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

Protein crystallography data

The structure of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form), PDB code: 2jih 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) 56.90 / 2.10
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 (%) 22.4 / 28.2

Other elements in 2jih:

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

Nickel (Ni) 12 atoms
Magnesium (Mg) 6 atoms
Zinc (Zn) 2 atoms
Sodium (Na) 5 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form) (pdb code 2jih). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form), PDB code: 2jih:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 2jih

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Cadmium binding site 1 out of 6 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-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 (Complex-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1554

b:38.2
occ:1.00
OD1 A:ASP344 2.2 49.6 1.0
O A:HOH2038 2.3 28.1 1.0
OD2 A:ASP465 2.4 42.8 1.0
OE2 A:GLU261 2.5 31.4 1.0
OE1 A:GLU261 2.5 38.1 1.0
O A:ASP344 2.6 51.3 1.0
O A:HOH2081 2.8 26.9 1.0
CD A:GLU261 2.8 34.1 1.0
CG A:ASP344 3.2 49.6 1.0
CG A:ASP465 3.5 43.1 1.0
C A:ASP344 3.7 50.7 1.0
OD2 A:ASP344 3.9 47.6 1.0
CD A:CD1558 4.0 44.2 1.0
O A:HOH2039 4.0 31.3 1.0
CB A:ASP344 4.0 50.6 1.0
OD1 A:ASP465 4.1 43.6 1.0
CA A:ASP344 4.1 50.7 1.0
O A:HIS349 4.1 35.9 1.0
CG A:GLU261 4.3 34.3 1.0
O A:ASP346 4.3 47.9 1.0
O A:LYS466 4.4 43.4 1.0
CB A:ASP465 4.6 41.9 1.0
O A:HOH2080 4.8 30.3 1.0
N A:ARG345 4.9 50.5 1.0
CB A:HIS349 5.0 38.1 1.0

Cadmium binding site 2 out of 6 in 2jih

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Cadmium binding site 2 out of 6 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-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 (Complex-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1555

b:45.4
occ:1.00
O A:HOH2026 2.0 35.2 1.0
O A:HOH2023 2.4 25.8 1.0
OE1 A:GLU320 2.5 41.5 1.0
OE1 A:GLU315 2.6 38.4 1.0
O A:HOH2024 3.2 39.2 1.0
CD A:GLU315 3.3 41.4 1.0
OE2 A:GLU315 3.4 40.7 1.0
NI A:NI1559 3.7 71.0 1.0
CD A:GLU320 3.7 42.0 1.0
CB A:GLU320 4.5 40.1 1.0
O A:HOH2025 4.5 46.7 1.0
OE2 A:GLU320 4.5 42.2 1.0
O A:HOH2027 4.6 38.5 1.0
CG A:GLU320 4.6 40.9 1.0
CA A:GLU320 4.7 39.8 1.0
CG A:GLU315 4.7 41.0 1.0

Cadmium binding site 3 out of 6 in 2jih

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Cadmium binding site 3 out of 6 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-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 (Complex-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1557

b:42.3
occ:1.00
OD1 B:ASP483 2.3 36.1 1.0
ND1 A:HIS280 2.3 26.3 1.0
O A:HOH2046 3.0 31.1 1.0
CE1 A:HIS280 3.1 27.8 1.0
CG B:ASP483 3.2 33.3 1.0
OD2 B:ASP483 3.3 32.2 1.0
CG A:HIS280 3.4 29.7 1.0
CB A:HIS280 3.8 31.3 1.0
CA A:HIS280 4.2 31.8 1.0
O B:HOH2070 4.3 34.2 1.0
NE2 A:HIS280 4.3 31.5 1.0
CD2 A:HIS280 4.4 28.4 1.0
CB B:ASN485 4.5 33.1 1.0
CG B:ARG486 4.6 30.9 1.0
CB B:ASP483 4.6 34.0 1.0
ND2 B:ASN485 4.7 31.6 1.0
CD B:ARG486 4.9 33.1 1.0

