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Sodium 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
Cadmium (Cd) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Complex-Form), PDB code: 2jih:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2jih

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Sodium binding site 1 out of 5 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 Sodium with other atoms in the Na 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:Na1565

b:37.9
occ:1.00
OE2 A:GLU389 2.1 32.1 1.0
OD1 A:ASP360 2.2 43.2 1.0
O A:CYS367 2.4 50.5 1.0
O A:THR369 2.4 42.0 1.0
O A:LEU361 2.5 44.2 1.0
CD A:GLU389 3.1 35.4 1.0
N A:LEU361 3.3 43.2 1.0
C A:CYS367 3.4 50.8 1.0
CG A:ASP360 3.4 43.5 1.0
OE1 A:GLU389 3.4 35.6 1.0
C A:THR369 3.6 41.9 1.0
C A:LEU361 3.6 44.5 1.0
NA A:NA1566 3.6 35.0 1.0
C A:ASP368 3.8 47.5 1.0
N A:THR369 3.8 45.6 1.0
C A:ASP360 3.9 42.4 1.0
CA A:LEU361 3.9 43.2 1.0
O A:ASP368 4.0 47.4 1.0
CA A:ASP360 4.1 42.0 1.0
CA A:THR369 4.2 43.9 1.0
CA A:CYS367 4.2 51.7 1.0
OD2 A:ASP360 4.2 46.0 1.0
N A:ASP368 4.3 49.8 1.0
CA A:ASP368 4.3 49.2 1.0
CB A:LEU361 4.3 42.5 1.0
CB A:ASP360 4.3 42.5 1.0
CB A:CYS367 4.4 51.5 1.0
CG A:GLU389 4.5 33.1 1.0
CB A:THR369 4.6 43.5 1.0
N A:LEU370 4.6 39.6 1.0
N A:CYS362 4.8 46.2 1.0
CD2 A:LEU370 4.8 39.0 1.0
O A:ASP360 4.8 42.1 1.0
CA A:LEU370 4.9 38.7 1.0

Sodium binding site 2 out of 5 in 2jih

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Sodium binding site 2 out of 5 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 Sodium with other atoms in the Na 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:Na1566

b:35.0
occ:1.00
O A:CYS367 2.6 50.5 1.0
OD2 A:ASP360 2.7 46.0 1.0
O A:HOH2050 2.8 43.5 1.0
OD1 A:ASP360 2.9 43.2 1.0
CG A:ASP360 3.2 43.5 1.0
C A:CYS367 3.5 50.8 1.0
NA A:NA1565 3.6 37.9 1.0
CB A:CYS367 3.9 51.5 1.0
N A:ASP368 4.2 49.8 1.0
CA A:ASP368 4.3 49.2 1.0
CA A:CYS367 4.3 51.7 1.0
OD1 A:ASP368 4.7 52.7 1.0
CB A:ASP360 4.7 42.5 1.0
C A:ASP368 4.9 47.5 1.0

Sodium binding site 3 out of 5 in 2jih

Go back to Sodium Binding Sites List in 2jih
Sodium binding site 3 out of 5 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 Sodium with other atoms in the Na 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:Na1567

