Calcium in PDB 6rbf: Mucin 2 D3 Domain

The structure of Mucin 2 D3 Domain, PDB code: 6rbf was solved by G.Javitt, D.Fass, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	152.461, 156.925, 93.584, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 28.3

The binding sites of Calcium atom in the Mucin 2 D3 Domain (pdb code 6rbf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Mucin 2 D3 Domain, PDB code: 6rbf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Mucin 2 D3 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mucin 2 D3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:66.1 occ:1.00 OD1 A:ASN994 2.4 61.0 1.0 O A:ARG998 2.5 59.1 1.0 OD1 A:ASN1001 2.5 68.1 1.0 OD1 A:ASP996 2.6 67.4 1.0 OD1 A:ASP1002 2.6 60.3 1.0 OD2 A:ASP872 2.7 56.7 1.0 CG A:ASP996 3.2 63.8 1.0 H A:ASP996 3.4 76.8 1.0 CG A:ASN994 3.4 57.2 1.0 CG A:ASP1002 3.4 57.6 1.0 H A:ASN994 3.4 55.1 1.0 OD2 A:ASP996 3.4 70.2 1.0 CG A:ASP872 3.5 55.3 1.0 CG A:ASN1001 3.5 64.6 1.0 H A:ARG998 3.6 80.3 1.0 HD21 A:ASN994 3.6 71.3 1.0 C A:ARG998 3.6 63.7 1.0 HD21 A:ASN1001 3.7 83.1 1.0 HA A:ASP1002 3.7 72.0 1.0 H A:PHE995 3.8 70.7 1.0 ND2 A:ASN994 3.9 59.5 1.0 OD2 A:ASP1002 3.9 49.2 1.0 HB2 A:ASP872 4.0 67.0 1.0 ND2 A:ASN1001 4.0 69.2 1.0 N A:ASP996 4.1 64.0 1.0 HB3 A:ARG998 4.1 90.9 1.0 N A:ASP1002 4.2 66.0 1.0 N A:PHE995 4.2 58.9 1.0 N A:ARG998 4.2 66.9 1.0 CB A:ASP872 4.2 55.8 1.0 OD1 A:ASP872 4.2 59.9 1.0 CA A:ASP1002 4.3 60.0 1.0 H A:ASP1002 4.3 79.2 1.0 N A:ASN994 4.3 45.9 1.0 H A:ASN1001 4.3 87.6 1.0 CA A:ARG998 4.3 67.0 1.0 HB2 A:ARG998 4.3 90.9 1.0 HB3 A:ASP872 4.3 67.0 1.0 HA A:SER999 4.4 82.8 1.0 CB A:ASP996 4.4 54.5 1.0 CB A:ASP1002 4.4 60.8 1.0 C A:ASN1001 4.4 58.5 1.0 CB A:ARG998 4.5 75.7 1.0 O A:HOH1402 4.5 45.4 1.0 CA A:ASP996 4.6 57.7 1.0 HB3 A:ASP996 4.6 65.4 1.0 C A:ASN994 4.6 55.8 1.0 CB A:ASN994 4.7 53.7 1.0 N A:SER999 4.7 76.1 1.0 C A:ASP996 4.7 64.9 1.0 HD22 A:ASN994 4.7 71.3 1.0 CA A:ASN994 4.7 47.4 1.0 HA3 A:GLY993 4.8 58.5 1.0 O A:ASN1001 4.8 53.7 1.0 CB A:ASN1001 4.8 70.8 1.0 HD22 A:ASN1001 4.9 83.1 1.0 HA A:PHE995 4.9 75.2 1.0 CA A:SER999 4.9 69.0 1.0 HB2 A:ASP1002 4.9 72.9 1.0 CA A:PHE995 5.0 62.6 1.0 N A:ASN1001 5.0 73.0 1.0 C A:PHE995 5.0 62.2 1.0 H A:HIS997 5.0 75.8 1.0 CA A:ASN1001 5.0 60.9 1.0 N A:HIS997 5.0 63.1 1.0

