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Calcium in PDB 4pbp: Crystal Structure of Zebrafish Short-Chain Pentraxin Protein

Protein crystallography data

The structure of Crystal Structure of Zebrafish Short-Chain Pentraxin Protein, PDB code: 4pbp was solved by R.Chen, J.X.Qi, F.G.George, C.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.14 / 1.65
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 153.623, 153.623, 62.330, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 17.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein (pdb code 4pbp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein, PDB code: 4pbp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4pbp

Go back to Calcium Binding Sites List in 4pbp
Calcium binding site 1 out of 6 in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein


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 Zebrafish Short-Chain Pentraxin Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:24.9
occ:1.00
 O A:HOH489 2.3 28.4 1.0
OE1 A:GLN151 2.4 25.6 1.0
O A:HOH482 2.4 24.5 1.0
OD2 A:ASP139 2.4 23.9 1.0
O A:HOH504 2.4 26.5 1.0
OD2 A:ASP141 2.5 26.4 1.0
OD1 A:ASP141 2.6 25.0 1.0
CG A:ASP141 2.9 25.5 1.0
CD A:GLN151 3.3 27.2 1.0
CG A:ASP139 3.5 22.0 1.0
NE2 A:GLN151 3.6 25.0 1.0
O A:HOH485 3.9 26.2 1.0
O A:HOH610 4.0 50.1 1.0
CA A:CA302 4.1 23.9 1.0
CB A:ASP139 4.1 21.6 1.0
O A:ASP139 4.2 25.1 1.0
CB A:ASP148 4.2 27.6 1.0
CB A:ASP141 4.3 25.7 1.0
OD2 A:ASP148 4.5 30.5 1.0
OD1 A:ASP139 4.6 22.2 1.0
O A:HOH588 4.6 46.6 1.0
CG A:GLN151 4.7 22.9 1.0
CH2 A:TRP65 4.7 22.8 1.0
O A:SER146 4.8 27.3 1.0
C A:ASP139 4.8 24.2 1.0
O A:PRO140 4.9 22.5 1.0
CG A:ASP148 5.0 34.2 1.0

Calcium binding site 2 out of 6 in 4pbp

Go back to Calcium Binding Sites List in 4pbp
Calcium binding site 2 out of 6 in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein


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 Zebrafish Short-Chain Pentraxin Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:23.9
occ:1.00
 O A:PRO140 2.4 22.5 1.0
O A:HOH485 2.4 26.2 1.0
OD1 A:ASP141 2.4 25.0 1.0
O A:HOH484 2.5 26.5 1.0
OD1 A:ASP60 2.5 24.8 1.0
OD1 A:ASP139 2.5 22.2 1.0
OD2 A:ASP139 2.5 23.9 1.0
OD2 A:ASP60 2.6 25.6 1.0
CG A:ASP139 2.8 22.0 1.0
CG A:ASP60 2.9 23.7 1.0
C A:PRO140 3.5 23.6 1.0
CG A:ASP141 3.7 25.5 1.0
CA A:ASP141 4.0 24.5 1.0
CA A:CA301 4.1 24.9 1.0
N A:ASP141 4.1 24.3 1.0
CB A:ASP139 4.3 21.6 1.0
OG A:SER79 4.3 29.1 0.6
O A:HOH504 4.4 26.5 1.0
CB A:ASP60 4.4 22.1 1.0
CB A:ASP141 4.4 25.7 1.0
ND2 A:ASN63 4.5 24.2 1.0
N A:PRO140 4.5 21.1 1.0
C A:ASP139 4.5 24.2 1.0
O A:HOH572 4.6 54.0 1.0
OD2 A:ASP141 4.6 26.4 1.0
O A:HOH493 4.6 24.4 1.0
CA A:PRO140 4.6 22.5 1.0
O A:HOH535 4.6 35.5 1.0
CZ2 A:TRP65 4.7 24.0 1.0
O A:ASP139 4.7 25.1 1.0
CE1 A:TYR55 4.8 26.9 1.0
O3 A:GOL304 4.8 31.8 1.0
O A:HOH645 4.9 53.6 1.0
CD1 A:TYR55 4.9 23.3 1.0
CA A:ASP139 4.9 23.8 1.0
O A:HOH497 5.0 22.8 1.0

