Sodium 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
Cadmium	(Cd)	4 atoms

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

Sodium 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 Sodium with other atoms in the Na 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:Na1566 b:29.1 occ:1.00 O A:THR369 2.2 37.5 1.0 OD1 A:ASP360 2.2 41.4 1.0 O A:HOH2049 2.2 35.4 1.0 O A:LEU361 2.3 40.0 1.0 O A:CYS367 2.4 45.5 1.0 OE2 A:GLU389 2.4 36.8 1.0 CD A:GLU389 3.4 35.8 1.0 C A:THR369 3.4 38.4 1.0 C A:LEU361 3.4 40.6 1.0 C A:CYS367 3.4 45.8 1.0 N A:LEU361 3.4 38.7 1.0 CG A:ASP360 3.5 40.4 1.0 OE1 A:GLU389 3.6 38.3 1.0 NA A:NA1567 3.8 40.9 1.0 CA A:LEU361 3.8 39.6 1.0 N A:THR369 4.0 41.0 1.0 C A:ASP368 4.1 42.2 1.0 C A:ASP360 4.1 38.4 1.0 CA A:CYS367 4.1 46.8 1.0 CB A:CYS367 4.2 46.9 1.0 CA A:THR369 4.2 40.3 1.0 OD2 A:ASP360 4.2 43.4 1.0 CB A:LEU361 4.2 39.6 1.0 CA A:ASP360 4.3 38.4 1.0 O A:ASP368 4.3 41.9 1.0 N A:ASP368 4.4 44.4 1.0 N A:LEU370 4.4 36.8 1.0 CB A:ASP360 4.5 39.0 1.0 CD2 A:LEU370 4.6 34.8 1.0 CA A:ASP368 4.6 43.5 1.0 N A:CYS362 4.6 41.8 1.0 CA A:LEU370 4.6 35.7 1.0 CB A:THR369 4.7 40.3 1.0 CG A:GLU389 4.8 32.6 1.0 O A:ASP360 5.0 37.3 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1567 b:40.9 occ:1.00 O A:HOH2049 2.5 35.4 1.0 O A:CYS367 2.9 45.5 1.0 OD2 A:ASP360 3.0 43.4 1.0 OD1 A:ASP360 3.2 41.4 1.0 CG A:ASP360 3.4 40.4 1.0 NA A:NA1566 3.8 29.1 1.0 C A:CYS367 3.8 45.8 1.0 CB A:CYS367 4.1 46.9 1.0 CA A:CYS367 4.6 46.8 1.0 N A:ASP368 4.6 44.4 1.0 OE1 A:GLU389 4.7 38.3 1.0 CB A:ASP360 4.8 39.0 1.0 CA A:ASP368 4.8 43.5 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1562 b:45.1 occ:1.00 O B:THR369 2.3 51.9 1.0 OD1 B:ASP360 2.3 55.4 1.0 O B:LEU361 2.4 56.0 1.0 O B:CYS367 2.6 58.4 1.0 OE2 B:GLU389 2.8 41.7 1.0 NA B:NA1563 3.4 45.0 1.0 C B:THR369 3.5 52.1 1.0 C B:CYS367 3.5 58.5 1.0 CG B:ASP360 3.5 54.7 1.0 C B:LEU361 3.5 56.1 1.0 N B:LEU361 3.6 54.8 1.0 CD B:GLU389 3.6 41.3 1.0 OE1 B:GLU389 3.8 42.1 1.0 SG B:CYS367 3.9 61.4 1.0 N B:THR369 4.0 54.3 1.0 C B:ASP368 4.0 55.6 1.0 CA B:LEU361 4.1 55.4 1.0 C B:ASP360 4.2 54.0 1.0 O B:ASP368 4.2 55.4 1.0 CA B:THR369 4.2 53.4 1.0 OD2 B:ASP360 4.3 55.8 1.0 CD2 B:LEU370 4.3 49.0 1.0 N B:ASP368 4.3 57.5 1.0 CA B:CYS367 4.4 59.4 1.0 CA B:ASP360 4.4 53.5 1.0 CA B:ASP368 4.4 56.7 1.0 N B:LEU370 4.5 50.5 1.0 CB B:ASP360 4.6 53.8 1.0 CB B:CYS367 4.6 59.4 1.0 CB B:LEU361 4.6 55.4 1.0 N B:CYS362 4.7 56.8 1.0 CB B:THR369 4.7 53.4 1.0 CA B:LEU370 4.7 49.4 1.0 CA B:CYS362 5.0 57.5 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1563 b:45.0 occ:1.00 O B:CYS367 2.8 58.4 1.0 OD1 B:ASP360 2.8 55.4 1.0 OD2 B:ASP360 3.2 55.8 1.0 CG B:ASP360 3.3 54.7 1.0 NA B:NA1562 3.4 45.1 1.0 C B:CYS367 3.9 58.5 1.0 OE1 B:GLU389 4.6 42.1 1.0 CB B:CYS367 4.6 59.4 1.0 CB B:ASP360 4.6 53.8 1.0 SG B:CYS367 4.6 61.4 1.0 CA B:ASP368 4.7 56.7 1.0 N B:ASP368 4.7 57.5 1.0 CA B:CYS367 4.9 59.4 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