b:37.0
occ:1.00
O A:PRO410 2.7 32.6 1.0
OD1 A:ASP412 2.8 39.8 1.0
OG A:SER447 2.8 34.8 1.0
N A:SER447 3.5 39.2 1.0
CG A:ASP412 3.7 37.6 1.0
CB A:MET430 3.7 39.3 1.0
CA A:SER447 3.7 37.8 1.0
C A:PRO410 3.8 33.8 1.0
CB A:SER447 3.8 37.8 1.0
OG A:SER444 3.8 38.6 1.0
CG A:MET430 3.9 37.0 1.0
CB A:CYS446 3.9 41.1 1.0
SG A:CYS417 4.0 45.2 1.0
CD A:PRO410 4.0 33.0 1.0
SG A:CYS446 4.0 44.5 1.0
C A:CYS446 4.0 39.6 1.0
N A:ASP412 4.1 36.6 1.0
C A:HIS411 4.1 36.4 1.0
CA A:ASP412 4.1 37.6 1.0
O A:HIS411 4.2 36.5 1.0
CB A:MET409 4.2 33.8 1.0
N A:PRO410 4.2 33.0 1.0
O A:HOH2075 4.4 38.2 1.0
CG A:PRO410 4.4 32.7 1.0
OD2 A:ASP412 4.4 35.7 1.0
CB A:ASP412 4.5 37.3 1.0
O A:CYS446 4.6 39.3 1.0
CA A:PRO410 4.6 33.2 1.0
CA A:CYS446 4.6 40.8 1.0
N A:HIS411 4.6 34.9 1.0
C A:MET409 4.7 33.3 1.0
CA A:HIS411 4.7 35.6 1.0
CA A:MET409 4.8 33.8 1.0

Sodium binding site 4 out of 5 in 2jih

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Sodium binding site 4 out of 5 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 Sodium with other atoms in the Na 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
B:Na1564

b:51.9
occ:1.00
O B:LEU361 2.3 48.5 1.0
OE2 B:GLU389 2.4 39.8 1.0
OD1 B:ASP360 2.4 42.1 1.0
O B:CYS367 2.5 52.2 1.0
O B:THR369 2.6 44.7 1.0
O B:HOH2039 2.6 50.7 1.0
N B:THR369 3.3 47.6 1.0
N B:LEU361 3.3 45.8 1.0
C B:LEU361 3.4 48.2 1.0
C B:CYS367 3.4 52.5 1.0
CD B:GLU389 3.5 40.4 1.0
C B:ASP368 3.5 49.1 1.0
C B:THR369 3.5 44.8 1.0
CG B:ASP360 3.6 45.3 1.0
NA B:NA1565 3.6 38.0 1.0
CA B:LEU361 3.8 46.8 1.0
OE1 B:GLU389 3.8 40.9 1.0
CA B:THR369 3.9 46.6 1.0
CA B:ASP368 3.9 50.2 1.0
O B:ASP368 4.0 48.9 1.0
C B:ASP360 4.0 44.8 1.0
N B:ASP368 4.0 51.5 1.0
CA B:ASP360 4.2 44.1 1.0
CB B:LEU361 4.3 46.4 1.0
OD2 B:ASP360 4.4 47.7 1.0
CB B:THR369 4.4 46.5 1.0
CA B:CYS367 4.5 53.8 1.0
CB B:ASP360 4.5 44.7 1.0
N B:CYS362 4.5 49.8 1.0
N B:LEU370 4.7 42.9 1.0
SG B:CYS367 4.8 56.1 1.0
CG B:GLU389 4.8 36.3 1.0
O B:ASP360 4.9 44.5 1.0
CA B:CYS362 5.0 51.1 1.0

Sodium binding site 5 out of 5 in 2jih

Go back to Sodium Binding Sites List in 2jih
Sodium binding site 5 out of 5 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 Sodium with other atoms in the Na 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:Na1565

b:38.0
occ:1.00
O B:HOH2039 2.6 50.7 1.0
OD2 B:ASP360 2.8 47.7 1.0
O B:CYS367 2.9 52.2 1.0
OD1 B:ASP360 3.0 42.1 1.0
CG B:ASP360 3.2 45.3 1.0
NA B:NA1564 3.6 51.9 1.0
C B:CYS367 3.8 52.5 1.0
CA B:ASP368 4.0 50.2 1.0
N B:ASP368 4.3 51.5 1.0
O B:HOH2030 4.4 40.8 1.0
CB B:ASP360 4.7 44.7 1.0
OD1 B:ASP368 4.7 49.9 1.0
C B:ASP368 4.8 49.1 1.0
OE2 B:GLU389 4.9 39.8 1.0
OE1 B:GLU389 4.9 40.9 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: Thu Oct 29 04:12:35 2020

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