Calcium in PDB 7kbu: Structure of Hevin Fs-Ec

The structure of Structure of Hevin Fs-Ec, PDB code: 7kbu was solved by M.Machius, S.Fan, G.Rudenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 2.27
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.657, 132.289, 149.225, 90, 90, 90
R / Rfree (%)	18.7 / 23.8

The structure of Structure of Hevin Fs-Ec also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Structure of Hevin Fs-Ec (pdb code 7kbu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Hevin Fs-Ec, PDB code: 7kbu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Hevin Fs-Ec


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Hevin Fs-Ec within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:33.6 occ:1.00 OD1 A:ASP600 2.2 33.0 1.0 O A:HOH861 2.3 35.7 1.0 O A:VAL607 2.3 32.3 1.0 OE2 A:GLU612 2.3 32.4 1.0 O A:PRO603 2.4 44.6 1.0 OD1 A:ASP605 2.5 35.6 1.0 OE1 A:GLU612 2.5 26.5 1.0 CD A:GLU612 2.8 30.3 1.0 H A:ASP605 3.4 49.0 1.0 CG A:ASP605 3.4 35.6 1.0 HA A:ASP600 3.4 33.2 1.0 CG A:ASP600 3.5 34.7 1.0 C A:VAL607 3.5 31.2 1.0 HA A:LEU608 3.6 28.9 1.0 HD2 A:PRO603 3.6 49.7 1.0 H A:VAL607 3.6 34.9 1.0 C A:PRO603 3.7 43.1 1.0 OD2 A:ASP605 3.8 40.8 1.0 HA A:MET604 3.8 55.5 1.0 HG22 A:VAL607 3.9 37.5 1.0 N A:ASP605 3.9 40.7 1.0 H A:HIS602 4.0 53.6 1.0 HD23 A:LEU608 4.0 27.8 1.0 CA A:ASP600 4.1 27.5 1.0 HG23 A:VAL607 4.2 37.5 1.0 CB A:ASP600 4.3 32.8 1.0 CG A:GLU612 4.3 34.5 1.0 N A:PRO603 4.3 41.8 1.0 N A:VAL607 4.3 29.2 1.0 OD2 A:ASP600 4.3 35.4 1.0 CD A:PRO603 4.4 41.3 1.0 CA A:LEU608 4.4 24.6 1.0 N A:LEU608 4.4 25.9 1.0 H A:THR609 4.4 32.0 1.0 C A:ASP600 4.4 36.4 1.0 H A:GLN601 4.4 44.1 1.0 HB2 A:ASP600 4.5 39.5 1.0 CA A:MET604 4.5 46.1 1.0 CG2 A:VAL607 4.5 31.2 1.0 HG23 A:THR609 4.5 36.0 1.0 N A:MET604 4.5 43.0 1.0 CA A:VAL607 4.5 28.0 1.0 CB A:ASP605 4.6 45.2 1.0 N A:GLN601 4.6 36.6 1.0 HG3 A:GLU612 4.6 41.6 1.0 CA A:PRO603 4.6 36.8 1.0 H A:ARG606 4.6 49.3 1.0 C A:MET604 4.6 46.0 1.0 O A:HOH804 4.7 43.4 1.0 HG2 A:GLU612 4.7 41.6 1.0 CA A:ASP605 4.7 40.5 1.0 N A:HIS602 4.7 44.5 1.0 C A:HIS602 4.7 40.2 1.0 HG2 A:PRO603 4.8 55.6 1.0 HB3 A:ASP605 4.9 54.4 1.0 N A:ARG606 4.9 41.0 1.0 N A:THR609 4.9 26.6 1.0 O A:ASP600 4.9 38.2 1.0 C A:ASP605 5.0 39.9 1.0 CD2 A:LEU608 5.0 23.5 1.0 O A:HIS602 5.0 41.6 1.0

