Calcium in PDB 6ype: Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain.

The structure of Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain., PDB code: 6ype was solved by J.Elegheert, A.J.Clayton, A.R.Aricescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.69 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.220, 36.060, 92.170, 90.00, 97.47, 90.00
R / Rfree (%)	15.3 / 17.8

The structure of Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain. also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain. (pdb code 6ype). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain., PDB code: 6ype:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain.


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 the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:9.0 occ:1.00 O A:GLN359 2.3 8.8 1.0 O2 A:CAC502 2.3 21.0 1.0 OD1 A:ASN280 2.3 10.0 1.0 OE1 A:GLU358 2.4 9.8 1.0 OD1 A:ASP360 2.4 9.6 1.0 O A:HOH746 2.4 13.1 1.0 OE2 A:GLU358 2.6 9.6 1.0 CD A:GLU358 2.8 12.7 1.0 CG A:ASN280 3.3 7.7 1.0 C A:GLN359 3.3 9.6 1.0 ND2 A:ASN280 3.6 10.2 1.0 CG A:ASP360 3.6 9.5 1.0 AS A:CAC502 3.6 20.5 1.0 O1 A:CAC502 3.8 21.0 1.0 CA A:ASP360 3.8 7.7 1.0 CA A:CA501 3.8 9.0 1.0 N A:ASP360 3.9 8.8 1.0 O A:HOH675 4.0 9.1 1.0 CB A:ASP360 4.3 10.9 1.0 CG A:GLU358 4.3 8.6 1.0 C1 A:CAC502 4.4 20.7 1.0 N A:GLN359 4.4 8.7 1.0 CA A:GLN359 4.5 8.9 1.0 CB A:ALA279 4.5 8.8 1.0 OD2 A:ASP360 4.5 11.5 1.0 CB A:ASN280 4.7 7.8 1.0 O A:ALA279 4.7 9.3 1.0 O A:HOH669 4.7 19.8 1.0 C A:ALA279 4.8 8.8 1.0 O A:HOH654 4.8 29.1 1.0 N A:ASN280 4.9 9.6 1.0 O A:HOH763 4.9 35.5 1.0 O A:HOH624 5.0 10.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain.


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 the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:9.0 occ:1.00 O1 A:CAC502 2.2 21.0 1.0 OE2 A:GLU358 2.3 9.6 1.0 OE1 A:GLN370 2.4 9.4 1.0 O A:HOH635 2.4 14.5 1.0 O A:HOH624 2.4 10.4 1.0 OD2 A:ASP360 2.5 11.5 1.0 OD1 A:ASP360 2.6 9.6 1.0 CG A:ASP360 2.9 9.5 1.0 CD A:GLN370 3.3 12.7 1.0 CD A:GLU358 3.5 12.7 1.0 NE2 A:GLN370 3.6 13.0 1.0 AS A:CAC502 3.7 20.5 1.0 CA A:CA500 3.8 9.0 1.0 CB A:ASP367 4.1 9.3 1.0 O2 A:CAC502 4.2 21.0 1.0 CG A:GLU358 4.3 8.6 1.0 CB A:ASP360 4.3 10.9 1.0 CB A:GLU358 4.3 8.2 1.0 OE1 A:GLU358 4.4 9.8 1.0 O A:GLY365 4.5 13.5 1.0 OD2 A:ASP367 4.5 15.5 1.0 O A:GLU358 4.5 10.3 1.0 O A:HOH767 4.6 44.8 1.0 CG A:GLN370 4.7 8.8 1.0 O A:GLN359 4.7 8.8 1.0 C1 A:CAC502 4.7 20.7 1.0 C A:GLU358 4.8 8.9 1.0 C A:GLN359 4.8 9.6 1.0 N A:ASP360 4.8 8.8 1.0 O A:HOH642 4.9 19.5 1.0 CG A:ASP367 4.9 16.7 1.0 CA A:ASP360 5.0 7.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain.


