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Calcium in PDB 3flp: Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus

Protein crystallography data

The structure of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus, PDB code: 3flp was solved by A.K.Shrive, T.J.Greenhough, P.B.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.27 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.320, 167.560, 140.870, 90.00, 92.50, 90.00
R / Rfree (%) 20.1 / 22.3

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus (pdb code 3flp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 28 binding sites of Calcium where determined in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus, PDB code: 3flp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 28 in 3flp

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Calcium binding site 1 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:11.9
occ:1.00
 OD1 A:ASN60 2.3 12.0 1.0
O A:HOH228 2.3 3.6 1.0
O A:GLN146 2.4 9.2 1.0
OD2 A:ASP59 2.4 14.9 1.0
OD1 A:ASP147 2.4 12.8 1.0
OE1 A:GLU145 2.5 12.0 1.0
OE2 A:GLU145 2.6 12.9 1.0
CD A:GLU145 2.9 12.3 1.0
CG A:ASN60 3.3 12.7 1.0
C A:GLN146 3.4 10.7 1.0
CG A:ASP59 3.5 16.3 1.0
ND2 A:ASN60 3.6 8.5 1.0
CG A:ASP147 3.6 11.8 1.0
CA A:ASP147 3.7 13.3 1.0
CA A:CA302 3.9 15.1 1.0
N A:ASP147 3.9 11.9 1.0
CB A:ASP59 4.2 14.4 1.0
O A:HOH237 4.2 8.4 1.0
CB A:ASP147 4.2 12.2 1.0
O A:HOH604 4.3 13.1 1.0
O A:ASP59 4.3 12.0 1.0
OD1 A:ASP59 4.4 16.7 1.0
CG A:GLU145 4.4 10.7 1.0
C A:ASP59 4.5 13.8 1.0
OD2 A:ASP147 4.6 13.0 1.0
CA A:GLN146 4.6 10.0 1.0
N A:GLN146 4.6 10.1 1.0
CB A:ASN60 4.7 11.5 1.0
N A:ASN60 4.9 11.9 1.0
C A:GLU145 4.9 9.8 1.0
C A:ASP147 4.9 14.2 1.0

Calcium binding site 2 out of 28 in 3flp

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Calcium binding site 2 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:15.1
occ:1.00
 OE1 A:GLU154 2.3 20.9 1.0
O A:HOH604 2.4 13.1 1.0
O A:HOH221 2.4 6.3 1.0
OE1 A:GLU157 2.4 18.4 1.0
OD2 A:ASP147 2.4 13.0 1.0
OE1 A:GLU145 2.5 12.0 1.0
OD1 A:ASP147 2.6 12.8 1.0
CG A:ASP147 2.8 11.8 1.0
CD A:GLU154 3.4 24.0 1.0
CD A:GLU157 3.4 18.0 1.0
O A:HOH228 3.6 3.6 1.0
CD A:GLU145 3.7 12.3 1.0
OE2 A:GLU157 3.7 20.9 1.0
CA A:CA301 3.9 11.9 1.0
CG A:GLU154 3.9 23.4 1.0
O A:GLU145 4.2 11.0 1.0
CB A:ASP147 4.2 12.2 1.0
O A:GLY152 4.4 13.6 1.0
CB A:GLU145 4.4 10.0 1.0
CB A:GLU154 4.4 19.5 1.0
CG A:GLU145 4.4 10.7 1.0
OE2 A:GLU154 4.4 25.3 1.0
OE2 A:GLU145 4.7 12.9 1.0
CG A:GLU157 4.7 17.3 1.0
O A:HOH781 4.8 14.8 1.0
C A:GLU145 4.8 9.8 1.0
O A:GLN146 4.9 9.2 1.0
CA A:ASP147 4.9 13.3 1.0
N A:ASP147 4.9 11.9 1.0
C A:GLN146 5.0 10.7 1.0