Calcium binding site 2 out of 6 in the Structure of Hevin Fs-Ec


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Hevin Fs-Ec within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:26.4 occ:1.00 OD1 A:ASP635 2.2 26.6 1.0 O A:HIS641 2.2 27.8 1.0 O A:HOH816 2.3 31.1 1.0 OD1 A:ASP639 2.4 29.5 1.0 OD1 A:ASN637 2.5 30.7 1.0 OE2 A:GLU646 2.5 30.1 1.0 OE1 A:GLU646 2.5 27.4 1.0 CD A:GLU646 2.9 30.1 1.0 CG A:ASP639 3.3 31.2 1.0 CG A:ASP635 3.4 30.1 1.0 C A:HIS641 3.4 30.4 1.0 CG A:ASN637 3.5 31.8 1.0 HD21 A:ASN637 3.5 40.0 1.0 H A:HIS641 3.5 35.0 1.0 OD2 A:ASP639 3.6 34.4 1.0 H A:ASP639 3.6 40.5 1.0 HA A:ILE642 3.6 28.8 1.0 HA A:ASP635 3.6 38.8 1.0 ND2 A:ASN637 3.9 33.2 1.0 H A:ASN637 4.0 35.2 1.0 HG23 A:THR643 4.2 36.3 1.0 N A:HIS641 4.2 29.1 1.0 HB2 A:HIS641 4.2 36.8 1.0 OD2 A:ASP635 4.2 32.0 1.0 H A:THR643 4.2 30.8 1.0 CB A:ASP635 4.3 28.2 1.0 CA A:ASP635 4.3 32.2 1.0 N A:ILE642 4.4 31.2 1.0 CA A:HIS641 4.4 32.2 1.0 CG A:GLU646 4.4 26.8 1.0 CA A:ILE642 4.4 24.6 1.0 N A:ASP639 4.4 33.6 1.0 HB2 A:ASP635 4.5 34.0 1.0 H A:LYS640 4.5 34.5 1.0 H A:LYS638 4.5 35.6 1.0 CB A:ASP639 4.6 32.2 1.0 HD2 A:PRO636 4.6 35.6 1.0 C A:ASP635 4.7 30.4 1.0 HD22 A:ASN637 4.7 40.0 1.0 O A:HOH833 4.7 28.6 1.0 N A:ASN637 4.8 29.8 1.0 HG1 A:THR643 4.8 33.4 1.0 CB A:HIS641 4.8 30.6 1.0 HG2 A:GLU646 4.8 31.5 1.0 N A:LYS640 4.8 28.6 1.0 CB A:ASN637 4.8 32.7 1.0 HG3 A:GLU646 4.8 31.5 1.0 N A:LYS638 4.9 29.5 1.0 N A:THR643 4.9 26.2 1.0 HB3 A:ASP639 4.9 38.0 1.0 CA A:ASP639 4.9 41.5 1.0 HG12 A:ILE642 5.0 28.1 1.0 C A:ASP639 5.0 30.4 1.0 HG13 A:ILE642 5.0 28.1 1.0

Calcium binding site 3 out of 6 in the Structure of Hevin Fs-Ec


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Hevin Fs-Ec within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:41.7 occ:1.00 O B:HOH811 2.4 44.8 1.0 OD1 B:ASP600 2.4 36.5 1.0 O B:PRO603 2.4 55.9 1.0 OE2 B:GLU612 2.4 47.8 1.0 O B:VAL607 2.4 41.3 1.0 OD2 B:ASP605 2.5 54.6 1.0 OE1 B:GLU612 2.6 36.5 1.0 CD B:GLU612 2.8 43.1 1.0 OD1 B:ASP605 3.0 68.1 1.0 CG B:ASP605 3.0 54.4 1.0 HD2 B:PRO603 3.5 57.4 1.0 HA B:ASP600 3.5 43.1 1.0 H B:ASP605 3.5 61.8 1.0 CG B:ASP600 3.6 44.5 1.0 C B:PRO603 3.6 50.8 1.0 C B:VAL607 3.6 40.3 1.0 HA B:LEU608 3.7 49.2 1.0 H B:VAL607 3.7 53.4 1.0 H B:HIS602 4.0 59.1 1.0 HG23 B:VAL607 4.0 58.4 1.0 HA B:MET604 4.0 62.2 1.0 N B:ASP605 4.1 51.4 1.0 N B:PRO603 4.1 49.0 1.0 HD23 B:LEU608 4.1 48.7 1.0 CA B:ASP600 4.2 35.8 1.0 CD B:PRO603 4.2 47.7 1.0 HG22 B:VAL607 4.3 58.4 1.0 CB B:ASP605 4.3 49.5 1.0 CB B:ASP600 4.3 33.7 1.0 CG B:GLU612 4.3 44.0 1.0 HG23 B:THR609 4.4 54.5 1.0 C B:ASP600 4.4 47.5 1.0 H B:GLN601 4.4 53.4 1.0 OD2 B:ASP600 4.4 40.5 1.0 N B:VAL607 4.4 44.4 1.0 CA B:PRO603 4.5 57.3 1.0 H B:THR609 4.5 51.5 1.0 HB2 B:ASP600 4.5 40.5 1.0 N B:LEU608 4.5 35.8 1.0 CA B:LEU608 4.5 40.9 1.0 HG2 B:PRO603 4.5 56.5 1.0 C B:HIS602 4.5 51.5 1.0 N B:MET604 4.5 53.2 1.0 N B:GLN601 4.6 44.4 1.0 CA B:MET604 4.6 51.7 1.0 CG2 B:VAL607 4.6 48.5 1.0 HB3 B:ASP605 4.6 59.5 1.0 CA B:VAL607 4.6 44.6 1.0 HG3 B:GLU612 4.6 53.0 1.0 N B:HIS602 4.6 49.1 1.0 CA B:ASP605 4.7 52.4 1.0 HG2 B:GLU612 4.7 53.0 1.0 C B:MET604 4.7 54.4 1.0 O B:HIS602 4.7 57.1 1.0 H B:ARG606 4.8 57.3 1.0 CG B:PRO603 4.9 47.6 1.0 O B:ASP600 5.0 47.9 1.0 HD3 B:PRO603 5.0 57.4 1.0 C B:ASP605 5.0 55.4 1.0 N B:THR609 5.0 42.8 1.0