Cadmium binding site 4 out of 6 in 2jih

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Cadmium binding site 4 out of 6 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-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 (Complex-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1558

b:44.2
occ:1.00
OE1 A:GLU261 2.2 38.1 1.0
O A:CYS462 2.3 36.5 1.0
O A:HOH2080 2.3 30.3 1.0
OD1 A:ASP465 2.4 43.6 1.0
OD2 A:ASP351 2.5 27.0 1.0
OD2 A:ASP344 2.5 47.6 1.0
OD1 A:ASP351 2.7 30.0 1.0
CG A:ASP351 2.9 27.5 1.0
CG A:ASP344 3.2 49.6 1.0
OD1 A:ASP344 3.2 49.6 1.0
CG A:ASP465 3.3 43.1 1.0
CD A:GLU261 3.3 34.1 1.0
OD2 A:ASP465 3.4 42.8 1.0
C A:CYS462 3.5 37.3 1.0
CG A:GLU261 3.9 34.3 1.0
CD A:CD1554 4.0 38.2 1.0
CB A:GLU261 4.2 35.0 1.0
CA A:LEU463 4.3 38.1 1.0
OE2 A:GLU261 4.3 31.4 1.0
O A:ASP465 4.3 42.9 1.0
O A:TYR259 4.3 38.4 1.0
N A:LEU463 4.3 37.5 1.0
CB A:ASP351 4.4 29.0 1.0
CA A:CYS462 4.6 37.1 1.0
CB A:ASP344 4.6 50.6 1.0
O A:HOH2044 4.6 43.0 1.0
CB A:ASP465 4.7 41.9 1.0
CB A:CYS462 4.7 36.9 1.0
C A:LEU463 4.8 38.9 1.0
N A:ASP465 4.9 41.6 1.0
N A:GLU261 4.9 35.8 1.0
SG A:CYS462 5.0 36.0 1.0

Cadmium binding site 5 out of 6 in 2jih

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Cadmium binding site 5 out of 6 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1555

b:47.2
occ:1.00
OD1 A:ASP483 2.2 34.6 1.0
ND1 B:HIS280 2.2 35.4 1.0
O A:HOH2089 2.5 30.0 1.0
CG A:ASP483 3.0 33.6 1.0
CE1 B:HIS280 3.0 34.7 1.0
OD2 A:ASP483 3.0 35.9 1.0
O A:HOH2088 3.2 46.9 1.0
CG B:HIS280 3.3 34.3 1.0
CB B:HIS280 3.8 35.5 1.0
O A:HOH2087 4.0 39.5 1.0
NE2 B:HIS280 4.2 32.5 1.0
CG A:ARG486 4.2 32.9 1.0
CA B:HIS280 4.2 34.2 1.0
CD2 B:HIS280 4.4 36.5 1.0
CB A:ASP483 4.4 31.8 1.0
CB A:ASN485 4.4 29.3 1.0
ND2 A:ASN485 4.5 33.1 1.0
O A:HOH2091 4.7 36.5 1.0
O B:HOH2067 4.7 39.9 1.0
CD A:ARG486 4.8 37.4 1.0
CG B:PRO474 5.0 41.9 1.0
N A:ARG486 5.0 29.7 1.0

Cadmium binding site 6 out of 6 in 2jih

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Cadmium binding site 6 out of 6 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1557

b:43.4
occ:1.00
OD1 B:ASP344 2.1 44.6 1.0
O B:HOH2026 2.2 45.5 1.0
OD2 B:ASP465 2.3 42.5 1.0
OE2 B:GLU261 2.6 34.9 1.0
O B:HOH2063 2.6 32.9 1.0
OE1 B:GLU261 2.7 38.5 1.0
CD B:GLU261 3.0 36.3 1.0
O B:ASP344 3.0 50.9 1.0
CG B:ASP344 3.1 50.3 1.0
CG B:ASP465 3.3 41.9 1.0
OD1 B:ASP465 3.7 40.4 1.0
OD2 B:ASP344 3.7 44.5 1.0
NI B:NI1558 4.0 26.8 1.0
C B:ASP344 4.1 50.9 1.0
O B:LYS466 4.1 45.6 1.0
O B:HOH2064 4.2 35.8 1.0
CB B:ASP344 4.2 51.0 1.0
O B:HIS349 4.3 42.7 1.0
O B:ASP346 4.3 50.6 1.0
O B:HOH2062 4.3 41.0 1.0
CA B:ASP344 4.4 51.1 1.0
CG B:GLU261 4.4 35.7 1.0
OE1 B:GLN468 4.5 52.8 1.0
CB B:ASP465 4.6 41.9 1.0
O B:HOH2061 4.7 30.1 1.0
O B:ASP465 4.7 43.1 1.0
C B:LYS466 4.9 45.6 1.0

Reference:

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
Page generated: Wed Oct 28 09:59:37 2020
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