Calcium binding site 2 out of 4 in the Mucin 2 D3 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mucin 2 D3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1308 b:65.8 occ:1.00 O B:ARG998 2.3 68.2 1.0 OD2 B:ASP872 2.4 56.0 1.0 OD1 B:ASN994 2.4 62.6 1.0 OD1 B:ASN1001 2.5 68.4 1.0 OD1 B:ASP1002 2.7 62.0 1.0 OD1 B:ASP996 3.0 60.8 1.0 H B:ASP996 3.1 68.6 1.0 H B:ARG998 3.1 82.9 1.0 CG B:ASP996 3.2 64.8 1.0 OD2 B:ASP996 3.2 66.0 1.0 C B:ARG998 3.4 73.3 1.0 CG B:ASP872 3.5 56.9 1.0 CG B:ASN994 3.5 62.6 1.0 CG B:ASN1001 3.6 70.6 1.0 HD21 B:ASN1001 3.6 79.8 1.0 HD21 B:ASN994 3.6 73.2 1.0 HB3 B:ARG998 3.7 98.4 1.0 H B:ASN994 3.7 59.2 1.0 HB2 B:ASP872 3.7 69.5 1.0 CG B:ASP1002 3.7 59.9 1.0 N B:ARG998 3.9 69.1 1.0 HB2 B:ARG998 3.9 98.4 1.0 N B:ASP996 3.9 57.2 1.0 ND2 B:ASN994 3.9 61.0 1.0 HA B:ASP1002 3.9 63.4 1.0 ND2 B:ASN1001 4.0 66.5 1.0 CA B:ARG998 4.0 72.8 1.0 CB B:ASP872 4.0 57.9 1.0 CB B:ARG998 4.1 82.0 1.0 H B:PHE995 4.1 77.3 1.0 HB3 B:ASP872 4.1 69.5 1.0 H B:ASN1001 4.3 77.6 1.0 OD2 B:ASP1002 4.3 57.5 1.0 CB B:ASP996 4.3 66.0 1.0 N B:ASP1002 4.3 53.4 1.0 C B:ASP996 4.4 63.9 1.0 CA B:ASP996 4.4 64.9 1.0 HA B:SER999 4.4 81.4 1.0 OD1 B:ASP872 4.4 62.1 1.0 N B:PHE995 4.4 64.5 1.0 N B:ASN994 4.5 49.3 1.0 H B:ASP1002 4.5 64.1 1.0 C B:ASN1001 4.5 58.0 1.0 CA B:ASP1002 4.5 52.8 1.0 N B:SER999 4.6 71.8 1.0 O B:ASP996 4.6 63.2 1.0 N B:HIS997 4.7 62.0 1.0 CB B:ASN994 4.7 55.5 1.0 C B:ASN994 4.7 57.1 1.0 O B:ASN1001 4.7 54.1 1.0 CB B:ASP1002 4.7 55.5 1.0 HD22 B:ASN994 4.8 73.2 1.0 HB3 B:ASP996 4.8 79.2 1.0 HD22 B:ASN1001 4.8 79.8 1.0 H B:HIS997 4.9 74.4 1.0 CA B:ASN994 4.9 50.0 1.0 CB B:ASN1001 4.9 66.7 1.0 HA B:ARG998 4.9 87.3 1.0 CA B:SER999 4.9 67.8 1.0 N B:ASN1001 5.0 64.7 1.0

Calcium binding site 3 out of 4 in the Mucin 2 D3 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mucin 2 D3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1302 b:57.6 occ:1.00 OD2 C:ASP872 2.2 47.1 1.0 OD1 C:ASN994 2.5 47.9 1.0 H C:ASP996 2.7 53.7 1.0 O C:ARG998 2.7 47.7 1.0 OD1 C:ASP1002 2.7 38.8 1.0 OD1 C:ASP996 2.8 54.9 1.0 H C:ASN994 3.1 37.6 1.0 H C:PHE995 3.2 55.1 1.0 CG C:ASP872 3.3 45.9 1.0 CG C:ASP996 3.3 53.3 1.0 H C:ARG998 3.4 64.0 1.0 HB2 C:ASN1001 3.4 61.9 1.0 HA C:ASP1002 3.4 49.9 1.0 CG C:ASP1002 3.5 42.9 1.0 CG C:ASN994 3.5 45.5 1.0 N C:ASP996 3.5 44.7 1.0 N C:PHE995 3.6 45.9 1.0 HB2 C:ASP872 3.6 52.8 1.0 C C:ARG998 3.8 51.9 1.0 O C:HOH1410 3.8 31.9 1.0 N C:ASN994 3.9 31.4 1.0 OD2 C:ASP996 3.9 55.4 1.0 C C:ASN994 4.0 47.2 1.0 N C:ASP1002 4.0 44.5 1.0 CB C:ASP872 4.0 44.0 1.0 HB3 C:ASP996 4.0 56.0 1.0 OD2 C:ASP1002 4.1 44.4 1.0 CA C:ASP1002 4.1 41.6 1.0 HD21 C:ASN994 4.1 64.7 1.0 CB C:ASP996 4.1 46.6 1.0 C C:ASN1001 4.2 48.3 1.0 N C:ARG998 4.2 53.4 1.0 OD1 C:ASP872 4.2 44.9 1.0 ND2 C:ASN994 4.2 53.9 1.0 H C:ASP1002 4.2 53.4 1.0 CA C:ASP996 4.3 44.5 1.0 CA C:ASN994 4.3 41.4 1.0 CB C:ASN1001 4.3 51.6 1.0 HA C:PHE995 4.3 48.7 1.0 H C:ASN1001 4.3 54.9 1.0 CA C:PHE995 4.3 40.6 1.0 HA C:SER999 4.4 56.1 1.0 HB2 C:ARG998 4.4 66.1 1.0 CB C:ASP1002 4.4 46.0 1.0 HB3 C:ASP872 4.4 52.8 1.0 O C:ASN1001 4.4 51.7 1.0 C C:PHE995 4.4 41.0 1.0 HA3 C:GLY993 4.5 48.4 1.0 HB3 C:ASN1001 4.5 61.9 1.0 CB C:ASN994 4.5 43.7 1.0 H C:HIS997 4.5 61.9 1.0 CA C:ARG998 4.5 56.3 1.0 C C:ASP996 4.7 46.5 1.0 CA C:ASN1001 4.7 46.9 1.0 N C:HIS997 4.7 51.5 1.0 O C:ASN994 4.7 45.3 1.0 HD22 C:ASN1001 4.8 70.8 1.0 N C:SER999 4.8 50.6 1.0 H C:ASP872 4.8 46.8 1.0 HB2 C:ASP1002 4.9 55.2 1.0 N C:ASN1001 4.9 45.7 1.0 C C:GLY993 4.9 38.9 1.0 CA C:SER999 5.0 46.7 1.0 CB C:ARG998 5.0 55.1 1.0

