Calcium in PDB 5ik8: Laminin A2LG45 I-Form, G6/7 Bound.

The structure of Laminin A2LG45 I-Form, G6/7 Bound., PDB code: 5ik8 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)	55.77 / 2.00
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.540, 126.290, 144.000, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21

The binding sites of Calcium atom in the Laminin A2LG45 I-Form, G6/7 Bound. (pdb code 5ik8). 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, G6/7 Bound., PDB code: 5ik8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Laminin A2LG45 I-Form, G6/7 Bound.


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, G6/7 Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4001 b:0.7 occ:1.00 OD2 A:ASP2876 2.4 87.7 1.0 OD2 A:ASP2808 2.4 60.9 1.0 O A:ILE2874 2.4 67.5 1.0 O A:LEU2825 2.4 65.3 1.0 C A:ILE2874 3.4 66.5 1.0 H A:ASP2876 3.5 69.5 1.0 CG A:ASP2808 3.5 60.4 1.0 CG A:ASP2876 3.5 82.0 1.0 C A:LEU2825 3.6 64.2 1.0 HB2 A:ASP2876 3.6 84.2 1.0 H A:ILE2874 3.7 76.6 1.0 HB A:ILE2874 3.8 83.6 1.0 HG22 A:ILE2874 3.8 83.7 1.0 HB3 A:LEU2825 4.0 79.3 1.0 HA A:LEU2825 4.0 74.0 1.0 OD1 A:ASP2808 4.0 65.0 1.0 N A:ASP2876 4.0 57.9 1.0 CB A:ASP2876 4.1 70.2 1.0 HA A:LEU2875 4.1 71.7 1.0 HA3 A:GLY2826 4.1 92.0 1.0 CA A:ILE2874 4.2 65.7 1.0 CA A:LEU2825 4.3 61.7 1.0 N A:LEU2875 4.3 61.4 1.0 N A:ILE2874 4.3 63.8 1.0 CB A:ILE2874 4.3 69.7 1.0 N A:GLY2826 4.5 73.9 1.0 CA A:LEU2875 4.5 59.7 1.0 OD1 A:ASP2876 4.6 85.7 1.0 CG2 A:ILE2874 4.6 69.8 1.0 CB A:LEU2825 4.6 66.1 1.0 C A:LEU2875 4.6 56.5 1.0 CA A:GLY2826 4.7 76.6 1.0 CA A:ASP2876 4.7 60.8 1.0 HB1 A:ALA2872 4.7 94.3 1.0 HB3 A:ASP2808 4.7 64.1 1.0 CB A:ASP2808 4.7 53.4 1.0 HA2 A:GLY2826 4.8 92.0 1.0 O A:HOH4116 4.8 85.2 1.0 HB3 A:ASP2876 4.9 84.2 1.0 O A:HOH4344 4.9 70.8 1.0 H A:ASP2873 4.9 88.1 1.0 HG21 A:ILE2874 5.0 83.7 1.0

Calcium binding site 2 out of 4 in the Laminin A2LG45 I-Form, G6/7 Bound.


