Calcium in PDB 5ik7: Laminin A2LG45 I-Form, Apo.

The structure of Laminin A2LG45 I-Form, Apo., PDB code: 5ik7 was solved by D.C.Briggs, E.Hohenester, K.P.Campbell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.10 / 2.00
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	112.068, 129.083, 147.054, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.9

The binding sites of Calcium atom in the Laminin A2LG45 I-Form, Apo. (pdb code 5ik7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Laminin A2LG45 I-Form, Apo., PDB code: 5ik7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Laminin A2LG45 I-Form, Apo.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Laminin A2LG45 I-Form, Apo. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4001 b:0.9 occ:1.00 OD2 A:ASP2808 2.3 70.0 1.0 O A:HOH4248 2.3 0.5 1.0 OG1 A:FLC4007 2.4 85.1 0.4 OD1 A:ASP2876 2.4 0.7 1.0 O A:ILE2874 2.4 60.5 1.0 O A:LEU2825 2.7 56.0 1.0 HG1 A:FLC4007 3.1 0.2 0.4 H A:ASP2876 3.3 71.7 1.0 OB1 A:FLC4007 3.3 84.1 0.4 CGC A:FLC4007 3.4 84.5 0.4 CG A:ASP2876 3.4 0.9 1.0 CBC A:FLC4007 3.4 84.1 0.4 C A:ILE2874 3.4 62.7 1.0 CG A:ASP2808 3.5 68.5 1.0 OB2 A:FLC4007 3.5 83.7 0.4 CG A:FLC4007 3.6 84.3 0.4 C A:LEU2825 3.8 55.1 1.0 HA A:LEU2875 3.8 66.9 1.0 HB A:ILE2874 3.9 91.8 1.0 H A:ILE2874 3.9 83.0 1.0 N A:ASP2876 4.0 59.8 1.0 OD1 A:ASP2808 4.0 77.5 1.0 OD2 A:ASP2876 4.0 0.4 1.0 HG22 A:ILE2874 4.1 92.5 1.0 HA A:LEU2825 4.1 67.6 1.0 CB A:FLC4007 4.2 84.6 0.4 HB3 A:LEU2825 4.2 73.9 1.0 N A:LEU2875 4.3 58.6 1.0 HB3 A:ASP2876 4.3 0.0 1.0 CA A:ILE2874 4.3 70.0 1.0 HA3 A:GLY2826 4.4 85.3 1.0 CB A:ASP2876 4.4 87.5 1.0 CA A:LEU2875 4.4 55.7 1.0 CA A:LEU2825 4.5 56.4 1.0 CB A:ILE2874 4.5 76.5 1.0 OG2 A:FLC4007 4.5 84.2 0.4 N A:ILE2874 4.5 69.2 1.0 HG2 A:FLC4007 4.6 0.2 0.4 C A:LEU2875 4.6 53.4 1.0 HB3 A:ASP2808 4.6 67.7 1.0 CB A:ASP2808 4.7 56.4 1.0 CG2 A:ILE2874 4.8 77.0 1.0 N A:GLY2826 4.8 60.4 1.0 CA A:ASP2876 4.8 71.2 1.0 HB1 A:ALA2872 4.8 94.1 1.0 CB A:LEU2825 4.9 61.6 1.0 CA A:GLY2826 4.9 71.0 1.0 HB2 A:ASP2808 5.0 67.7 1.0 OHB A:FLC4007 5.0 85.9 0.4

