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Calcium in PDB 7pkb: C-Reactive Protein Pentamer at pH 7.5

Calcium Binding Sites:

The binding sites of Calcium atom in the C-Reactive Protein Pentamer at pH 7.5 (pdb code 7pkb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the C-Reactive Protein Pentamer at pH 7.5, PDB code: 7pkb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7pkb

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Calcium binding site 1 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:83.5
occ:1.00
OE1 E:GLU147 2.3 83.7 1.0
OD1 E:ASP140 2.3 81.9 1.0
OE1 E:GLN150 2.5 78.3 1.0
OD2 E:ASP140 2.5 81.9 1.0
CG E:ASP140 2.7 81.9 1.0
HG2 E:GLU138 3.2 77.9 1.0
OE2 E:GLU138 3.2 77.9 1.0
HE22 E:GLN150 3.3 78.3 1.0
CD E:GLN150 3.3 78.3 1.0
CD E:GLU147 3.4 83.7 1.0
CD E:GLU138 3.5 77.9 1.0
HG3 E:GLU147 3.5 83.7 1.0
NE2 E:GLN150 3.6 78.3 1.0
HB3 E:GLU138 3.7 77.9 1.0
CG E:GLU138 3.7 77.9 1.0
CG E:GLU147 4.0 83.7 1.0
CB E:ASP140 4.2 81.9 1.0
OE1 E:GLU138 4.2 77.9 1.0
CB E:GLU138 4.2 77.9 1.0
CA E:CA302 4.3 83.2 1.0
HB2 E:GLU147 4.4 83.7 1.0
HE21 E:GLN150 4.4 78.3 1.0
OE2 E:GLU147 4.4 83.7 1.0
O E:GLU138 4.5 77.9 1.0
HB3 E:ASP140 4.5 81.9 1.0
CG E:GLN150 4.6 78.3 1.0
HG3 E:GLU138 4.6 77.9 1.0
HB2 E:ASP140 4.6 81.9 1.0
HG3 E:GLN150 4.7 78.3 1.0
HG2 E:GLU147 4.8 83.7 1.0
CB E:GLU147 4.8 83.7 1.0
HB2 E:GLU138 4.8 77.9 1.0
HB2 E:GLN150 5.0 78.3 1.0
C E:GLU138 5.0 77.9 1.0
HA E:ASP140 5.0 81.9 1.0

Calcium binding site 2 out of 10 in 7pkb

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Calcium binding site 2 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:83.2
occ:1.00
OD1 E:ASN61 2.3 78.7 1.0
OD2 E:ASP140 2.5 81.9 1.0
HA E:ASP140 2.7 81.9 1.0
OD2 E:ASP60 2.9 82.0 1.0
CG E:ASP60 3.0 82.0 1.0
OE2 E:GLU138 3.1 77.9 1.0
CG E:ASN61 3.2 78.7 1.0
OD1 E:ASP60 3.2 82.0 1.0
O E:GLN139 3.3 77.6 1.0
HG2 E:GLU138 3.3 77.9 1.0
HB2 E:ASP60 3.3 82.0 1.0
O E:ASP60 3.5 82.0 1.0
CG E:ASP140 3.5 81.9 1.0
ND2 E:ASN61 3.5 78.7 1.0
CA E:ASP140 3.5 81.9 1.0
CB E:ASP60 3.7 82.0 1.0
C E:ASP60 3.8 82.0 1.0
HG3 E:GLU138 3.8 77.9 1.0
CG E:GLU138 3.9 77.9 1.0
C E:GLN139 3.9 77.6 1.0
CB E:ASP140 3.9 81.9 1.0
CD E:GLU138 3.9 77.9 1.0
HB3 E:ASP140 4.0 81.9 1.0
N E:ASP140 4.0 81.9 1.0
HD21 E:ASN61 4.3 78.7 1.0
CA E:CA301 4.3 83.5 1.0
N E:ASN61 4.3 78.7 1.0
CA E:ASP60 4.4 82.0 1.0
CB E:ASN61 4.4 78.7 1.0
OD1 E:ASP140 4.5 81.9 1.0
HB3 E:ASP60 4.5 82.0 1.0
HA E:ASN61 4.5 78.7 1.0
HD23 E:LEU64 4.7 71.6 1.0
CA E:ASN61 4.7 78.7 1.0
H E:ASP140 4.7 81.9 1.0
C E:ASP140 4.7 81.9 1.0
H E:ASN61 4.8 78.7 1.0
HB2 E:ASP140 4.8 81.9 1.0
HB2 E:ASN61 4.8 78.7 1.0
O E:ASP140 5.0 81.9 1.0
N E:GLN139 5.0 77.6 1.0

