Potassium in PDB 1ovl: Crystal Structure of NURR1 Lbd
Protein crystallography data
The structure of Crystal Structure of NURR1 Lbd, PDB code: 1ovl
was solved by
Z.Wang,
J.Liu,
N.Walker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
500.00 /
2.20
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.383,
80.383,
227.370,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1ovl:
The structure of Crystal Structure of NURR1 Lbd also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of NURR1 Lbd
(pdb code 1ovl). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the
Crystal Structure of NURR1 Lbd, PDB code: 1ovl:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Potassium binding site 1 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 1 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K707
b:57.6
occ:1.00
|
O
|
A:HOH900
|
3.6
|
50.7
|
1.0
|
CG
|
A:MSE496
|
4.0
|
35.1
|
1.0
|
CA
|
A:MSE496
|
4.1
|
28.8
|
1.0
|
CD2
|
A:TYR551
|
4.2
|
22.7
|
1.0
|
CE2
|
A:TYR551
|
4.2
|
24.4
|
1.0
|
BR
|
A:BR818
|
4.2
|
67.7
|
1.0
|
CB
|
A:MSE496
|
4.3
|
30.7
|
1.0
|
CE
|
A:MSE496
|
4.3
|
35.4
|
1.0
|
O
|
A:MSE496
|
4.5
|
26.0
|
1.0
|
NZ
|
A:LYS554
|
4.6
|
47.0
|
1.0
|
O
|
A:ASN495
|
4.6
|
31.5
|
1.0
|
C
|
A:MSE496
|
4.8
|
27.1
|
1.0
|
CG
|
A:LYS554
|
4.8
|
41.2
|
1.0
|
|
Potassium binding site 2 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 2 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K703
b:41.4
occ:1.00
|
OE1
|
B:GLN405
|
3.4
|
45.8
|
1.0
|
CD1
|
B:PHE479
|
3.7
|
32.6
|
1.0
|
CE1
|
B:PHE479
|
3.7
|
32.8
|
1.0
|
O
|
B:HIS402
|
3.8
|
38.9
|
1.0
|
CG
|
B:GLN405
|
4.0
|
41.8
|
1.0
|
N
|
B:PHE406
|
4.0
|
32.2
|
1.0
|
CD
|
B:GLN405
|
4.1
|
44.1
|
1.0
|
CA
|
B:CYS475
|
4.1
|
33.3
|
1.0
|
CB
|
B:GLN405
|
4.1
|
36.6
|
1.0
|
CA
|
B:PHE406
|
4.2
|
30.0
|
1.0
|
CA
|
B:GLY478
|
4.2
|
31.7
|
1.0
|
CD1
|
B:LEU409
|
4.4
|
28.2
|
1.0
|
CB
|
B:PHE406
|
4.4
|
31.1
|
1.0
|
C
|
B:GLN405
|
4.4
|
32.5
|
1.0
|
O
|
B:CYS475
|
4.4
|
33.3
|
1.0
|
O
|
B:GLN474
|
4.4
|
36.4
|
1.0
|
N
|
B:GLY478
|
4.5
|
32.4
|
1.0
|
CB
|
B:CYS475
|
4.6
|
31.8
|
1.0
|
N
|
B:PHE479
|
4.6
|
31.5
|
1.0
|
C
|
B:CYS475
|
4.7
|
32.8
|
1.0
|
SG
|
B:CYS475
|
4.8
|
34.7
|
1.0
|
O
|
B:GLN405
|
4.8
|
31.9
|
1.0
|
C
|
B:GLY478
|
4.8
|
31.4
|
1.0
|
C
|
B:HIS402
|
4.8
|
39.5
|
1.0
|
N
|
B:CYS475
|
4.9
|
33.5
|
1.0
|
CA
|
B:GLN405
|
4.9
|
33.9
|
1.0
|
|
Potassium binding site 3 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 3 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K704
b:44.8
occ:1.00
|
O
|
B:HOH985
|
3.3
|
42.0
|
1.0
|
CA
|
B:TYR551