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, G6/7 Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4002 b:41.1 occ:1.00 OD2 A:ASP2982 2.3 36.4 1.0 OD2 A:ASP3055 2.3 49.4 1.0 O A:SER3053 2.4 38.5 1.0 O A:ASN2999 2.4 39.5 1.0 OB2 A:FLC4004 2.4 64.2 1.0 O A:HOH4131 2.4 35.1 1.0 OHB A:FLC4004 2.5 76.2 1.0 HOB A:FLC4004 3.2 91.5 1.0 CBC A:FLC4004 3.3 66.5 1.0 CG A:ASP2982 3.3 37.3 1.0 C A:ASN2999 3.4 38.9 1.0 H A:ASP3055 3.4 46.1 1.0 CB A:FLC4004 3.5 76.8 1.0 CG A:ASP3055 3.5 48.1 1.0 C A:SER3053 3.6 38.1 1.0 OD1 A:ASP2982 3.6 36.1 1.0 HB3 A:SER3053 3.8 50.2 1.0 H A:SER3053 3.8 48.9 1.0 HB3 A:ASN2999 3.8 47.5 1.0 HA A:ASN2999 3.8 43.4 1.0 HB2 A:ASP3055 3.9 53.7 1.0 HA3 A:GLY3000 3.9 48.8 1.0 HA A:ALA3054 4.0 43.0 1.0 HB3 A:SER3051 4.0 66.9 1.0 OA2 A:FLC4004 4.1 88.1 1.0 CA A:ASN2999 4.1 36.2 1.0 HG1 A:FLC4004 4.1 92.9 1.0 N A:ASP3055 4.1 38.4 1.0 CB A:ASP3055 4.2 44.8 1.0 CG A:FLC4004 4.3 77.4 1.0 OD1 A:ASP3055 4.3 46.1 1.0 N A:GLY3000 4.4 37.9 1.0 CA A:SER3053 4.4 39.3 1.0 N A:SER3053 4.4 40.7 1.0 O A:HOH4243 4.4 57.7 1.0 OB1 A:FLC4004 4.5 56.7 1.0 CB A:ASN2999 4.5 39.6 1.0 N A:ALA3054 4.5 36.9 1.0 CB A:SER3053 4.5 41.9 1.0 CA A:ALA3054 4.6 35.8 1.0 CA A:GLY3000 4.6 40.6 1.0 CB A:ASP2982 4.6 34.4 1.0 CAC A:FLC4004 4.6 88.5 1.0 CA A:FLC4004 4.7 83.0 1.0 HB3 A:ASP2982 4.7 41.2 1.0 CGC A:FLC4004 4.7 82.3 1.0 HG A:SER3053 4.7 53.5 1.0 CA A:ASP3055 4.8 40.4 1.0 C A:ALA3054 4.9 38.3 1.0 OG2 A:FLC4004 4.9 85.6 1.0 HB2 A:ASP2982 5.0 41.2 1.0 CB A:SER3051 5.0 55.7 1.0

Calcium binding site 3 out of 4 in the Laminin A2LG45 I-Form, G6/7 Bound.


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, G6/7 Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4001 b:57.6 occ:1.00 O4 B:XYS4006 1.9 73.6 1.0 OD2 B:ASP2808 2.3 63.9 1.0 O B:LEU2825 2.3 71.0 1.0 OD2 B:ASP2876 2.4 70.0 1.0 O6B B:BDP4007 2.5 82.0 1.0 O B:ILE2874 2.6 64.2 1.0 OD1 B:ASP2808 2.7 60.8 1.0 CG B:ASP2808 2.8 63.7 1.0 O5 B:BDP4007 3.0 78.1 1.0 C4 B:XYS4006 3.0 78.5 1.0 H4 B:XYS4006 3.1 94.1 1.0 C B:LEU2825 3.3 70.5 1.0 H B:ASP2876 3.4 74.2 1.0 HB2 B:ASP2876 3.4 79.9 1.0 CG B:ASP2876 3.5 69.6 1.0 O3 B:XYS4006 3.6 78.4 1.0 C6 B:BDP4007 3.6 82.9 1.0 HA3 B:GLY2826 3.6 78.8 1.0 C B:ILE2874 3.7 64.7 1.0 C3 B:XYS4006 3.8 79.5 1.0 HA B:LEU2825 3.8 81.7 1.0 C5 B:BDP4007 3.9 80.7 1.0 CB B:ASP2876 4.0 66.6 1.0 N B:ASP2876 4.0 61.8 1.0 C1 B:BDP4007 4.0 79.0 1.0 HB B:ILE2874 4.0 84.1 1.0 HB3 B:LEU2825 4.1 84.1 1.0 H3 B:XYS4006 4.1 95.4 1.0 H B:ILE2874 4.1 82.1 1.0 HA B:LEU2875 4.1 76.8 1.0 CA B:LEU2825 4.1 68.1 1.0 N B:GLY2826 4.2 65.3 1.0 C5 B:XYS4006 4.2 78.2 1.0 H51 B:XYS4006 4.2 93.9 1.0 CB B:ASP2808 4.3 61.4 1.0 CA B:GLY2826 4.3 65.6 1.0 HB1 B:ALA2872 4.4 83.8 1.0 HA2 B:GLY2826 4.5 78.8 1.0 H2 B:BDP4007 4.5 95.5 1.0 H52 B:XYS4006 4.6 93.9 1.0 H4 B:BDP4007 4.6 98.4 1.0 HB2 B:ASP2808 4.6 73.7 1.0 CA B:ILE2874 4.6 67.2 1.0 CA B:ASP2876 4.6 63.9 1.0 N B:LEU2875 4.6 65.8 1.0 H5 B:BDP4007 4.6 96.8 1.0 CB B:LEU2825 4.6 70.1 1.0 HB3 B:ASP2808 4.6 73.7 1.0 OD1 B:ASP2876 4.6 75.4 1.0 CA B:LEU2875 4.7 64.0 1.0 N B:ILE2874 4.7 68.4 1.0 O6A B:BDP4007 4.7 79.5 1.0 C B:LEU2875 4.7 62.5 1.0 CB B:ILE2874 4.7 70.0 1.0 H1 B:BDP4007 4.8 94.8 1.0 HB3 B:ASP2876 4.8 79.9 1.0 HG22 B:ILE2874 4.8 84.1 1.0 HD2 B:ARG2803 4.9 86.0 1.0 C4 B:BDP4007 4.9 82.0 1.0 C2 B:BDP4007 4.9 79.6 1.0 H B:GLY2826 5.0 78.4 1.0