Calcium binding site 2 out of 4 in the Laminin A2LG45 I-Form, Apo.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Laminin A2LG45 I-Form, Apo. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4002 b:55.9 occ:1.00 OD2 A:ASP3055 2.4 56.9 1.0 OHB A:FLC4003 2.4 95.0 1.0 O A:HOH4141 2.4 47.2 1.0 O A:SER3053 2.4 35.8 1.0 OD2 A:ASP2982 2.4 32.1 1.0 O A:ASN2999 2.5 41.3 1.0 OB2 A:FLC4003 2.5 74.6 1.0 HOB A:FLC4003 3.0 1.0 1.0 CG A:ASP2982 3.4 33.6 1.0 CBC A:FLC4003 3.4 81.2 1.0 CB A:FLC4003 3.5 91.9 1.0 C A:ASN2999 3.5 39.5 1.0 H A:ASP3055 3.5 50.4 1.0 CG A:ASP3055 3.5 55.3 1.0 OA2 A:FLC4003 3.6 0.1 1.0 C A:SER3053 3.6 37.6 1.0 OD1 A:ASP2982 3.7 34.8 1.0 H A:SER3053 3.9 46.1 1.0 HA A:ASN2999 3.9 42.2 1.0 HB3 A:SER3053 3.9 49.8 1.0 HA3 A:GLY3000 3.9 47.6 1.0 HB3 A:ASN2999 3.9 45.5 1.0 HA A:ALA3054 4.0 47.9 1.0 HB2 A:ASP3055 4.0 57.5 1.0 HB3 A:SER3051 4.0 65.0 1.0 N A:ASP3055 4.2 42.0 1.0 CA A:ASN2999 4.2 35.2 1.0 CB A:ASP3055 4.3 47.9 1.0 OD1 A:ASP3055 4.4 53.6 1.0 CAC A:FLC4003 4.4 0.3 1.0 CG A:FLC4003 4.4 93.3 1.0 N A:GLY3000 4.4 40.4 1.0 CA A:SER3053 4.5 36.6 1.0 O A:HOH4108 4.5 60.5 1.0 HG2 A:FLC4003 4.5 0.9 1.0 N A:SER3053 4.5 38.4 1.0 N A:ALA3054 4.5 39.6 1.0 CA A:FLC4003 4.5 95.5 1.0 CB A:ASN2999 4.6 37.9 1.0 HG A:SER3053 4.6 52.0 1.0 CB A:SER3053 4.6 41.5 1.0 OB1 A:FLC4003 4.6 75.9 1.0 CA A:ALA3054 4.6 39.9 1.0 HB3 A:ASP2982 4.6 34.3 1.0 CGC A:FLC4003 4.6 96.0 1.0 CA A:GLY3000 4.7 39.6 1.0 CB A:ASP2982 4.7 28.6 1.0 OG2 A:FLC4003 4.8 99.9 1.0 C A:ALA3054 4.9 41.1 1.0 CA A:ASP3055 4.9 41.3 1.0 CB A:SER3051 5.0 54.1 1.0

Calcium binding site 3 out of 4 in the Laminin A2LG45 I-Form, Apo.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Laminin A2LG45 I-Form, Apo. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4001 b:0.8 occ:1.00 OD2 B:ASP2808 2.4 82.6 1.0 O B:HOH4250 2.4 61.0 1.0 OD2 B:ASP2876 2.4 0.7 1.0 O B:ILE2874 2.6 64.2 1.0 O B:LEU2825 2.7 77.2 1.0 H B:ASP2876 3.3 92.3 1.0 CG B:ASP2808 3.5 87.7 1.0 HB2 B:ASP2876 3.5 0.8 1.0 CG B:ASP2876 3.6 0.8 1.0 C B:ILE2874 3.6 72.7 1.0 HB B:ILE2874 3.7 0.6 1.0 C B:LEU2825 3.8 78.3 1.0 HG22 B:ILE2874 3.9 0.7 1.0 OD1 B:ASP2808 3.9 95.4 1.0 N B:ASP2876 4.0 76.9 1.0 H B:ILE2874 4.0 91.2 1.0 HA3 B:GLY2826 4.0 0.9 1.0 CB B:ASP2876 4.0 98.1 1.0 HA B:LEU2825 4.2 83.7 1.0 HA B:LEU2875 4.3 85.9 1.0 CB B:ILE2874 4.4 86.3 1.0 HB3 B:LEU2825 4.4 80.7 1.0 CA B:ILE2874 4.4 79.7 1.0 CG2 B:ILE2874 4.5 88.9 1.0 CA B:LEU2825 4.6 69.8 1.0 N B:ILE2874 4.6 76.0 1.0 N B:LEU2875 4.6 73.1 1.0 N B:GLY2826 4.6 86.8 1.0 CA B:ASP2876 4.6 83.2 1.0 OD1 B:ASP2876 4.6 0.1 1.0 CA B:GLY2826 4.7 93.2 1.0 HA2 B:GLY2826 4.7 0.9 1.0 HB1 B:ALA2872 4.7 0.9 1.0 HB3 B:ASP2808 4.7 96.2 1.0 CB B:ASP2808 4.7 80.2 1.0 C B:LEU2875 4.7 72.6 1.0 CA B:LEU2875 4.8 71.6 1.0 HB3 B:ASP2876 4.9 0.8 1.0 HG21 B:ILE2874 4.9 0.7 1.0