|
3.7
|
24.0
|
1.0
|
N
|
B:TYR551
|
3.9
|
23.1
|
1.0
|
C
|
B:ASN550
|
4.1
|
23.8
|
1.0
|
O
|
B:ASN550
|
4.1
|
24.1
|
1.0
|
CB
|
B:TYR551
|
4.3
|
24.8
|
1.0
|
CB
|
B:LYS554
|
4.4
|
34.5
|
1.0
|
CD2
|
B:TYR551
|
4.5
|
28.0
|
1.0
|
CB
|
B:ASN550
|
4.5
|
28.1
|
1.0
|
CG
|
B:LYS554
|
4.6
|
40.4
|
1.0
|
NE2
|
F:HIS516
|
4.6
|
66.1
|
1.0
|
CG
|
B:TYR551
|
4.9
|
28.5
|
1.0
|
CA
|
B:ASN550
|
5.0
|
25.3
|
1.0
|
C
|
B:TYR551
|
5.0
|
22.7
|
1.0
|
|
Potassium binding site 4 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 4 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K705
b:41.9
occ:1.00
|
BR
|
B:BR800
|
3.2
|
21.3
|
1.0
|
O
|
B:HOH989
|
3.3
|
47.7
|
1.0
|
O
|
B:HOH962
|
3.3
|
43.5
|
1.0
|
ND2
|
B:ASN547
|
3.5
|
15.7
|
1.0
|
O
|
E:HOH851
|
3.7
|
25.9
|
1.0
|
CD1
|
B:LEU552
|
3.8
|
21.6
|
1.0
|
CE
|
B:LYS536
|
3.9
|
31.3
|
1.0
|
CB
|
B:ASN547
|
4.1
|
14.0
|
1.0
|
CA
|
B:PRO549
|
4.1
|
22.1
|
1.0
|
CD
|
B:LYS536
|
4.2
|
29.1
|
1.0
|
CG
|
B:ASN547
|
4.2
|
18.6
|
1.0
|
CG
|
B:LYS536
|
4.3
|
26.3
|
1.0
|
N
|
B:PRO549
|
4.3
|
23.1
|
1.0
|
CB
|
B:PRO549
|
4.3
|
21.9
|
1.0
|
O
|
B:HOH963
|
4.4
|
38.4
|
1.0
|
CG
|
B:LEU552
|
4.4
|
25.3
|
1.0
|
O
|
B:HOH994
|
4.4
|
40.4
|
1.0
|
NZ
|
B:LYS536
|
4.6
|
34.1
|
1.0
|
CB
|
B:LEU552
|
4.6
|
23.4
|
1.0
|
C
|
B:ARG548
|
4.7
|
21.3
|
1.0
|
CD
|
B:PRO549
|
4.8
|
23.4
|
1.0
|
N
|
B:ARG548
|
4.8
|
20.8
|
1.0
|
O
|
B:ARG548
|
4.9
|
21.6
|
1.0
|
|
Potassium binding site 5 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 5 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K702
b:29.4
occ:1.00
|
OG
|
D:SER501
|
3.3
|
21.7
|
1.0
|
O
|
D:HOH872
|
3.4
|
43.0
|
1.0
|
O
|
D:HOH861
|
3.5
|
38.7
|
1.0
|
N
|
E:ILE500
|
3.8
|
27.8
|
1.0
|
CG2
|
E:ILE500
|
3.8
|
27.1
|
1.0
|
CB
|
E:ILE500
|
3.9
|
28.2
|
1.0
|
CB
|
D:SER501
|
4.0
|
21.2
|
1.0
|
CA
|
E:ILE500
|
4.5
|
26.9
|
1.0
|
CB
|
E:ASP499
|
4.5
|
30.7
|
1.0
|
CG2
|
D:ILE365
|
4.5
|
35.2
|
1.0
|
O
|
D:HOH818
|
4.5
|
11.9
|
1.0
|
CA
|
E:ASP499
|
4.6
|
28.7
|
1.0
|
C
|
E:ASP499
|
4.7
|
27.3
|
1.0
|
CG2
|
D:VAL369
|
4.7
|
22.0
|
1.0
|
CD2
|
D:HIS538
|
4.8
|
20.1
|
1.0
|
CG1
|
D:ILE365
|
4.8
|
34.0
|
1.0
|
CD1
|
D:ILE365
|
5.0
|
32.4
|
1.0
|
|
Potassium binding site 6 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 6 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K706
b:37.3
occ:1.00
|
NZ
|
D:LYS554
|
3.1
|
33.5
|
1.0
|
CE
|
D:LYS554
|
3.6
|
38.3
|
1.0
|
CG
|
D:MSE496
|
4.1
|
34.4
|
1.0
|
CD
|
D:LYS554
|
4.1
|
36.4
|
1.0
|
CD2
|
D:TYR551
|
4.2
|
21.2
|
1.0
|
CA
|
D:MSE496
|
4.3
|
32.4
|
1.0
|
CB
|
D:MSE496
|
4.3
|
33.7