Calcium binding site 4 out of 6 in the Structure of Hevin Fs-Ec


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Hevin Fs-Ec within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:43.6 occ:1.00 O B:HIS641 2.3 57.2 1.0 OD1 B:ASP635 2.3 49.3 1.0 OE2 B:GLU646 2.4 51.9 1.0 OD1 B:ASP639 2.4 60.2 1.0 OD1 B:ASN637 2.4 55.9 1.0 OE1 B:GLU646 2.5 50.8 1.0 CD B:GLU646 2.8 50.8 1.0 HD21 B:ASN637 3.2 63.1 1.0 CG B:ASN637 3.4 51.5 1.0 CG B:ASP639 3.4 61.6 1.0 C B:HIS641 3.5 48.1 1.0 CG B:ASP635 3.5 52.2 1.0 HA B:ILE642 3.5 51.3 1.0 ND2 B:ASN637 3.7 53.1 1.0 HA B:ASP635 3.7 64.5 1.0 H B:HIS641 3.7 66.2 1.0 OD2 B:ASP639 3.8 63.6 1.0 H B:ASP639 3.8 68.9 1.0 H B:THR643 4.0 45.1 1.0 H B:ASN637 4.1 60.1 1.0 HB2 B:HIS641 4.2 69.0 1.0 CG B:GLU646 4.3 45.1 1.0 HG23 B:THR643 4.3 53.5 1.0 HD2 B:PRO636 4.3 63.3 1.0 OD2 B:ASP635 4.3 48.1 1.0 CA B:ILE642 4.3 42.6 1.0 N B:ILE642 4.4 40.0 1.0 N B:HIS641 4.4 55.0 1.0 CA B:ASP635 4.4 53.7 1.0 CB B:ASP635 4.4 46.3 1.0 CA B:HIS641 4.5 52.9 1.0 HD22 B:ASN637 4.5 63.1 1.0 HB2 B:ASP635 4.5 55.7 1.0 HG3 B:GLU646 4.6 54.3 1.0 N B:ASP639 4.6 57.3 1.0 CB B:ASP639 4.7 53.4 1.0 HG2 B:GLU646 4.7 54.3 1.0 H B:LYS638 4.7 61.3 1.0 N B:THR643 4.7 37.7 1.0 CB B:ASN637 4.8 53.1 1.0 C B:ASP635 4.8 49.1 1.0 CB B:HIS641 4.8 57.4 1.0 HB3 B:ASP639 4.8 64.2 1.0 H B:LYS640 4.8 74.5 1.0 N B:ASN637 4.9 50.0 1.0 HG12 B:ILE642 4.9 51.2 1.0 HG13 B:ILE642 5.0 51.2 1.0 HB2 B:GLU646 5.0 43.4 1.0

