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:
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
|