Calcium binding site 3 out of 10 in 7pkb

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Calcium binding site 3 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:81.9
occ:1.00
OD1 D:ASP140 2.3 82.4 1.0
OE1 D:GLN150 2.4 78.2 1.0
OD2 D:ASP140 2.9 82.4 1.0
CG D:ASP140 2.9 82.4 1.0
CD D:GLN150 3.3 78.2 1.0
HE22 D:GLN150 3.4 78.2 1.0
OE1 D:GLU147 3.5 84.4 1.0
HG3 D:GLU147 3.6 84.4 1.0
CD D:GLU147 3.6 84.4 1.0
NE2 D:GLN150 3.7 78.2 1.0
HG2 D:GLU138 3.8 78.0 1.0
CD D:GLU138 3.8 78.0 1.0
HB3 D:GLU138 3.8 78.0 1.0
OE1 D:GLU138 3.9 78.0 1.0
OE2 D:GLU147 3.9 84.4 1.0
CG D:GLU147 4.1 84.4 1.0
OE2 D:GLU138 4.1 78.0 1.0
HB2 D:GLU147 4.2 84.4 1.0
CG D:GLU138 4.2 78.0 1.0
CB D:ASP140 4.4 82.4 1.0
HE21 D:GLN150 4.5 78.2 1.0
CG D:GLN150 4.5 78.2 1.0
CB D:GLU138 4.5 78.0 1.0
HG3 D:GLN150 4.5 78.2 1.0
CA D:CA302 4.6 81.2 1.0
HB2 D:ASP140 4.6 82.4 1.0
CB D:GLU147 4.7 84.4 1.0
O D:GLU138 4.8 78.0 1.0
HB3 D:ASP140 4.8 82.4 1.0
HB2 D:GLN150 4.8 78.2 1.0
HG2 D:GLU147 4.9 84.4 1.0

Calcium binding site 4 out of 10 in 7pkb

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Calcium binding site 4 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:81.2
occ:1.00
OD1 D:ASN61 2.2 78.7 1.0
OD2 D:ASP140 2.3 82.4 1.0
HA D:ASP140 2.7 82.4 1.0
OD2 D:ASP60 3.0 83.1 1.0
CG D:ASP60 3.1 83.1 1.0
O D:GLN139 3.1 77.8 1.0
CG D:ASN61 3.1 78.7 1.0
HB2 D:ASP60 3.3 83.1 1.0
OE2 D:GLU138 3.3 78.0 1.0
HG2 D:GLU138 3.3 78.0 1.0
CG D:ASP140 3.3 82.4 1.0
O D:ASP60 3.4 83.1 1.0
OD1 D:ASP60 3.4 83.1 1.0
ND2 D:ASN61 3.5 78.7 1.0
CA D:ASP140 3.5 82.4 1.0
CB D:ASP60 3.7 83.1 1.0
C D:GLN139 3.8 77.8 1.0
C D:ASP60 3.8 83.1 1.0
CB D:ASP140 3.9 82.4 1.0
CG D:GLU138 3.9 78.0 1.0
N D:ASP140 4.0 82.4 1.0
CD D:GLU138 4.0 78.0 1.0
HG3 D:GLU138 4.1 78.0 1.0
HB3 D:ASP140 4.1 82.4 1.0
OD1 D:ASP140 4.3 82.4 1.0
HD21 D:ASN61 4.3 78.7 1.0
N D:ASN61 4.4 78.7 1.0
CB D:ASN61 4.4 78.7 1.0
CA D:ASP60 4.4 83.1 1.0
HA D:ASN61 4.5 78.7 1.0
HB3 D:ASP60 4.5 83.1 1.0
HD23 D:LEU64 4.6 71.2 1.0
CA D:CA301 4.6 81.9 1.0
CA D:ASN61 4.7 78.7 1.0
H D:ASP140 4.7 82.4 1.0
C D:ASP140 4.7 82.4 1.0
HB2 D:ASP140 4.8 82.4 1.0
HB2 D:ASN61 4.8 78.7 1.0
H D:ASN61 4.9 78.7 1.0
H D:GLN139 4.9 77.8 1.0
N D:GLN139 5.0 77.8 1.0