Calcium binding site 3 out of 6 in 4pbp

Go back to Calcium Binding Sites List in 4pbp
Calcium binding site 3 out of 6 in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein


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 Zebrafish Short-Chain Pentraxin Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:22.7
occ:1.00
 OD2 B:ASP139 2.4 22.4 1.0
O B:HOH492 2.4 26.6 1.0
OE1 B:GLN151 2.4 22.2 1.0
O B:HOH494 2.4 27.3 1.0
O B:HOH478 2.4 22.1 1.0
OD2 B:ASP141 2.4 25.0 1.0
OD1 B:ASP141 2.6 22.6 1.0
CG B:ASP141 2.8 24.1 1.0
CD B:GLN151 3.4 20.0 1.0
CG B:ASP139 3.5 21.7 1.0
NE2 B:GLN151 3.7 23.2 1.0
O B:HOH483 3.8 24.3 1.0
CA B:CA302 4.0 21.5 1.0
CB B:ASP139 4.1 20.1 1.0
O B:ASP139 4.2 23.0 1.0
CB B:ASP141 4.3 24.7 1.0
CB B:ASP148 4.3 25.9 1.0
OD1 B:ASP139 4.5 20.2 1.0
OD2 B:ASP148 4.6 29.6 1.0
O B:HOH634 4.6 57.0 1.0
O B:HOH543 4.6 37.7 1.0
CG B:GLN151 4.7 21.7 1.0
CH2 B:TRP65 4.8 21.7 1.0
O B:SER146 4.8 23.9 1.0
C B:ASP139 4.9 20.9 1.0
O B:PRO140 4.9 21.7 1.0

Calcium binding site 4 out of 6 in 4pbp

Go back to Calcium Binding Sites List in 4pbp
Calcium binding site 4 out of 6 in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein


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 Zebrafish Short-Chain Pentraxin Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:21.5
occ:1.00
 O B:PRO140 2.4 21.7 1.0
OD1 B:ASP141 2.4 22.6 1.0
O B:HOH486 2.5 23.7 1.0
O B:HOH483 2.5 24.3 1.0
OD1 B:ASP139 2.5 20.2 1.0
OD1 B:ASP60 2.5 22.2 1.0
OD2 B:ASP60 2.5 23.0 1.0
OD2 B:ASP139 2.5 22.4 1.0
CG B:ASP139 2.8 21.7 1.0
CG B:ASP60 2.9 22.3 1.0
C B:PRO140 3.5 22.7 1.0
CG B:ASP141 3.6 24.1 1.0
CA B:ASP141 4.0 23.2 1.0
CA B:CA301 4.0 22.7 1.0
N B:ASP141 4.2 22.7 1.0
OG B:SER79 4.2 35.1 1.0
CB B:ASP139 4.3 20.1 1.0
CB B:ASP60 4.4 18.6 1.0
O B:HOH492 4.4 26.6 1.0
CB B:ASP141 4.4 24.7 1.0
N B:PRO140 4.5 22.0 1.0
ND2 B:ASN63 4.5 21.1 1.0
C B:ASP139 4.5 20.9 1.0
OD2 B:ASP141 4.6 25.0 1.0
O B:HOH480 4.6 21.9 1.0
O B:HOH548 4.6 42.5 1.0
CA B:PRO140 4.7 21.8 1.0
O B:HOH405 4.7 32.8 1.0
O B:ASP139 4.8 23.0 1.0
CZ2 B:TRP65 4.8 22.1 1.0
O1 B:GOL303 4.9 44.0 1.0
CA B:ASP139 4.9 20.3 1.0
O B:HOH479 4.9 22.7 1.0
CD1 B:TYR55 5.0 21.0 1.0

Calcium binding site 5 out of 6 in 4pbp

Go back to Calcium Binding Sites List in 4pbp
Calcium binding site 5 out of 6 in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein


