1.0
CB B:ASN61 4.1 123.5 1.0
OD1 B:ASP60 4.1 127.1 1.0
OE1 B:GLU138 4.1 119.9 1.0
O B:ASP60 4.1 127.1 1.0
CB B:ASP140 4.3 125.9 1.0
CB B:ASP60 4.3 127.1 1.0
OD2 B:ASP140 4.3 125.9 1.0
C B:ASP60 4.4 127.1 1.0
C B:GLN139 4.5 119.8 1.0
N B:ASP140 4.5 125.9 1.0
N B:ASN61 4.7 123.5 1.0
CG B:GLU138 4.7 119.9 1.0
CA B:ASN61 4.7 123.5 1.0
CA B:CA301 4.8 137.2 1.0
C B:ASP140 5.0 125.9 1.0

Calcium binding site 7 out of 20 in 8wv5

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Calcium binding site 7 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:146.5
occ:1.00
OE1 C:GLU138 2.4 136.7 1.0
OE2 C:GLU147 2.4 145.2 1.0
OD2 C:ASP140 2.4 141.0 1.0
OE1 C:GLN150 2.4 131.7 1.0
CD C:GLU147 2.7 145.2 1.0
CG C:GLU147 2.8 145.2 1.0
CG C:ASP140 3.3 141.0 1.0
CD C:GLN150 3.4 131.7 1.0
CD C:GLU138 3.5 136.7 1.0
OD1 C:ASP140 3.5 141.0 1.0
OE1 C:GLU147 3.6 145.2 1.0
CB C:GLU147 3.8 145.2 1.0
OE2 C:GLU138 3.9 136.7 1.0
NE2 C:GLN150 4.0 131.7 1.0
O C:GLU138 4.5 136.7 1.0
CG C:GLN150 4.6 131.7 1.0
CB C:ASP140 4.6 141.0 1.0
CG C:GLU138 4.7 136.7 1.0
CA C:CA302 4.9 144.3 1.0
CB C:GLU138 5.0 136.7 1.0

Calcium binding site 8 out of 20 in 8wv5

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Calcium binding site 8 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:144.3
occ:1.00
ND2 C:ASN61 2.3 136.9 1.0
OD1 C:ASP140 2.4 141.0 1.0
OD2 C:ASP60 2.4 141.4 1.0
OD1 C:ASN61 2.4 136.9 1.0
OE2 C:GLU138 2.4 136.7 1.0
CG C:ASN61 2.6 136.9 1.0
CG C:ASP60 3.4 141.4 1.0
CG C:ASP140 3.5 141.0 1.0
CD C:GLU138 3.6 136.7 1.0
O C:GLN139 3.6 137.0 1.0
CA C:ASP140 3.8 141.0 1.0
CB C:ASN61 4.0 136.9 1.0
OD1 C:ASP60 4.1 141.4 1.0
OE1 C:GLU138 4.1 136.7 1.0
O C:ASP60 4.2 141.4 1.0
CB C:ASP140 4.2 141.0 1.0
CB C:ASP60 4.3 141.4 1.0
OD2 C:ASP140 4.3 141.0 1.0
C C:GLN139 4.3 137.0 1.0
C C:ASP60 4.4 141.4 1.0
N C:ASP140 4.4 141.0 1.0
N C:ASN61 4.7 136.9 1.0
CA C:ASN61 4.7 136.9 1.0
CG C:GLU138 4.7 136.7 1.0
C C:ASP140 4.8 141.0 1.0
CA C:CA301 4.9 146.5 1.0

Calcium binding site 9 out of 20 in 8wv5

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Calcium binding site 9 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:141.0
occ:1.00
OE1 D:GLU138 2.4 139.5 1.0
OE2 D:GLU147 2.4 141.1 1.0
OD2 D:ASP140 2.4 141.3 1.0
OE1 D:GLN150 2.4 131.4 1.0
CD D:GLU147 2.6 141.1 1.0
CG D:GLU147 2.8 141.1 1.0
CG D:ASP140 3.3 141.3 1.0
CD D:GLN150 3.4 131.4 1.0
CD D:GLU138 3.5 139.5 1.0
OE1 D:GLU147 3.5 141.1 1.0
OD1 D:ASP140 3.6 141.3 1.0
CB D:GLU147 3.8 141.1 1.0
OE2 D:GLU138 3.9 139.5 1.0
NE2 D:GLN150 4.1 131.4 1.0
O D:GLU138 4.4 139.5 1.0
CG D:GLN150 4.6 131.4 1.0
CB D:ASP140 4.6 141.3 1.0
CG D:GLU138 4.7 139.5 1.0
CA D:CA302 4.9 146.8 1.0
CB D:GLU138 5.0 139.5 1.0

Calcium binding site 10 out of 20 in 8wv5

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Calcium binding site 10 out of 20 in the C-Reactive Protein, Decamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of C-Reactive Protein, Decamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:146.8
occ:1.00
ND2 D:ASN61 2.3 143.5 1.0
OD1 D:ASP140 2.4 141.3 1.0
OD1 D:ASN61 2.4 143.5 1.0
OD2 D:ASP60 2.4 146.3 1.0
OE2 D:GLU138 2.4 139.5 1.0
CG D:ASN61 2.6 143.5 1.0
CG D:ASP60 3.4 146.3 1.0
CG D:ASP140 3.5 141.3 1.0
CD D:GLU138 3.6 139.5 1.0
O D:GLN139 3.9 136.4 1.0
OD1 D:ASP60 4.1 146.3 1.0
CA D:ASP140 4.1 141.3 1.0
CB D:ASN61 4.1 143.5 1.0
OE1 D:GLU138 4.2 139.5 1.0
CB D:ASP140 4.4 141.3 1.0
OD2 D:ASP140 4.4 141.3 1.0
O D:ASP60 4.4 146.3 1.0
CB D:ASP60 4.5 146.3 1.0
C D:ASP60 4.6 146.3 1.0
C D:GLN139 4.6 136.4 1.0
N D:ASP140 4.7 141.3 1.0
CG D:GLU138 4.7 139.5 1.0
N D:ASN61 4.8 143.5 1.0
CA D:ASN61 4.9 143.5 1.0
CA D:CA301 4.9 141.0 1.0
CD1 D:LEU64 4.9 123.9 1.0

Reference:

S.Yadav, K.R.Vinothkumar. Factors Affecting Macromolecule Orientations in Thin Films Formed in Cryo-Em. Acta Crystallogr D Struct V. 80 535 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38935342
DOI: 10.1107/S2059798324005229
Page generated: Sat Sep 28 09:20:27 2024

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