Cadmium in PDB 2v4b: Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)

The structure of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form), PDB code: 2v4b was solved by S.Gerhardt, G.Hassall, P.Hawtin, E.Mccall, L.Flavell, C.Minshull, D.Hargreaves, A.Ting, R.A.Pauptit, A.E.Parker, W.M.Abbott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.26 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.579, 64.396, 113.524, 90.00, 90.91, 90.00
R / Rfree (%)	22 / 26.3

The structure of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) also contains other interesting chemical elements:

Nickel	(Ni)	14 atoms
Magnesium	(Mg)	3 atoms
Zinc	(Zn)	2 atoms
Sodium	(Na)	4 atoms

The binding sites of Cadmium atom in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) (pdb code 2v4b). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form), PDB code: 2v4b:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1553 b:38.0 occ:1.00 OD2 A:ASP465 2.2 34.1 1.0 OD1 A:ASP344 2.3 48.4 1.0 O A:HOH2044 2.3 20.3 1.0 O A:HOH2091 2.4 30.1 1.0 OE2 A:GLU261 2.6 38.3 1.0 OE1 A:GLU261 2.6 31.6 1.0 O A:ASP344 2.8 48.8 1.0 CD A:GLU261 3.0 34.2 1.0 CG A:ASP344 3.2 49.9 1.0 CG A:ASP465 3.3 36.9 1.0 OD1 A:ASP465 3.8 39.5 1.0 C A:ASP344 3.8 48.1 1.0 O A:HOH2041 3.8 50.2 1.0 OD2 A:ASP344 3.9 50.6 1.0 NI A:NI1557 4.0 28.2 1.0 O A:HOH2090 4.0 45.1 1.0 CB A:ASP344 4.2 49.0 1.0 CA A:ASP344 4.2 48.8 1.0 O A:ASP346 4.2 41.6 1.0 O A:HIS349 4.3 35.2 1.0 O A:LYS466 4.3 40.2 1.0 CG A:GLU261 4.5 32.4 1.0 CB A:ASP465 4.6 36.5 1.0 O A:HOH2089 4.8 33.9 1.0 CB A:HIS349 4.9 36.4 1.0 N A:ARG345 5.0 47.4 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1554 b:35.4 occ:1.00 O A:HOH2027 2.2 35.4 1.0 OE1 A:GLU320 2.3 39.6 1.0 OE1 A:GLU315 2.3 34.0 1.0 CD A:GLU315 3.2 34.9 1.0 OE2 A:GLU315 3.4 32.3 1.0 CD A:GLU320 3.5 37.5 1.0 NI A:NI1559 3.8 59.6 1.0 OE2 A:GLU320 4.0 37.3 1.0 CG A:GLU315 4.6 35.3 1.0 O A:HOH2031 4.6 28.9 1.0 CG A:GLU320 4.7 34.5 1.0 CB A:GLU320 4.7 34.5 1.0 CA A:GLU320 4.8 34.5 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1554 b:43.5 occ:1.00 ND1 B:HIS280 2.2 29.7 1.0 OD1 A:ASP483 2.3 28.6 1.0 O B:HOH2010 2.3 33.1 1.0 OD2 A:ASP483 2.9 35.2 1.0 CG A:ASP483 3.0 32.4 1.0 CE1 B:HIS280 3.1 32.0 1.0 CG B:HIS280 3.3 31.0 1.0 CB B:HIS280 3.7 29.8 1.0 CG A:ARG486 4.2 36.1 1.0 NE2 B:HIS280 4.3 31.9 1.0 O A:HOH2098 4.3 39.6 1.0 CA B:HIS280 4.3 30.1 1.0 CB A:ASN485 4.4 32.7 1.0 CD2 B:HIS280 4.4 31.5 1.0 CB A:ASP483 4.5 32.2 1.0 ND2 A:ASN485 4.5 30.8 1.0 CD A:ARG486 4.6 40.2 1.0 O A:HOH2100 4.9 39.9 1.0 N A:ARG486 4.9 33.1 1.0 CG A:ASN485 5.0 33.3 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1556 b:41.5 occ:1.00 OD2 B:ASP465 2.1 40.3 1.0 OD1 B:ASP344 2.2 41.3 1.0 O B:HOH2024 2.4 29.0 1.0 OE1 B:GLU261 2.4 37.1 1.0 OE2 B:GLU261 2.5 37.6 1.0 CD B:GLU261 2.8 36.4 1.0 O B:ASP344 3.0 48.3 1.0 CG B:ASP344 3.1 46.9 1.0 CG B:ASP465 3.2 41.3 1.0 OD2 B:ASP344 3.6 45.9 1.0 OD1 B:ASP465 3.6 42.1 1.0 O B:HOH2023 4.0 39.0 1.0 NI B:NI1557 4.0 29.4 1.0 OE1 B:GLN468 4.0 51.6 1.0 C B:ASP344 4.0 48.3 1.0 O B:LYS466 4.1 44.6 1.0 CB B:ASP344 4.2 48.0 1.0 O B:HIS349 4.2 40.7 1.0 CG B:GLU261 4.3 35.6 1.0 O B:ASP346 4.3 47.5 1.0 CA B:ASP344 4.4 48.3 1.0 CB B:ASP465 4.4 41.1 1.0 O B:HOH2046 4.8 22.6 1.0 C B:LYS466 5.0 45.0 1.0

S.Gerhardt, G.Hassall, P.Hawtin, E.Mccall, L.Flavell, C.Minshull, D.Hargreaves, A.Ting, R.A.Pauptit, A.E.Parker, W.M.Abbott. Crystal Structures of Human Adamts-1 Reveal A Conserved Catalytic Domain and A Disintegrin-Like Domain with A Fold Homologous to Cysteine-Rich Domains. J.Mol.Biol. V. 373 891 2007.
ISSN: ISSN 0022-2836
PubMed: 17897672
DOI: 10.1016/J.JMB.2007.07.047