Calcium binding site 3 out of 28 in 3flp

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Calcium binding site 3 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:15.5
occ:1.00
 OD2 B:ASP59 2.3 16.0 1.0
OD1 B:ASN60 2.4 16.1 1.0
OD1 B:ASP147 2.4 11.9 1.0
O B:GLN146 2.4 14.0 1.0
OE2 B:GLU145 2.6 14.8 1.0
OE1 B:GLU145 2.6 8.2 1.0
CD B:GLU145 3.0 13.3 1.0
CG B:ASP59 3.4 17.8 1.0
C B:GLN146 3.4 13.6 1.0
CG B:ASN60 3.4 16.2 1.0
CG B:ASP147 3.6 12.9 1.0
CA B:ASP147 3.7 15.1 1.0
ND2 B:ASN60 3.8 14.6 1.0
CA B:CA302 3.8 17.6 1.0
N B:ASP147 3.9 13.5 1.0
CB B:ASP59 4.1 17.4 1.0
CB B:ASP147 4.2 12.5 1.0
OD1 B:ASP59 4.3 17.9 1.0
O B:ASP59 4.3 16.6 1.0
CG B:GLU145 4.5 12.3 1.0
C B:ASP59 4.5 16.0 1.0
O B:HOH234 4.5 7.2 1.0
OD2 B:ASP147 4.6 12.5 1.0
CA B:GLN146 4.6 13.4 1.0
N B:GLN146 4.7 12.8 1.0
CB B:ASN60 4.8 14.3 1.0
N B:ASN60 4.9 14.4 1.0
C B:ASP147 4.9 16.6 1.0
C B:GLU145 5.0 12.3 1.0

Calcium binding site 4 out of 28 in 3flp

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Calcium binding site 4 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:17.6
occ:1.00
 O B:HOH236 2.3 15.6 1.0
OD1 B:ASP147 2.4 11.9 1.0
OE1 B:GLU157 2.4 19.9 1.0
OE1 B:GLU145 2.4 8.2 1.0
OD2 B:ASP147 2.5 12.5 1.0
OE1 B:GLU154 2.6 24.0 1.0
CG B:ASP147 2.7 12.9 1.0
CD B:GLU157 3.4 20.0 1.0
CD B:GLU145 3.6 13.3 1.0
CD B:GLU154 3.7 25.6 1.0
OE2 B:GLU157 3.7 21.7 1.0
CA B:CA301 3.8 15.5 1.0
O B:GLU145 4.1 14.3 1.0
CG B:GLU154 4.1 23.3 1.0
CB B:ASP147 4.2 12.5 1.0
O B:GLY152 4.3 13.8 1.0
CB B:GLU145 4.3 12.6 1.0
CG B:GLU145 4.4 12.3 1.0
CB B:GLU154 4.5 19.3 1.0
OE2 B:GLU145 4.6 14.8 1.0
C B:GLU145 4.7 12.3 1.0
CG B:GLU157 4.7 17.8 1.0
O B:GLN146 4.8 14.0 1.0
CA B:ASP147 4.8 15.1 1.0
OE2 B:GLU154 4.8 28.6 1.0
N B:ASP147 4.8 13.5 1.0
C B:GLN146 4.8 13.6 1.0

Calcium binding site 5 out of 28 in 3flp

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Calcium binding site 5 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:12.3
occ:1.00
 OD1 C:ASN60 2.3 11.5 1.0
O C:GLN146 2.4 12.7 1.0
OD2 C:ASP59 2.4 13.5 1.0
O C:HOH520 2.4 10.9 1.0
OD1 C:ASP147 2.5 17.6 1.0
OE1 C:GLU145 2.6 6.5 1.0
OE2 C:GLU145 2.6 10.0 1.0
CD C:GLU145 2.9 9.0 1.0
CG C:ASN60 3.3 11.0 1.0
C C:GLN146 3.4 11.8 1.0
CG C:ASP59 3.5 14.4 1.0
CA C:ASP147 3.7 15.4 1.0
ND2 C:ASN60 3.7 10.2 1.0
CG C:ASP147 3.7 15.8 1.0
CA C:CA302 3.9 12.6 1.0
N C:ASP147 3.9 14.0 1.0
CB C:ASP59 4.1 13.0 1.0
O C:HOH644 4.1 7.7 1.0
O C:HOH219 4.2 6.2 1.0
O C:ASP59 4.2 13.8 1.0
CB C:ASP147 4.3 15.3 1.0
C C:ASP59 4.4 13.7 1.0
OD1 C:ASP59 4.4 15.6 1.0
CG C:GLU145 4.5 7.9 1.0
CA C:GLN146 4.6 11.2 1.0
N C:GLN146 4.6 9.7 1.0
CB C:ASN60 4.7 10.8 1.0
OD2 C:ASP147 4.7 16.6 1.0
N C:ASN60 4.8 12.2 1.0
C C:ASP147 4.9 15.5 1.0
CA C:ASP59 4.9 14.3 1.0
C C:GLU145 4.9 9.9 1.0
CA C:ASN60 5.0 10.7 1.0

