Calcium in PDB 6byv: Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor

The binding sites of Calcium atom in the Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor (pdb code 6byv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor, PDB code: 6byv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:0.0 occ:1.00 HB3 A:ASP25 2.0 0.0 1.0 O A:TRP20 2.4 0.0 1.0 O A:ASP25 2.4 0.0 1.0 OE2 A:GLU34 2.5 0.0 1.0 OD2 A:ASP33 2.5 0.0 1.0 OD2 A:ASP27 2.5 0.0 1.0 OD1 A:ASP23 2.5 0.0 1.0 H A:ASP25 2.7 0.0 1.0 CB A:ASP25 3.0 0.0 1.0 HG2 A:GLU34 3.1 0.0 1.0 C A:ASP25 3.2 0.0 1.0 N A:ASP25 3.3 0.0 1.0 CA A:ASP25 3.3 0.0 1.0 HB3 A:TRP20 3.3 0.0 1.0 O A:LYS21 3.4 0.0 1.0 CG A:ASP27 3.4 0.0 1.0 H A:ASP23 3.5 0.0 1.0 CD A:GLU34 3.5 0.0 1.0 OD1 A:ASP27 3.5 0.0 1.0 HB2 A:ASP25 3.5 0.0 1.0 C A:TRP20 3.6 0.0 1.0 CG A:ASP23 3.7 0.0 1.0 CG A:GLU34 3.7 0.0 1.0 CG A:ASP33 3.7 0.0 1.0 H A:ASP27 3.9 0.0 1.0 HG3 A:GLU34 3.9 0.0 1.0 CG A:ASP25 4.0 0.0 1.0 C A:LYS21 4.1 0.0 1.0 HE3 A:TRP20 4.1 0.0 1.0 OD1 A:ASP25 4.2 0.0 1.0 OD2 A:ASP23 4.2 0.0 1.0 CB A:TRP20 4.2 0.0 1.0 HA A:TRP20 4.3 0.0 1.0 HB2 A:ASP33 4.3 0.0 1.0 HA A:CYS22 4.3 0.0 1.0 N A:ASP23 4.3 0.0 1.0 CA A:TRP20 4.3 0.0 1.0 HA A:ASP25 4.3 0.0 1.0 H A:GLY24 4.4 0.0 1.0 C A:GLY24 4.5 0.0 1.0 N A:PRO26 4.5 0.0 1.0 OD1 A:ASP33 4.6 0.0 1.0 N A:LYS21 4.6 0.0 1.0 N A:GLY24 4.6 0.0 1.0 OE1 A:GLU34 4.6 0.0 1.0 CB A:ASP33 4.6 0.0 1.0 N A:ASP27 4.7 0.0 1.0 HB2 A:TRP20 4.7 0.0 1.0 N A:CYS22 4.8 0.0 1.0 CB A:ASP27 4.8 0.0 1.0 CB A:ASP23 4.8 0.0 1.0 CA A:LYS21 4.9 0.0 1.0 C A:ASP23 4.9 0.0 1.0 CA A:CYS22 4.9 0.0 1.0 CA A:ASP23 4.9 0.0 1.0 HA A:LYS21 5.0 0.0 1.0 OD2 A:ASP25 5.0 0.0 1.0

Calcium binding site 2 out of 3 in the Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:0.0 occ:1.00 HG3 A:GLU77 1.9 0.0 1.0 OE2 A:GLU77 2.3 0.0 1.0 O A:GLU68 2.5 0.0 1.0 CG A:GLU77 2.5 0.0 1.0 OD1 A:ASP66 2.6 0.0 1.0 HA A:ARG64 2.6 0.0 1.0 OD2 A:ASP70 2.6 0.0 1.0 OD2 A:ASP76 2.6 0.0 1.0 HG2 A:GLU77 2.7 0.0 1.0 CD A:GLU77 2.7 0.0 1.0 O A:TRP63 2.7 0.0 1.0 H A:CYS65 2.8 0.0 1.0 HA A:ASN69 2.9 0.0 1.0 H A:ASP70 3.2 0.0 1.0 H A:ASP66 3.5 0.0 1.0 CA A:ARG64 3.6 0.0 1.0 CG A:ASP66 3.7 0.0 1.0 C A:GLU68 3.7 0.0 1.0 N A:CYS65 3.7 0.0 1.0 CG A:ASP70 3.8 0.0 1.0 C A:TRP63 3.8 0.0 1.0 CG A:ASP76 3.8 0.0 1.0 CA A:ASN69 3.9 0.0 1.0 OE1 A:GLU77 3.9 0.0 1.0 CB A:GLU77 3.9 0.0 1.0 N A:ASP70 4.0 0.0 1.0 HG2 A:ARG64 4.0 0.0 1.0 H A:GLU68 4.1 0.0 1.0 OD2 A:ASP66 4.1 0.0 1.0 HB3 A:ASP76 4.1 0.0 1.0 C A:ARG64 4.1 0.0 1.0 N A:ARG64 4.2 0.0 1.0 HB2 A:GLU77 4.2 0.0 1.0 HB3 A:GLU77 4.3 0.0 1.0 N A:ASN69 4.3 0.0 1.0 C A:ASN69 4.4 0.0 1.0 N A:ASP66 4.5 0.0 1.0 OD1 A:ASP70 4.5 0.0 1.0 CB A:ASP76 4.6 0.0 1.0 CB A:ARG64 4.7 0.0 1.0 SG A:CYS65 4.7 0.0 1.0 OD1 A:ASP76 4.7 0.0 1.0 HB3 A:TRP63 4.7 0.0 1.0 HB3 A:GLU68 4.7 0.0 1.0 HB2 A:ASP70 4.8 0.0 1.0 HB3 A:ARG64 4.8 0.0 1.0 CB A:ASP70 4.8 0.0 1.0 N A:GLU68 4.8 0.0 1.0 CA A:GLU68 4.8 0.0 1.0 CG A:ARG64 4.8 0.0 1.0 CA A:CYS65 4.8 0.0 1.0 CG A:ASN69 4.9 0.0 1.0 OD1 A:ASN69 4.9 0.0 1.0 CB A:ASP66 4.9 0.0 1.0