Calcium binding site 4 out of 4 in the Laminin A2LG45 I-Form, Apo.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Laminin A2LG45 I-Form, Apo. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:62.0 occ:1.00 O B:HOH4154 2.4 65.6 1.0 O B:SER3053 2.4 54.0 1.0 OD2 B:ASP3055 2.4 97.5 1.0 O B:ASN2999 2.5 63.5 1.0 OD2 B:ASP2982 2.6 67.5 1.0 OB2 B:FLC4003 2.6 91.1 1.0 OHB B:FLC4003 2.8 99.4 1.0 CG B:ASP3055 3.4 90.2 1.0 HOB B:FLC4003 3.4 0.3 1.0 H B:ASP3055 3.5 84.0 1.0 CBC B:FLC4003 3.5 95.2 1.0 C B:ASN2999 3.5 65.2 1.0 C B:SER3053 3.6 62.5 1.0 CG B:ASP2982 3.7 68.5 1.0 CB B:FLC4003 3.7 99.8 1.0 HG2 B:FLC4003 3.8 0.9 1.0 HA B:ASN2999 3.9 69.1 1.0 H B:SER3053 3.9 68.3 1.0 HA B:ALA3054 4.0 84.2 1.0 HB3 B:SER3053 4.0 82.8 1.0 O B:HOH4129 4.0 63.0 1.0 HA3 B:GLY3000 4.0 70.0 1.0 HB2 B:ASP3055 4.0 0.0 1.0 HB3 B:ASN2999 4.1 71.5 1.0 HG B:SER3051 4.1 83.5 1.0 OD1 B:ASP3055 4.1 78.8 1.0 N B:ASP3055 4.1 70.0 1.0 OD1 B:ASP2982 4.2 72.4 1.0 CA B:ASN2999 4.3 57.6 1.0 CB B:ASP3055 4.3 90.8 1.0 OA1 B:FLC4003 4.3 95.6 1.0 CG B:FLC4003 4.4 0.1 1.0 CA B:SER3053 4.5 59.9 1.0 N B:GLY3000 4.5 61.5 1.0 N B:ALA3054 4.5 68.6 1.0 CB B:SER3053 4.6 69.0 1.0 N B:SER3053 4.6 57.0 1.0 CA B:ALA3054 4.6 70.2 1.0 CB B:ASN2999 4.7 59.5 1.0 OG B:SER3051 4.7 69.6 1.0 OB1 B:FLC4003 4.7 90.5 1.0 CA B:GLY3000 4.7 58.3 1.0 HE3 B:MET2981 4.8 0.6 1.0 OG B:SER3053 4.8 74.3 1.0 C B:ALA3054 4.9 63.6 1.0 HB3 B:ASP2982 4.9 74.9 1.0 CA B:ASP3055 4.9 81.7 1.0 HG2 A:PRO2897 4.9 72.5 1.0 CB B:ASP2982 4.9 62.4 1.0

D.C.Briggs, T.Yoshida-Moriguchi, T.Zheng, D.Venzke, M.E.Anderson, A.Strazzulli, M.Moracci, L.Yu, E.Hohenester, K.P.Campbell. Structural Basis of Laminin Binding to the Large Glycans on Dystroglycan. Nat.Chem.Biol. V. 12 810 2016.
ISSN: ESSN 1552-4469
PubMed: 27526028
DOI: 10.1038/NCHEMBIO.2146