Calcium binding site 5 out of 10 in 7pkb

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Calcium binding site 5 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:79.0
occ:1.00
OD1 C:ASP140 2.3 81.5 1.0
OE1 C:GLN150 2.6 77.8 1.0
OD2 C:ASP140 2.8 81.5 1.0
CG C:ASP140 2.9 81.5 1.0
OE1 C:GLU138 3.0 77.2 1.0
HG3 C:GLU147 3.3 83.7 1.0
CD C:GLN150 3.4 77.8 1.0
HE22 C:GLN150 3.5 77.8 1.0
CD C:GLU147 3.6 83.7 1.0
HB3 C:GLU138 3.6 77.2 1.0
OE2 C:GLU147 3.6 83.7 1.0
NE2 C:GLN150 3.8 77.8 1.0
CG C:GLU147 3.9 83.7 1.0
CD C:GLU138 3.9 77.2 1.0
OE1 C:GLU147 3.9 83.7 1.0
HB2 C:GLU147 4.2 83.7 1.0
CB C:ASP140 4.3 81.5 1.0
HG3 C:GLU138 4.4 77.2 1.0
CB C:GLU138 4.4 77.2 1.0
CG C:GLU138 4.5 77.2 1.0
HB2 C:ASP140 4.5 81.5 1.0
CA C:CA302 4.5 82.6 1.0
O C:GLU138 4.6 77.2 1.0
HE21 C:GLN150 4.6 77.8 1.0
HG3 C:GLN150 4.6 77.8 1.0
CG C:GLN150 4.6 77.8 1.0
HG2 C:GLU147 4.7 83.7 1.0
CB C:GLU147 4.7 83.7 1.0
HB3 C:ASP140 4.8 81.5 1.0
OE2 C:GLU138 4.8 77.2 1.0
HB2 C:GLN150 4.9 77.8 1.0
HB2 C:GLU138 5.0 77.2 1.0

Calcium binding site 6 out of 10 in 7pkb

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Calcium binding site 6 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:82.6
occ:1.00
OD1 C:ASN61 2.3 77.8 1.0
OD2 C:ASP140 2.3 81.5 1.0
OE2 C:GLU138 2.5 77.2 1.0
HA C:ASP140 2.7 81.5 1.0
OD2 C:ASP60 2.9 82.3 1.0
OE1 C:GLU138 2.9 77.2 1.0
CG C:ASP60 2.9 82.3 1.0
O C:GLN139 2.9 76.6 1.0
CD C:GLU138 3.0 77.2 1.0
OD1 C:ASP60 3.2 82.3 1.0
CG C:ASN61 3.2 77.8 1.0
O C:ASP60 3.3 82.3 1.0
CG C:ASP140 3.4 81.5 1.0
HB2 C:ASP60 3.4 82.3 1.0
CA C:ASP140 3.6 81.5 1.0
C C:GLN139 3.7 76.6 1.0
ND2 C:ASN61 3.7 77.8 1.0
CB C:ASP60 3.7 82.3 1.0
C C:ASP60 3.8 82.3 1.0
N C:ASP140 3.9 81.5 1.0
CB C:ASP140 4.0 81.5 1.0
HB3 C:ASP140 4.2 81.5 1.0
N C:ASN61 4.3 77.8 1.0
OD1 C:ASP140 4.4 81.5 1.0
CA C:ASP60 4.4 82.3 1.0
HA C:ASN61 4.5 77.8 1.0
HD21 C:ASN61 4.5 77.8 1.0
CB C:ASN61 4.5 77.8 1.0
CG C:GLU138 4.5 77.2 1.0
HB3 C:ASP60 4.5 82.3 1.0
CA C:CA301 4.5 79.0 1.0
HD23 C:LEU64 4.6 71.2 1.0
H C:ASP140 4.6 81.5 1.0
CA C:ASN61 4.7 77.8 1.0
H C:GLN139 4.7 76.6 1.0
C C:ASP140 4.8 81.5 1.0
N C:GLN139 4.8 76.6 1.0
HG3 C:GLU138 4.8 77.2 1.0
H C:ASN61 4.8 77.8 1.0
HB2 C:ASP140 4.8 81.5 1.0
CA C:GLN139 4.9 76.6 1.0
HG2 C:GLU138 4.9 77.2 1.0
HB2 C:ASN61 4.9 77.8 1.0
HA C:ASP60 4.9 82.3 1.0