Calcium binding site 3 out of 3 in the Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Solution uc(Nmr) Structure of Cysteine-Rich Calcium Bound Domains of Very Low Density Lipoprotein Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:0.0 occ:1.00 H A:ASN105 2.2 0.0 1.0 OD2 A:ASP109 2.3 0.0 1.0 OE2 A:GLU116 2.3 0.0 1.0 HA A:CYS104 2.3 0.0 1.0 OD1 A:ASN105 2.5 0.0 1.0 OD2 A:ASP115 2.5 0.0 1.0 O A:GLN107 2.5 0.0 1.0 O A:PHE102 2.5 0.0 1.0 N A:ASN105 3.1 0.0 1.0 CG A:ASP109 3.2 0.0 1.0 CA A:CYS104 3.2 0.0 1.0 HG2 A:GLU116 3.3 0.0 1.0 CG A:ASN105 3.3 0.0 1.0 H A:GLN107 3.3 0.0 1.0 CD A:GLU116 3.4 0.0 1.0 OD1 A:ASP109 3.4 0.0 1.0 N A:CYS104 3.5 0.0 1.0 O A:VAL103 3.5 0.0 1.0 HD22 A:ASN105 3.6 0.0 1.0 C A:VAL103 3.6 0.0 1.0 C A:PHE102 3.6 0.0 1.0 C A:GLN107 3.7 0.0 1.0 C A:CYS104 3.7 0.0 1.0 CG A:ASP115 3.7 0.0 1.0 CG A:GLU116 3.8 0.0 1.0 ND2 A:ASN105 3.8 0.0 1.0 HD2 A:PHE102 3.9 0.0 1.0 H A:CYS104 3.9 0.0 1.0 N A:GLN107 4.1 0.0 1.0 HB2 A:ASP115 4.1 0.0 1.0 HG3 A:GLN107 4.1 0.0 1.0 HG3 A:GLU116 4.2 0.0 1.0 CA A:ASN105 4.2 0.0 1.0 HA A:PHE102 4.2 0.0 1.0 H A:GLY106 4.2 0.0 1.0 HB3 A:PHE102 4.3 0.0 1.0 CB A:ASN105 4.3 0.0 1.0 HB3 A:CYS104 4.4 0.0 1.0 CA A:GLN107 4.4 0.0 1.0 OE1 A:GLU116 4.4 0.0 1.0 CB A:CYS104 4.4 0.0 1.0 CA A:PHE102 4.4 0.0 1.0 HA A:ASP108 4.5 0.0 1.0 N A:GLY106 4.5 0.0 1.0 N A:VAL103 4.5 0.0 1.0 CB A:ASP115 4.5 0.0 1.0 CB A:ASP109 4.6 0.0 1.0 C A:ASN105 4.6 0.0 1.0 CA A:VAL103 4.6 0.0 1.0 OD1 A:ASP115 4.6 0.0 1.0 HE2 A:PHE90 4.6 0.0 1.0 HD21 A:ASN105 4.7 0.0 1.0 HA A:VAL103 4.7 0.0 1.0 HB3 A:ASP109 4.7 0.0 1.0 N A:ASP108 4.7 0.0 1.0 C A:ASP108 4.7 0.0 1.0 HB3 A:GLN107 4.8 0.0 1.0 HB3 A:ASN105 4.8 0.0 1.0 CA A:ASP108 4.9 0.0 1.0 CB A:PHE102 4.9 0.0 1.0 O A:ASP108 4.9 0.0 1.0 O A:ASP115 4.9 0.0 1.0 CD2 A:PHE102 4.9 0.0 1.0 O A:CYS104 4.9 0.0 1.0 N A:ASP109 5.0 0.0 1.0

K.Banerjee, S.Yakovlev, J.M.Gruschus, L.Medved, N.Tjandra. Nuclear Magnetic Resonance Solution Structure of the Recombinant Fragment Containing Three Fibrin-Binding Cysteine-Rich Domains of the Very Low Density Lipoprotein Receptor. Biochemistry V. 57 4395 2018.
ISSN: ISSN 1520-4995
PubMed: 29965730
DOI: 10.1021/ACS.BIOCHEM.8B00349