|
1.0
|
CE
|
D:MSE496
|
4.5
|
31.4
|
1.0
|
CE2
|
D:TYR551
|
4.6
|
21.4
|
1.0
|
NH1
|
D:ARG548
|
4.6
|
33.6
|
1.0
|
O
|
D:MSE496
|
4.8
|
29.4
|
1.0
|
O
|
D:HOH890
|
5.0
|
58.9
|
1.0
|
|
Potassium binding site 7 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 7 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K700
b:17.4
occ:1.00
|
BR
|
E:BR802
|
3.1
|
28.7
|
1.0
|
N
|
E:ARG548
|
3.3
|
19.7
|
1.0
|
OG1
|
E:THR540
|
3.4
|
21.9
|
1.0
|
O
|
E:LYS536
|
3.9
|
21.2
|
1.0
|
CG1
|
E:VAL539
|
3.9
|
15.8
|
1.0
|
O
|
E:ARG548
|
3.9
|
22.8
|
1.0
|
CB
|
E:VAL539
|
4.0
|
14.7
|
1.0
|
C
|
E:ARG548
|
4.0
|
21.6
|
1.0
|
CA
|
E:ARG548
|
4.1
|
19.5
|
1.0
|
CA
|
E:ASN547
|
4.2
|
20.1
|
1.0
|
CB
|
E:ASN547
|
4.2
|
21.2
|
1.0
|
C
|
E:ASN547
|
4.3
|
19.8
|
1.0
|
CA
|
E:LYS536
|
4.3
|
21.6
|
1.0
|
CB
|
E:LEU552
|
4.3
|
31.2
|
1.0
|
N
|
E:THR540
|
4.3
|
17.4
|
1.0
|
CG
|
E:LEU552
|
4.3
|
34.1
|
1.0
|
CB
|
E:ARG548
|
4.4
|
21.2
|
1.0
|
O
|
E:HOH856
|
4.5
|
29.7
|
1.0
|
C
|
E:LYS536
|
4.5
|
20.9
|
1.0
|
N
|
E:PRO549
|
4.6
|
21.6
|
1.0
|
CB
|
E:LYS536
|
4.6
|
21.8
|
1.0
|
CB
|
E:THR540
|
4.6
|
18.6
|
1.0
|
CA
|
E:THR540
|
4.7
|
19.9
|
1.0
|
CG
|
E:LYS536
|
4.7
|
24.4
|
1.0
|
C
|
E:VAL539
|
4.8
|
18.4
|
1.0
|
CD2
|
E:LEU552
|
4.8
|
33.6
|
1.0
|
CG
|
E:ARG548
|
4.9
|
20.5
|
1.0
|
CG2
|
E:VAL539
|
4.9
|
17.0
|
1.0
|
CA
|
E:VAL539
|
5.0
|
16.9
|
1.0
|
|
Potassium binding site 8 out
of 8 in 1ovl
Go back to
Potassium Binding Sites List in 1ovl
Potassium binding site 8 out
of 8 in the Crystal Structure of NURR1 Lbd
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Crystal Structure of NURR1 Lbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K701
b:26.0
occ:1.00
|
OG
|
F:SER501
|
3.2
|
33.7
|
1.0
|
CG
|
F:ASP499
|
3.6
|
45.5
|
1.0
|
CB
|
F:SER501
|
3.7
|
34.0
|
1.0
|
CB
|
F:ASP499
|
3.7
|
42.4
|
1.0
|
OD1
|
F:ASP499
|
3.9
|
46.3
|
1.0
|
N
|
F:SER501
|
3.9
|
33.3
|
1.0
|
OD2
|
F:ASP499
|
4.0
|
47.8
|
1.0
|
CG2
|
F:ILE500
|
4.0
|
35.9
|
1.0
|
NE2
|
F:HIS538
|
4.1
|
48.1
|
1.0
|
CA
|
F:SER501
|
4.4
|
32.2
|
1.0
|
N
|
F:ILE500
|
4.5
|
39.3
|
1.0
|
O
|
F:HOH825
|
4.6
|
26.2
|
1.0
|
C
|
F:ASP499
|
4.8
|
40.3
|
1.0
|
CE1
|
F:HIS538
|
4.8
|
47.5
|
1.0
|
CA
|
F:ASP499
|
4.9
|
41.5
|
1.0
|
C
|
F:ILE500
|
4.9
|
35.2
|
1.0
|
|
Reference:
Z.Wang,
G.Benoit,
J.Liu,
S.Prasad,
P.Aarnisalo,
X.Liu,
H.Xu,
N.Walker,
T.Perlmann.
Structure and Function of NURR1 Identifies A Class of Ligand-Independent Nuclear Receptors Nature V. 423 555 2003.
ISSN: ISSN 0028-0836
PubMed: 12774125
DOI: 10.1038/NATURE01645
Page generated: Mon Aug 12 05:08:54 2024
|