Calcium binding site 4 out of 4 in the Laminin A2LG45 I-Form, G6/7 Bound.


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, G6/7 Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:44.0 occ:1.00 O B:SER3053 2.3 43.6 1.0 O B:HOH4225 2.4 39.0 1.0 OD2 B:ASP2982 2.4 44.8 1.0 O B:ASN2999 2.4 43.1 1.0 OD2 B:ASP3055 2.4 64.3 1.0 OB2 B:FLC4010 2.6 63.4 1.0 OHB B:FLC4010 2.6 68.2 1.0 HOB B:FLC4010 3.2 81.8 1.0 CG B:ASP3055 3.3 59.3 1.0 C B:ASN2999 3.4 45.2 1.0 CG B:ASP2982 3.4 44.5 1.0 CBC B:FLC4010 3.4 69.2 1.0 C B:SER3053 3.5 45.5 1.0 CB B:FLC4010 3.5 71.9 1.0 H B:ASP3055 3.6 57.5 1.0 HB3 B:SER3053 3.6 57.3 1.0 HG2 B:FLC4010 3.7 89.2 1.0 H B:SER3053 3.8 53.0 1.0 HB3 B:ASN2999 3.8 50.6 1.0 HA B:ASN2999 3.8 50.7 1.0 OD1 B:ASP2982 3.8 43.9 1.0 OD1 B:ASP3055 4.0 55.2 1.0 HA3 B:GLY3000 4.0 52.0 1.0 HA B:ALA3054 4.0 57.0 1.0 HB2 B:ASP3055 4.0 64.7 1.0 HG B:SER3051 4.1 61.3 1.0 CA B:ASN2999 4.1 42.3 1.0 OA1 B:FLC4010 4.2 54.0 1.0 N B:ASP3055 4.2 47.9 1.0 O B:HOH4116 4.2 98.8 1.0 CG B:FLC4010 4.2 74.3 1.0 CB B:ASP3055 4.3 53.9 1.0 CA B:SER3053 4.3 44.8 1.0 CB B:SER3053 4.3 47.7 1.0 N B:SER3053 4.4 44.1 1.0 N B:GLY3000 4.4 41.6 1.0 CB B:ASN2999 4.4 42.2 1.0 N B:ALA3054 4.5 45.3 1.0 HG B:SER3053 4.5 59.1 1.0 OB1 B:FLC4010 4.6 67.0 1.0 CA B:ALA3054 4.6 47.5 1.0 CA B:GLY3000 4.7 43.3 1.0 OG B:SER3051 4.7 51.1 1.0 OD1 A:ASN2816 4.7 44.4 1.0 CB B:ASP2982 4.7 42.0 1.0 HB3 B:ASP2982 4.7 50.4 1.0 CA B:FLC4010 4.8 67.3 1.0 CAC B:FLC4010 4.9 60.4 1.0 HG1 B:FLC4010 4.9 89.2 1.0 O A:HOH4159 4.9 53.9 1.0 CA B:ASP3055 4.9 50.8 1.0 C B:ALA3054 4.9 44.2 1.0 OG B:SER3053 4.9 49.3 1.0 HD21 A:ASN2816 5.0 54.8 1.0 HG2 A:PRO2897 5.0 67.9 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