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 the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:9.6 occ:1.00 O B:GLN359 2.3 10.7 1.0 O1 B:CAC502 2.3 16.0 1.0 OD1 B:ASP360 2.3 11.0 1.0 OD1 B:ASN280 2.4 8.7 1.0 O B:HOH748 2.4 11.5 1.0 OE2 B:GLU358 2.4 9.7 1.0 OE1 B:GLU358 2.5 9.9 1.0 CD B:GLU358 2.8 8.6 1.0 C B:GLN359 3.3 9.8 1.0 CG B:ASN280 3.4 9.3 1.0 CG B:ASP360 3.6 8.8 1.0 AS B:CAC502 3.6 15.8 1.0 ND2 B:ASN280 3.7 10.8 1.0 CA B:ASP360 3.8 9.5 1.0 CA B:CA501 3.8 11.1 1.0 N B:ASP360 3.9 9.3 1.0 O2 B:CAC502 3.9 15.9 1.0 O B:HOH677 4.0 8.5 1.0 CB B:ASP360 4.3 13.2 1.0 CG B:GLU358 4.3 10.4 1.0 C2 B:CAC502 4.3 15.8 1.0 O B:HOH700 4.4 24.7 1.0 N B:GLN359 4.4 7.0 1.0 CA B:GLN359 4.5 6.5 1.0 OD2 B:ASP360 4.5 10.8 1.0 CB B:ALA279 4.6 10.2 1.0 O B:HOH647 4.6 35.6 1.0 O B:ALA279 4.7 8.6 1.0 O B:HOH683 4.7 15.2 1.0 CB B:ASN280 4.7 7.0 1.0 C B:ALA279 4.8 8.5 1.0 N B:ASN280 4.9 7.3 1.0 O B:HOH646 4.9 9.2 1.0 C B:GLU358 5.0 7.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain.


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 the Human Neuronal Pentraxin 1 (NP1) Pentraxin (Ptx) Domain. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:11.1 occ:1.00 O2 B:CAC502 2.3 15.9 1.0 OE1 B:GLU358 2.3 9.9 1.0 O B:HOH640 2.4 12.9 1.0 O B:HOH646 2.4 9.2 1.0 OE1 B:GLN370 2.4 10.8 1.0 OD1 B:ASP360 2.5 11.0 1.0 OD2 B:ASP360 2.6 10.8 1.0 CG B:ASP360 2.9 8.8 1.0 CD B:GLN370 3.3 11.9 1.0 CD B:GLU358 3.5 8.6 1.0 NE2 B:GLN370 3.6 14.2 1.0 AS B:CAC502 3.7 15.8 1.0 CA B:CA500 3.8 9.6 1.0 O B:HOH638 4.1 21.9 1.0 O1 B:CAC502 4.1 16.0 1.0 CB B:ASP367 4.1 11.3 1.0 CG B:GLU358 4.3 10.4 1.0 CB B:ASP360 4.3 13.2 1.0 CB B:GLU358 4.3 9.6 1.0 OE2 B:GLU358 4.4 9.7 1.0 OD2 B:ASP367 4.5 16.0 1.0 O B:GLU358 4.5 7.9 1.0 O B:GLY365 4.6 11.7 1.0 C2 B:CAC502 4.6 15.8 1.0 CG B:GLN370 4.7 10.4 1.0 O B:GLN359 4.8 10.7 1.0 C B:GLU358 4.8 7.1 1.0 C B:GLN359 4.8 9.8 1.0 N B:ASP360 4.8 9.3 1.0 CG B:ASP367 4.9 17.9 1.0 O B:HOH635 4.9 20.9 1.0 CA B:ASP360 5.0 9.5 1.0

K.Suzuki, J.Elegheert, I.Song, H.Sasakura, O.Senkov, W.Kakegawa, A.J.Clayton, V.T.Chang, M.Ferrer-Ferrer, E.Miura, R.Kaushik, M.Ikeno, Y.Morioka, Y.Takeuchi, T.Shimada, S.Otsuka, S.Stoyanov, M.Watanabe, K.Takeuchi, A.Dityatev, A.R.Aricescu, M.Yuzaki. A Synthetic Synaptic Organizer Protein Restores Glutamatergic Neuronal Circuits. To Be Published.