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

Protein crystallography data

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

Other elements in 2v4b:

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
Zinc (Zn) 2 atoms
Cadmium (Cd) 4 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 3 in 2v4b

Go back to Magnesium Binding Sites List in 2v4b
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg1560

b:40.0
occ:1.00
ND1 A:HIS339 2.6 39.5 1.0
O A:HOH2038 3.1 58.3 1.0
NZ A:LYS308 3.3 40.4 1.0
CE1 A:HIS339 3.4 39.6 1.0
CG A:HIS339 3.7 37.7 1.0
CB A:HIS339 4.0 38.1 1.0
CA A:HIS339 4.0 37.9 1.0
CE A:LYS308 4.2 39.4 1.0
O A:HOH2037 4.4 42.6 1.0
O A:HIS339 4.5 39.5 1.0
NE2 A:HIS339 4.6 39.3 1.0
C A:HIS339 4.7 38.8 1.0
CD2 A:HIS339 4.8 39.3 1.0
O A:GLN338 4.9 37.4 1.0

Magnesium binding site 2 out of 3 in 2v4b

Go back to Magnesium Binding Sites List in 2v4b
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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:Mg1565

b:52.6
occ:1.00
O A:HOH2126 2.2 43.8 1.0
OD1 A:ASN542 2.5 40.3 1.0
CD2 A:HIS439 2.6 56.6 1.0
OD2 A:ASP530 2.6 39.5 1.0
NE2 A:HIS439 2.7 56.9 1.0
CG A:ASP530 3.3 35.1 1.0
OD1 A:ASP530 3.4 38.0 1.0
CG A:HIS439 3.5 55.4 1.0
CE1 A:HIS439 3.5 57.0 1.0
CG A:ASN542 3.7 39.5 1.0
ND1 A:HIS439 3.9 56.7 1.0
CA A:ASN542 4.2 37.5 1.0
O A:HOH2120 4.2 34.0 1.0
N A:ASN542 4.3 37.1 1.0
O A:HOH2116 4.4 42.4 1.0
CB A:HIS439 4.4 54.6 1.0
CB A:ASN542 4.5 38.2 1.0
ND2 A:ASN542 4.7 39.7 1.0
O A:HOH2118 4.7 34.6 1.0
CB A:ASP530 4.7 34.3 1.0
O A:HOH2119 5.0 36.6 1.0

Magnesium binding site 3 out of 3 in 2v4b

Go back to Magnesium Binding Sites List in 2v4b
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg 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:Mg1558

b:51.4
occ:1.00
OD1 B:ASN542 2.5 43.6 1.0
OD2 B:ASP530 2.5 37.2 1.0
O B:HOH2071 3.1 38.8 1.0
CG B:ASP530 3.3 35.3 1.0
OD1 B:ASP530 3.3 35.7 1.0
CD2 B:HIS439 3.6 59.0 1.0
CG B:ASN542 3.6 41.3 1.0
CA B:ASN542 4.0 39.8 1.0
O B:HOH2073 4.1 47.0 1.0
CG B:HIS439 4.1 57.0 1.0
NE2 B:HIS439 4.2 60.2 1.0
N B:ASN542 4.2 39.4 1.0
CB B:ASN542 4.4 40.4 1.0
CB B:HIS439 4.6 55.0 1.0
ND2 B:ASN542 4.6 45.0 1.0
CB B:ASP530 4.7 35.1 1.0
O B:HOH2072 4.9 39.7 1.0
ND1 B:HIS439 4.9 58.9 1.0
CE1 B:HIS439 4.9 59.7 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: Mon Dec 14 07:40:48 2020

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