Calcium binding site 5 out of 6 in the Structure of Hevin Fs-Ec


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Hevin Fs-Ec within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:52.2 occ:1.00 OD1 B:ASP517 2.5 27.6 1.0 O B:CYS650 2.5 26.8 1.0 O B:HOH877 2.6 41.9 1.0 O B:HOH871 2.7 41.8 1.0 O B:HOH803 2.8 33.6 1.0 O2 B:FMT707 3.4 50.5 1.0 CG B:ASP517 3.6 22.5 1.0 C B:CYS650 3.7 26.3 1.0 HA B:PHE651 3.8 31.0 1.0 SG B:CYS650 4.0 68.1 1.0 OD2 B:ASP517 4.1 29.1 1.0 O B:HOH846 4.2 30.8 1.0 C B:FMT707 4.2 54.7 1.0 HA B:CYS650 4.3 37.3 1.0 H B:FMT707 4.3 65.8 1.0 H B:ASP517 4.4 20.1 1.0 CA B:CYS650 4.5 31.0 1.0 HA B:ASP517 4.5 21.8 1.0 N B:PHE651 4.5 29.4 1.0 CA B:PHE651 4.6 25.8 1.0 N B:ASP517 4.7 16.6 1.0 HA B:THR516 4.8 23.8 1.0 CB B:CYS650 4.8 38.8 1.0 CB B:ASP517 4.8 20.2 1.0 CA B:ASP517 4.9 18.0 1.0

Calcium binding site 6 out of 6 in the Structure of Hevin Fs-Ec


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Hevin Fs-Ec within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca704 b:17.8 occ:1.00 OE2 A:GLU519 2.3 24.9 1.0 O B:HOH859 2.3 22.0 1.0 OE2 B:GLU519 2.3 18.0 1.0 O A:GLU624 2.4 14.3 1.0 O B:GLU624 2.4 14.8 1.0 OE1 B:GLU624 2.5 22.1 1.0 HG2 B:GLU519 3.2 23.0 1.0 HB3 B:GLU624 3.4 23.9 1.0 CD B:GLU519 3.4 20.4 1.0 C B:GLU624 3.5 17.8 1.0 HB3 A:HIS625 3.5 21.4 1.0 CD A:GLU519 3.6 26.2 1.0 HA B:GLU624 3.6 20.8 1.0 C A:GLU624 3.6 17.5 1.0 CD B:GLU624 3.7 26.4 1.0 OE2 A:GLU624 3.8 36.5 1.0 CG B:GLU519 3.8 19.1 1.0 HB3 A:CYS626 3.9 25.0 1.0 CA B:GLU624 3.9 17.2 1.0 HB3 A:GLU624 4.0 27.4 1.0 HB2 B:HIS625 4.0 24.2 1.0 CB B:GLU624 4.0 19.8 1.0 HG2 A:GLU519 4.1 25.3 1.0 HA A:GLU624 4.1 20.4 1.0 O A:HOH802 4.3 23.6 1.0 HB3 B:CYS626 4.3 18.8 1.0 O A:HIS625 4.3 16.5 1.0 CA A:GLU624 4.4 16.9 1.0 CB A:HIS625 4.4 17.7 1.0 OE1 A:GLU519 4.4 21.5 1.0 HB3 B:GLU519 4.5 24.4 1.0 C A:HIS625 4.5 18.8 1.0 CG A:GLU519 4.5 21.0 1.0 CG B:GLU624 4.5 21.2 1.0 HG3 B:GLU519 4.5 23.0 1.0 OE1 B:GLU519 4.5 22.4 1.0 N A:HIS625 4.6 15.9 1.0 CB A:GLU624 4.6 22.8 1.0 N B:HIS625 4.7 18.0 1.0 OE2 B:GLU624 4.7 33.2 1.0 HB2 A:HIS625 4.7 21.4 1.0 CA A:HIS625 4.7 17.9 1.0 CB A:CYS626 4.7 20.7 1.0 CB B:GLU519 4.8 20.2 1.0 CB B:HIS625 4.9 20.1 1.0 HB2 B:GLU624 4.9 23.9 1.0 CD A:GLU624 4.9 25.7 1.0 N A:CYS626 4.9 19.5 1.0 C B:HIS625 5.0 17.8 1.0 HG3 B:GLU624 5.0 25.6 1.0 O B:HIS625 5.0 15.7 1.0

S.Fan, S.P.Gangwar, M.Machius, G.Rudenko. Interplay Between Hevin, Sparc, and Mdgas: Modulators of Neurexin-Neuroligin Transsynaptic Bridges Structure 2021.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2021.01.003