Calcium binding site 6 out of 28 in 3flp

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Calcium binding site 6 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:12.6
occ:1.00
 O C:HOH644 2.2 7.7 1.0
O C:HOH674 2.2 13.2 1.0
OE1 C:GLU154 2.3 23.5 1.0
OE1 C:GLU157 2.3 13.0 1.0
OD1 C:ASP147 2.4 17.6 1.0
OE1 C:GLU145 2.5 6.5 1.0
OD2 C:ASP147 2.7 16.6 1.0
CG C:ASP147 2.8 15.8 1.0
CD C:GLU154 3.3 24.1 1.0
CD C:GLU157 3.3 13.2 1.0
OE2 C:GLU157 3.6 13.8 1.0
CD C:GLU145 3.7 9.0 1.0
O C:HOH520 3.7 10.9 1.0
CG C:GLU154 3.9 22.7 1.0
CA C:CA301 3.9 12.3 1.0
O C:GLU145 4.2 10.7 1.0
CB C:ASP147 4.3 15.3 1.0
OE2 C:GLU154 4.3 27.7 1.0
CB C:GLU145 4.4 7.8 1.0
CG C:GLU145 4.4 7.9 1.0
O C:GLY152 4.4 12.3 1.0
CB C:GLU154 4.5 20.0 1.0
OE2 C:GLU145 4.6 10.0 1.0
CG C:GLU157 4.7 12.2 1.0
C C:GLU145 4.8 9.9 1.0
O C:GLN146 4.8 12.7 1.0
CA C:ASP147 4.9 15.4 1.0
N C:ASP147 4.9 14.0 1.0
C C:GLN146 5.0 11.8 1.0

Calcium binding site 7 out of 28 in 3flp

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Calcium binding site 7 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:14.9
occ:1.00
 O D:GLN146 2.3 12.1 1.0
OD1 D:ASN60 2.4 16.2 1.0
OE1 D:GLU145 2.4 5.9 1.0
O D:HOH624 2.4 12.4 1.0
OD1 D:ASP147 2.5 12.4 1.0
OD2 D:ASP59 2.5 14.5 1.0
OE2 D:GLU145 2.5 6.0 1.0
CD D:GLU145 2.8 6.7 1.0
C D:GLN146 3.3 10.9 1.0
CG D:ASN60 3.4 15.8 1.0
CG D:ASP59 3.5 15.9 1.0
CG D:ASP147 3.6 12.6 1.0
CA D:ASP147 3.7 14.2 1.0
CA D:CA302 3.8 13.3 1.0
ND2 D:ASN60 3.8 12.5 1.0
N D:ASP147 3.9 11.3 1.0
CB D:ASP59 4.1 14.4 1.0
O D:ASP59 4.2 13.2 1.0
CB D:ASP147 4.2 12.1 1.0
O D:HOH814 4.3 22.4 1.0
CG D:GLU145 4.3 8.4 1.0
O D:HOH225 4.4 7.2 1.0
C D:ASP59 4.4 13.3 1.0
OD1 D:ASP59 4.5 15.6 1.0
CA D:GLN146 4.5 10.4 1.0
N D:GLN146 4.6 9.1 1.0
OD2 D:ASP147 4.6 14.0 1.0
CB D:ASN60 4.8 12.5 1.0
N D:ASN60 4.8 12.0 1.0
C D:ASP147 4.9 14.9 1.0
C D:GLU145 4.9 10.1 1.0
CA D:ASP59 5.0 13.9 1.0
CA D:ASN60 5.0 11.6 1.0

Calcium binding site 8 out of 28 in 3flp

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Calcium binding site 8 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:13.3
occ:1.00
 OE1 D:GLU154 2.2 13.0 1.0
OE1 D:GLU157 2.4 18.3 1.0
O D:HOH230 2.4 9.9 1.0
OD1 D:ASP147 2.4 12.4 1.0
OE1 D:GLU145 2.4 5.9 1.0
O D:HOH814 2.5 22.4 1.0
OD2 D:ASP147 2.5 14.0 1.0
CG D:ASP147 2.8 12.6 1.0
CD D:GLU154 3.3 14.6 1.0
CD D:GLU157 3.4 18.2 1.0
O D:HOH624 3.6 12.4 1.0
CD D:GLU145 3.6 6.7 1.0
OE2 D:GLU157 3.8 21.5 1.0
CA D:CA301 3.8 14.9 1.0
CG D:GLU154 4.0 16.2 1.0
CB D:ASP147 4.2 12.1 1.0
OE2 D:GLU154 4.2 16.7 1.0
O D:GLU145 4.3 11.7 1.0
CG D:GLU145 4.3 8.4 1.0
CB D:GLU145 4.4 8.7 1.0
O D:GLY152 4.5 13.7 1.0
OE2 D:GLU145 4.6 6.0 1.0
CB D:GLU154 4.6 15.8 1.0
CG D:GLU157 4.7 16.9 1.0
O D:GLN146 4.7 12.1 1.0
C D:GLU145 4.8 10.1 1.0
CA D:ASP147 4.8 14.2 1.0
C D:GLN146 4.9 10.9 1.0
N D:ASP147 4.9 11.3 1.0

