Atomistry » Sodium » PDB 2isz-2jln » 2jih
Atomistry »
  Sodium »
    PDB 2isz-2jln »
      2jih »

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

Go back to Sodium Binding Sites List in 2jih
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

Go back to Sodium Binding Sites List in 2jih
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

Go back to Sodium Binding Sites List in 2jih
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: Mon Oct 7 03:01:27 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy