Calcium in PDB 7jud: C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside

The structure of C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside, PDB code: 7jud was solved by W.I.Weis, H.Feinberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.93 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.137, 37.836, 55.065, 94.08, 99.63, 104.98
R / Rfree (%)	14.8 / 18

The binding sites of Calcium atom in the C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside (pdb code 7jud). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside, PDB code: 7jud:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:8.7 occ:1.00 OD1 A:ASP748 2.4 9.7 1.0 OD1 A:ASN747 2.4 9.5 1.0 OE1 A:GLU733 2.4 9.8 1.0 OD1 A:ASN727 2.4 10.0 1.0 O3 A:MMA803 2.5 10.0 1.0 O A:ASP748 2.5 8.6 1.0 O4 A:MMA803 2.5 11.4 1.0 OE1 A:GLU725 2.5 12.5 1.0 CG A:ASP748 3.4 10.5 1.0 CD A:GLU725 3.4 12.9 1.0 C3 A:MMA803 3.4 11.3 1.0 C4 A:MMA803 3.4 12.0 1.0 CD A:GLU733 3.4 9.9 1.0 CG A:ASN747 3.4 10.1 1.0 CG A:ASN727 3.5 10.8 1.0 C A:ASP748 3.6 8.0 1.0 OE2 A:GLU725 3.6 14.7 1.0 OE2 A:GLU733 3.7 11.6 1.0 N A:ASP748 3.8 8.2 1.0 ND2 A:ASN747 3.8 13.4 1.0 ND2 A:ASN727 4.0 12.8 1.0 CA A:ASP748 4.1 8.7 1.0 OD2 A:ASP748 4.1 10.5 1.0 N A:ASN727 4.2 10.0 1.0 CB A:ASP748 4.3 9.2 1.0 CG A:GLU725 4.6 11.9 1.0 CB A:ASN727 4.6 11.7 1.0 CB A:TYR729 4.6 10.9 1.0 N A:TYR729 4.7 9.0 1.0 C A:ASN747 4.7 8.7 1.0 N A:ASN728 4.7 10.3 1.0 CG A:GLU733 4.7 9.5 1.0 C2 A:MMA803 4.7 12.1 1.0 N A:ILE749 4.7 8.5 1.0 CB A:ASN747 4.7 10.4 1.0 C5 A:MMA803 4.8 13.7 1.0 CA A:ASN727 4.8 11.3 1.0 CB A:GLU733 4.9 9.6 1.0 CA A:ASN747 4.9 9.2 1.0

Calcium binding site 2 out of 3 in the C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:26.1 occ:0.75 OD1 A:ASN673 2.3 26.8 1.0 O A:HOH907 2.3 27.4 1.0 O A:HOH927 2.5 35.2 1.0 O A:HOH929 2.5 35.8 1.0 OE1 A:GLU677 2.5 26.6 0.8 OE2 A:GLU677 2.5 25.2 0.8 O A:SER671 2.5 15.5 1.0 OG A:SER671 2.6 19.6 0.8 OE1 A:GLU677 2.6 14.4 0.2 CD A:GLU677 2.9 24.4 0.8 C A:SER671 3.3 13.3 1.0 CG A:ASN673 3.4 25.1 1.0 CD A:GLU677 3.4 14.2 0.2 CB A:SER671 3.5 11.3 0.2 OE2 A:GLU677 3.5 14.4 0.2 CB A:SER671 3.6 16.2 0.8 CB A:ASN673 3.9 22.9 1.0 N A:ASN673 3.9 17.1 1.0 O A:HOH908 3.9 37.5 1.0 CA A:SER671 3.9 11.9 0.2 CA A:SER671 4.0 12.9 0.8 N A:ILE672 4.1 12.4 1.0 OE1 A:GLN760 4.3 18.6 1.0 CG A:GLU677 4.4 22.6 0.8 N A:SER671 4.4 12.3 1.0 CA A:ILE672 4.4 13.5 1.0 ND2 A:ASN673 4.5 26.0 1.0 CA A:ASN673 4.5 20.3 1.0 C A:ILE672 4.5 14.8 1.0 OG A:SER671 4.7 10.4 0.2 CZ A:PHE642 4.7 18.9 1.0 OD2 A:ASP712 4.7 23.4 1.0 CG A:GLU677 4.7 14.9 0.2 OG A:SER714 4.9 25.2 1.0

Calcium binding site 3 out of 3 in the C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C-Type Carbohydrate-Recognition Domain 4 of the Mannose Receptor Complexed with Methyl-Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:9.2 occ:1.00 OD1 B:ASP748 2.4 8.8 1.0 OD1 B:ASN747 2.4 9.5 1.0 OD1 B:ASN727 2.4 10.1 1.0 OE1 B:GLU733 2.4 11.7 1.0 O B:ASP748 2.5 9.2 1.0 OE1 B:GLU725 2.5 11.5 1.0 O3 B:MMA802 2.5 11.1 1.0 O4 B:MMA802 2.5 10.5 1.0 CG B:ASP748 3.4 9.0 1.0 C3 B:MMA802 3.4 12.2 1.0 C4 B:MMA802 3.4 11.8 1.0 CD B:GLU725 3.4 12.1 1.0 CD B:GLU733 3.4 11.7 1.0 CG B:ASN747 3.4 10.7 1.0 CG B:ASN727 3.4 10.6 1.0 C B:ASP748 3.5 8.5 1.0 OE2 B:GLU733 3.7 13.0 1.0 OE2 B:GLU725 3.7 14.4 1.0 N B:ASP748 3.8 8.5 1.0 ND2 B:ASN747 3.9 14.3 1.0 ND2 B:ASN727 4.0 11.3 1.0 CA B:ASP748 4.0 8.3 1.0 OD2 B:ASP748 4.1 10.5 1.0 N B:ASN727 4.2 9.9 1.0 CB B:ASP748 4.3 8.8 1.0 CB B:TYR729 4.6 12.6 1.0 CG B:GLU725 4.6 12.4 1.0 CB B:ASN727 4.6 11.1 1.0 N B:TYR729 4.6 11.5 1.0 C B:ASN747 4.6 9.1 1.0 N B:ILE749 4.7 9.1 1.0 N B:ASN728 4.7 11.3 1.0 CG B:GLU733 4.7 11.8 1.0 C2 B:MMA802 4.7 13.7 1.0 CB B:ASN747 4.7 10.1 1.0 C5 B:MMA802 4.8 15.4 1.0 CA B:ASN727 4.8 9.8 1.0 CB B:GLU733 4.9 11.1 1.0 CA B:ASN747 4.9 9.0 1.0 CG2 B:ILE749 5.0 14.1 0.5 O2 B:MMA802 5.0 15.5 1.0

H.Feinberg, S.A.F.Jegouzo, Y.Lasanajak, D.F.Smith, K.Drickamer, M.E.Taylor, W.I.Weis. Structural Analysis of Carbohydrate Binding By the Macrophage Mannose Receptor CD206 J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X