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 Zebrafish Short-Chain Pentraxin Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:28.4
occ:1.00
 O C:HOH435 2.4 30.5 1.0
OD2 C:ASP139 2.4 25.9 1.0
O C:HOH439 2.4 30.0 1.0
O C:HOH438 2.4 30.4 1.0
OD2 C:ASP141 2.4 29.9 1.0
OE1 C:GLN151 2.4 28.2 1.0
OD1 C:ASP141 2.6 27.7 1.0
CG C:ASP141 2.8 29.3 1.0
CD C:GLN151 3.4 28.6 1.0
CG C:ASP139 3.5 22.8 1.0
NE2 C:GLN151 3.8 28.4 1.0
O C:HOH443 3.8 32.8 1.0
CA C:CA302 4.0 27.2 1.0
CB C:ASP139 4.1 23.9 1.0
O C:ASP139 4.1 27.9 1.0
CB C:ASP148 4.2 31.0 1.0
CB C:ASP141 4.3 29.4 1.0
O C:HOH616 4.3 61.8 1.0
OD1 C:ASP139 4.5 24.2 1.0
OD2 C:ASP148 4.5 36.7 1.0
O C:HOH411 4.5 39.2 1.0
CH2 C:TRP65 4.7 26.9 1.0
CG C:GLN151 4.7 26.7 1.0
O C:SER146 4.8 31.3 1.0
C C:ASP139 4.8 26.1 1.0
O C:PRO140 4.9 26.4 1.0
CG C:ASP148 4.9 32.9 1.0

Calcium binding site 6 out of 6 in 4pbp

Go back to Calcium Binding Sites List in 4pbp
Calcium binding site 6 out of 6 in the Crystal Structure of Zebrafish Short-Chain Pentraxin Protein


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 Zebrafish Short-Chain Pentraxin Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:27.2
occ:1.00
 OD1 C:ASP141 2.4 27.7 1.0
O C:HOH433 2.4 30.0 1.0
O C:HOH443 2.4 32.8 1.0
OD1 C:ASP139 2.4 24.2 1.0
O C:PRO140 2.5 26.4 1.0
OD1 C:ASP60 2.5 27.5 1.0
OD2 C:ASP60 2.6 28.4 1.0
OD2 C:ASP139 2.6 25.9 1.0
CG C:ASP139 2.8 22.8 1.0
CG C:ASP60 2.9 26.9 1.0
C C:PRO140 3.5 29.6 1.0
CG C:ASP141 3.6 29.3 1.0
CA C:CA301 4.0 28.4 1.0
CA C:ASP141 4.1 31.2 1.0
N C:ASP141 4.2 27.9 1.0
O C:HOH438 4.2 30.4 1.0
O C:HOH565 4.3 56.9 1.0
CB C:ASP139 4.3 23.9 1.0
OG C:SER79 4.4 41.6 1.0
CB C:ASP60 4.4 25.2 1.0
CB C:ASP141 4.4 29.4 1.0
C C:ASP139 4.5 26.1 1.0
ND2 C:ASN63 4.5 26.2 1.0
N C:PRO140 4.5 25.2 1.0
OD2 C:ASP141 4.6 29.9 1.0
O C:HOH489 4.6 39.0 1.0
O C:HOH442 4.6 25.9 1.0
CA C:PRO140 4.7 25.9 1.0
O C:HOH589 4.7 50.6 1.0
O C:ASP139 4.7 27.9 1.0
CZ2 C:TRP65 4.7 26.3 1.0
CA C:ASP139 4.9 22.9 1.0
CE1 C:TYR55 4.9 32.1 1.0
CD1 C:TYR55 5.0 25.0 1.0

Reference:

R.Chen, J.Qi, H.Yuan, Y.Wu, W.Hu, C.Xia. Crystal Structures For Short-Chain Pentraxin From Zebrafish Demonstrate A Cyclic Trimer with New Recognition and Effector Faces. J.Struct.Biol. V. 189 259 2015.
ISSN: ESSN 1095-8657
PubMed: 25592778
DOI: 10.1016/J.JSB.2015.01.001
Page generated: Wed Jul 9 01:16:09 2025

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