Calcium binding site 4 out of 4 in the Mucin 2 D3 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mucin 2 D3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1303 b:83.1 occ:1.00 OD1 D:ASN994 2.3 67.2 1.0 OD2 D:ASP872 2.4 73.0 1.0 O D:ARG998 2.5 75.5 1.0 OD1 D:ASP996 2.7 85.9 1.0 OD1 D:ASN1001 2.9 84.8 1.0 OD1 D:ASP1002 2.9 68.2 1.0 CG D:ASP1002 3.3 65.9 1.0 H D:ASP996 3.3 74.6 1.0 HA D:ASP1002 3.3 85.1 1.0 CG D:ASN994 3.4 73.9 1.0 CG D:ASP872 3.5 73.6 1.0 H D:ARG998 3.6 94.6 1.0 OD2 D:ASP1002 3.6 63.6 1.0 H D:ASN994 3.6 79.8 1.0 C D:ARG998 3.6 78.5 1.0 HB2 D:ASP872 3.6 81.4 1.0 H D:PHE995 3.6 75.6 1.0 HA D:SER999 3.7 96.4 1.0 CG D:ASP996 3.7 84.8 1.0 HD21 D:ASN994 3.8 79.8 1.0 CG D:ASN1001 3.8 88.2 1.0 H D:ASN1001 3.8 93.3 1.0 N D:ASP1002 3.9 76.2 1.0 CA D:ASP1002 3.9 70.9 1.0 H D:ASP1002 4.0 91.5 1.0 ND2 D:ASN994 4.0 66.5 1.0 CB D:ASP872 4.1 67.9 1.0 HD21 D:ASN1001 4.1 0.6 1.0 N D:ASP996 4.1 62.2 1.0 CB D:ASP1002 4.1 64.1 1.0 C D:ASN1001 4.2 76.8 1.0 HB3 D:ARG998 4.3 0.4 1.0 HB3 D:ASP872 4.3 81.4 1.0 N D:PHE995 4.3 63.0 1.0 N D:ARG998 4.3 78.8 1.0 ND2 D:ASN1001 4.3 90.5 1.0 CA D:SER999 4.4 80.3 1.0 N D:ASN994 4.4 66.5 1.0 OD2 D:ASP996 4.4 86.3 1.0 N D:SER999 4.4 70.7 1.0 O D:HOH1407 4.4 52.6 1.0 O D:ASN1001 4.5 66.3 1.0 CA D:ARG998 4.5 89.1 1.0 OD1 D:ASP872 4.5 69.1 1.0 HB2 D:ASP1002 4.5 77.0 1.0 N D:ASN1001 4.6 77.8 1.0 C D:SER999 4.6 83.3 1.0 CB D:ASP996 4.6 76.1 1.0 CB D:ASN994 4.7 72.2 1.0 HB3 D:ASP996 4.7 91.4 1.0 CA D:ASP996 4.8 63.9 1.0 CA D:ASN1001 4.8 78.8 1.0 O D:SER999 4.8 74.4 1.0 C D:ASP996 4.9 81.9 1.0 CA D:ASN994 4.9 71.6 1.0 HD22 D:ASN994 4.9 79.8 1.0 CB D:ASN1001 4.9 86.8 1.0 HB3 D:ASN994 4.9 86.7 1.0 CB D:ARG998 4.9 94.5 1.0 C D:ASN994 4.9 62.1 1.0 HB3 D:ASP1002 4.9 77.0 1.0 HA3 D:GLY993 5.0 68.7 1.0

G.Javitt, M.L.G.Calvo, L.Albert, N.Reznik, T.Ilani, R.Diskin, D.Fass. Intestinal Gel-Forming Mucins Polymerize By Disulfide-Mediated Dimerization of D3 Domains. J.Mol.Biol. V. 431 3740 2019.
ISSN: ESSN 1089-8638
PubMed: 31310764
DOI: 10.1016/J.JMB.2019.07.018