Calcium binding site 7 out of 10 in 7pkb

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Calcium binding site 7 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:73.4
occ:1.00
OE1 B:GLU138 2.4 76.5 1.0
OD2 B:ASP140 2.5 80.9 1.0
OE1 B:GLN150 2.5 76.5 1.0
OD1 B:ASP140 3.0 80.9 1.0
CG B:ASP140 3.1 80.9 1.0
HG3 B:GLU147 3.2 82.3 1.0
OE1 B:GLU147 3.3 82.3 1.0
CD B:GLN150 3.4 76.5 1.0
CD B:GLU138 3.4 76.5 1.0
HE22 B:GLN150 3.4 76.5 1.0
CD B:GLU147 3.6 82.3 1.0
NE2 B:GLN150 3.7 76.5 1.0
HB3 B:GLU138 3.8 76.5 1.0
CG B:GLU147 3.9 82.3 1.0
OE2 B:GLU138 4.2 76.5 1.0
OE2 B:GLU147 4.2 82.3 1.0
HB2 B:GLU147 4.3 82.3 1.0
HG3 B:GLU138 4.3 76.5 1.0
CG B:GLU138 4.3 76.5 1.0
CB B:GLU138 4.5 76.5 1.0
HE21 B:GLN150 4.5 76.5 1.0
CB B:ASP140 4.5 80.9 1.0
HG2 B:GLU147 4.6 82.3 1.0
CG B:GLN150 4.6 76.5 1.0
O B:GLU138 4.6 76.5 1.0
HG3 B:GLN150 4.6 76.5 1.0
CB B:GLU147 4.7 82.3 1.0
CA B:CA302 4.7 86.6 1.0
HB2 B:ASP140 4.8 80.9 1.0
HB2 B:GLN150 4.9 76.5 1.0

Calcium binding site 8 out of 10 in 7pkb

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Calcium binding site 8 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:86.6
occ:1.00
OE2 B:GLU138 2.2 76.5 1.0
OD1 B:ASN61 2.3 77.4 1.0
OD1 B:ASP140 2.3 80.9 1.0
OD2 B:ASP60 2.5 82.7 1.0
CG B:ASP60 2.7 82.7 1.0
HA B:ASP140 2.7 80.9 1.0
OD1 B:ASP60 2.9 82.7 1.0
CG B:ASN61 3.2 77.4 1.0
O B:GLN139 3.2 77.2 1.0
CD B:GLU138 3.2 76.5 1.0
CG B:ASP140 3.3 80.9 1.0
HB2 B:ASP60 3.4 82.7 1.0
O B:ASP60 3.4 82.7 1.0
OE1 B:GLU138 3.6 76.5 1.0
ND2 B:ASN61 3.6 77.4 1.0
CB B:ASP60 3.6 82.7 1.0
CA B:ASP140 3.6 80.9 1.0
C B:ASP60 3.8 82.7 1.0
CB B:ASP140 3.9 80.9 1.0
C B:GLN139 3.9 77.2 1.0
HB3 B:ASP140 4.0 80.9 1.0
N B:ASP140 4.1 80.9 1.0
N B:ASN61 4.3 77.4 1.0
OD2 B:ASP140 4.3 80.9 1.0
CA B:ASP60 4.3 82.7 1.0
HB3 B:ASP60 4.4 82.7 1.0
HD21 B:ASN61 4.4 77.4 1.0
CB B:ASN61 4.4 77.4 1.0
HA B:ASN61 4.5 77.4 1.0
CG B:GLU138 4.5 76.5 1.0
HG2 B:GLU138 4.6 76.5 1.0
CA B:ASN61 4.7 77.4 1.0
CA B:CA301 4.7 73.4 1.0
H B:ASN61 4.7 77.4 1.0
C B:ASP140 4.7 80.9 1.0
H B:ASP140 4.8 80.9 1.0
HB2 B:ASP140 4.8 80.9 1.0
HB2 B:ASN61 4.8 77.4 1.0
HG3 B:GLU138 4.8 76.5 1.0
HD22 B:LEU64 4.8 70.6 1.0
HA B:ASP60 4.9 82.7 1.0
O B:ASP140 5.0 80.9 1.0