Calcium binding site 9 out of 28 in 3flp

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Calcium binding site 9 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:10.0
occ:1.00
 O E:HOH223 2.3 6.1 1.0
OD1 E:ASN60 2.4 9.3 1.0
O E:GLN146 2.4 11.0 1.0
OD1 E:ASP147 2.4 11.5 1.0
OE2 E:GLU145 2.4 15.2 1.0
OD2 E:ASP59 2.5 11.8 1.0
OE1 E:GLU145 2.5 14.0 1.0
CD E:GLU145 2.8 14.8 1.0
CG E:ASN60 3.3 11.3 1.0
C E:GLN146 3.4 11.5 1.0
CG E:ASP59 3.6 14.7 1.0
CG E:ASP147 3.6 11.8 1.0
ND2 E:ASN60 3.7 9.1 1.0
CA E:ASP147 3.7 14.2 1.0
CA E:CA302 3.9 18.7 1.0
N E:ASP147 3.9 12.4 1.0
O E:HOH588 4.1 19.4 1.0
CB E:ASP59 4.2 13.8 1.0
CB E:ASP147 4.2 11.9 1.0
O E:ASP59 4.3 12.7 1.0
O E:HOH220 4.3 1.6 1.0
CG E:GLU145 4.3 12.1 1.0
OD1 E:ASP59 4.5 15.2 1.0
C E:ASP59 4.5 13.5 1.0
OD2 E:ASP147 4.6 9.7 1.0
CA E:GLN146 4.6 11.1 1.0
N E:GLN146 4.7 10.9 1.0
CB E:ASN60 4.7 11.3 1.0
N E:ASN60 4.9 12.3 1.0
C E:ASP147 4.9 14.5 1.0
C E:GLU145 4.9 11.9 1.0

Calcium binding site 10 out of 28 in 3flp

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Calcium binding site 10 out of 28 in the Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Native Heptameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:18.7
occ:1.00
 OE2 E:GLU154 2.4 22.4 1.0
OE1 E:GLU157 2.4 17.2 1.0
OE1 E:GLU145 2.4 14.0 1.0
OD1 E:ASP147 2.4 11.5 1.0
OD2 E:ASP147 2.4 9.7 1.0
O E:HOH588 2.6 19.4 1.0
CG E:ASP147 2.7 11.8 1.0
CD E:GLU154 3.3 24.5 1.0
CD E:GLU157 3.4 17.8 1.0
CD E:GLU145 3.6 14.8 1.0
CG E:GLU154 3.7 23.4 1.0
OE2 E:GLU157 3.8 18.5 1.0
CA E:CA301 3.9 10.0 1.0
O E:HOH223 3.9 6.1 1.0
O E:GLU145 4.0 13.7 1.0
CB E:ASP147 4.1 11.9 1.0
O E:GLY152 4.2 12.1 1.0
CB E:GLU145 4.3 11.1 1.0
CB E:GLU154 4.4 19.0 1.0
CG E:GLU145 4.4 12.1 1.0
OE1 E:GLU154 4.5 27.4 1.0
OE2 E:GLU145 4.5 15.2 1.0
C E:GLU145 4.6 11.9 1.0
CG E:GLU157 4.7 16.3 1.0
N E:ASP147 4.8 12.4 1.0
O E:GLN146 4.8 11.0 1.0
CA E:ASP147 4.8 14.2 1.0
C E:GLN146 4.8 11.5 1.0
N E:GLU154 5.0 16.6 1.0

Reference:

A.K.Shrive, I.Burns, H.T.Chou, H.Stahlberg, P.B.Armstrong, T.J.Greenhough. Crystal Structures of Limulus Sap-Like Pentraxin Reveal Two Molecular Aggregations. J.Mol.Biol. V. 386 1240 2009.
ISSN: ISSN 0022-2836
PubMed: 19452596
Page generated: Sat Jul 13 10:10:38 2024

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