Calcium binding site 9 out of 10 in 7pkb

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Calcium binding site 9 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:79.8
occ:1.00
OD1 A:ASP140 2.3 81.5 1.0
OD2 A:ASP140 2.5 81.5 1.0
OE1 A:GLN150 2.5 77.5 1.0
CG A:ASP140 2.7 81.5 1.0
OE1 A:GLU138 3.1 76.6 1.0
HG3 A:GLU147 3.2 84.1 1.0
CD A:GLN150 3.4 77.5 1.0
HB3 A:GLU138 3.4 76.6 1.0
OE1 A:GLU147 3.5 84.1 1.0
HE22 A:GLN150 3.6 77.5 1.0
CD A:GLU147 3.6 84.1 1.0
NE2 A:GLN150 3.8 77.5 1.0
CG A:GLU147 3.9 84.1 1.0
CD A:GLU138 4.0 76.6 1.0
HB2 A:GLU147 4.1 84.1 1.0
OE2 A:GLU147 4.1 84.1 1.0
CB A:ASP140 4.2 81.5 1.0
HG3 A:GLU138 4.3 76.6 1.0
CB A:GLU138 4.3 76.6 1.0
CG A:GLU138 4.4 76.6 1.0
O A:GLU138 4.5 76.6 1.0
CA A:CA302 4.5 82.5 1.0
HG3 A:GLN150 4.5 77.5 1.0
HB2 A:ASP140 4.5 81.5 1.0
CG A:GLN150 4.6 77.5 1.0
CB A:GLU147 4.6 84.1 1.0
HE21 A:GLN150 4.6 77.5 1.0
HG2 A:GLU147 4.7 84.1 1.0
HB3 A:ASP140 4.7 81.5 1.0
HB2 A:GLU138 4.8 76.6 1.0
HB2 A:GLN150 4.9 77.5 1.0
OE2 A:GLU138 5.0 76.6 1.0
HA A:ASP140 5.0 81.5 1.0
N A:ASP140 5.0 81.5 1.0

Calcium binding site 10 out of 10 in 7pkb

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Calcium binding site 10 out of 10 in the C-Reactive Protein Pentamer at pH 7.5


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 Pentamer at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:82.5
occ:1.00
OD1 A:ASN61 2.3 77.2 1.0
O A:GLN139 2.4 76.8 1.0
OD2 A:ASP140 2.5 81.5 1.0
HA A:ASP140 2.6 81.5 1.0
OE1 A:GLU138 2.7 76.6 1.0
OD2 A:ASP60 2.8 81.3 1.0
OE2 A:GLU138 2.9 76.6 1.0
CG A:ASP60 3.0 81.3 1.0
HB2 A:ASP60 3.1 81.3 1.0
CD A:GLU138 3.2 76.6 1.0
CG A:ASN61 3.2 77.2 1.0
C A:GLN139 3.3 76.8 1.0
OD1 A:ASP60 3.4 81.3 1.0
CA A:ASP140 3.5 81.5 1.0
CG A:ASP140 3.6 81.5 1.0
CB A:ASP60 3.6 81.3 1.0
ND2 A:ASN61 3.7 77.2 1.0
N A:ASP140 3.7 81.5 1.0
O A:ASP60 3.9 81.3 1.0
C A:ASP60 4.0 81.3 1.0
CB A:ASP140 4.0 81.5 1.0
HB3 A:ASP140 4.3 81.5 1.0
N A:ASN61 4.3 77.2 1.0
HB3 A:ASP60 4.3 81.3 1.0
CA A:ASP60 4.5 81.3 1.0
HA A:ASN61 4.5 77.2 1.0
HD21 A:ASN61 4.5 77.2 1.0
H A:ASP140 4.5 81.5 1.0
CB A:ASN61 4.5 77.2 1.0
CA A:CA301 4.5 79.8 1.0
C A:ASP140 4.6 81.5 1.0
OD1 A:ASP140 4.6 81.5 1.0
CA A:GLN139 4.6 76.8 1.0
CG A:GLU138 4.7 76.6 1.0
H A:ASN61 4.7 77.2 1.0
CA A:ASN61 4.7 77.2 1.0
HD23 A:LEU64 4.8 70.9 1.0
N A:GLN139 4.8 76.8 1.0
HB2 A:ASN61 4.9 77.2 1.0
HB2 A:ASP140 4.9 81.5 1.0
H A:GLN139 4.9 76.8 1.0
HG3 A:GLU138 5.0 76.6 1.0
O A:ASP140 5.0 81.5 1.0

Reference:

D.P.Noone, T.T.Velden, T.H.Sharp. Cryo-Electron Microscopy and Biochemical Analysis Offer Insights Into the Effects of Acidic pH, Such As Occur During Acidosis, on the Complement Binding Properties of C-Reactive Protein Front Immunol 2021.
ISSN: ESSN 1664-3224
DOI: 10.3389/FIMMU.2021.757633
Page generated: Fri Dec 24 05:21:19 2021

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