Potassium in PDB 6rvz: Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate
Protein crystallography data
The structure of Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate, PDB code: 6rvz
was solved by
A.Kroupova,
M.Jinek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.04 /
2.10
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.653,
99.653,
94.155,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.8 /
21.1
|
Other elements in 6rvz:
The structure of Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate
(pdb code 6rvz). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the
Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate, PDB code: 6rvz:
Jump to Potassium binding site number:
1;
2;
3;
Potassium binding site 1 out
of 3 in 6rvz
Go back to
Potassium Binding Sites List in 6rvz
Potassium binding site 1 out
of 3 in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate
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 ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K604
b:31.1
occ:1.00
|
HH12
|
A:ARG316
|
2.5
|
26.4
|
0.0
|
H
|
A:ARG390
|
2.7
|
30.4
|
1.0
|
O
|
A:HOH813
|
2.9
|
30.1
|
1.0
|
HA
|
A:GLN389
|
2.9
|
30.9
|
1.0
|
HD2
|
A:ARG316
|
3.1
|
25.3
|
1.0
|
HG2
|
A:ARG390
|
3.2
|
29.2
|
1.0
|
NH1
|
A:ARG316
|
3.3
|
25.0
|
1.0
|
HD12
|
A:ILE376
|
3.4
|
28.4
|
1.0
|
HH11
|
A:ARG316
|
3.6
|
26.4
|
0.0
|
N
|
A:ARG390
|
3.6
|
30.3
|
1.0
|
HG2
|
A:GLN389
|
3.7
|
30.8
|
1.0
|
HD13
|
A:ILE376
|
3.8
|
28.4
|
1.0
|
CA
|
A:GLN389
|
3.9
|
30.9
|
1.0
|
O
|
A:GLY388
|
4.0
|
31.0
|
1.0
|
CD
|
A:ARG316
|
4.0
|
25.2
|
1.0
|
CD1
|
A:ILE376
|
4.0
|
28.3
|
1.0
|
HE
|
A:ARG390
|
4.0
|
28.0
|
1.0
|
HB3
|
A:ARG390
|
4.1
|
29.9
|
1.0
|
CG
|
A:ARG390
|
4.1
|
29.2
|
1.0
|
C
|
A:GLN389
|
4.2
|
30.7
|
1.0
|
CZ
|
A:ARG316
|
4.3
|
25.1
|
1.0
|
HD3
|
A:ARG390
|
4.3
|
28.5
|
1.0
|
HG12
|
A:ILE376
|
4.3
|
28.6
|
1.0
|
HG2
|
A:ARG316
|
4.4
|
25.4
|
1.0
|
CB
|
A:ARG390
|
4.4
|
29.9
|
1.0
|
HB3
|
A:GLN389
|
4.5
|
30.8
|
1.0
|
HG3
|
A:ARG316
|
4.5
|
25.4
|
1.0
|
CG
|
A:GLN389
|
4.5
|
30.9
|
1.0
|
NE
|
A:ARG316
|
4.5
|
25.3
|
1.0
|
NE
|
A:ARG390
|
4.5
|
28.0
|
1.0
|
CB
|
A:GLN389
|
4.5
|
30.8
|
1.0
|
CD
|
A:ARG390
|
4.5
|
28.5
|
1.0
|
HD3
|
A:ARG316
|
4.6
|
25.3
|
1.0
|
CG
|
A:ARG316
|
4.6
|
25.5
|
1.0
|
CA
|
A:ARG390
|
4.6
|
30.5
|
1.0
|
CG1
|
A:ILE376
|
4.7
|
28.5
|
1.0
|
HG13
|
A:ILE376
|
4.8
|
28.5
|
1.0
|
HD11
|
A:ILE376
|
4.8
|
28.4
|
1.0
|
C
|
A:GLY388
|
4.8
|
32.0
|
1.0
|
HG3
|
A:ARG390
|
4.8
|
29.2
|
1.0
|
N
|
A:GLN389
|
4.8
|
31.2
|
1.0
|
HG3
|
A:GLN389
|
4.9
|
30.8
|
1.0
|
|
Potassium binding site 2 out
of 3 in 6rvz
Go back to
Potassium Binding Sites List in 6rvz
Potassium binding site 2 out
of 3 in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate
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 ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K605
b:45.3
occ:1.00
|
HH21
|
A:ARG246
|
2.5
|
29.0
|
0.0
|
HH11
|
A:ARG246
|
2.7
|
26.8
|
0.0
|
H8
|
A:KL2601
|
2.7
|
32.2
|
1.0
|
HO5'
|
A:KL2601
|
2.9
|
30.0
|
0.0
|
O5'
|
A:KL2601
|
2.9
|
30.5
|
1.0
|
HG3
|
A:LYS250
|
3.1
|
44.1
|
1.0
|
NH2
|
A:ARG246
|
3.4
|
25.2
|
1.0
|
NH1
|
A:ARG246
|
3.4
|
24.7
|
1.0
|
HZ3
|
A:LYS250
|
3.6
|
48.1
|
1.0
|
O
|
A:HOH725
|
3.6
|
48.0
|
1.0
|
O
|
A:HOH955
|
3.7
|
44.6
|
1.0
|
HE2
|
A:LYS250
|
3.7
|
46.9
|
1.0
|
C8
|
A:KL2601
|
3.7
|
32.1
|
1.0
|
HD22
|
A:LEU179
|
3.8
|
28.7
|
1.0
|
HZ2
|
A:LYS250
|
3.8
|
48.1
|
1.0
|
H5'2
|
A:KL2601
|
3.9
|
31.1
|
1.0
|
CZ
|
A:ARG246
|
3.9
|
25.6
|
1.0
|
C5'
|
A:KL2601
|
3.9
|
31.2
|
1.0
|
HD21
|
A:LEU179
|
4.0
|
28.7
|
1.0
|
HH22
|
A:ARG246
|
4.0
|
29.0
|
0.0
|
CG
|
A:LYS250
|
4.0
|
44.1
|
1.0
|
NZ
|
A:LYS250
|
4.0
|
48.6
|
1.0
|
O4'
|
A:KL2601
|
4.0
|
31.3
|
1.0
|
HH12
|
A:ARG246
|
4.2
|
26.8
|
0.0
|
HG2
|
A:LYS250
|
4.2
|
44.1
|
1.0
|
CE
|
A:LYS250
|
4.3
|
47.0
|
1.0
|
CD2
|
A:LEU179
|
4.3
|
28.6
|
1.0
|
O
|
A:HOH855
|
4.4
|
28.2
|
1.0
|
N7
|
A:KL2601
|
4.5
|
32.5
|
1.0
|
C4'
|
A:KL2601
|
4.6
|
31.3
|
1.0
|
HD12
|
A:LEU179
|
4.7
|
28.6
|
1.0
|
O
|
A:HOH871
|
4.7
|
47.5
|
1.0
|
N9
|
A:KL2601
|
4.7
|
32.0
|
1.0
|
CD
|
A:LYS250
|
4.8
|
45.1
|
1.0
|
HB3
|
A:LYS250
|
4.8
|
43.0
|
1.0
|
H5'1
|
A:KL2601
|
4.8
|
31.0
|
1.0
|
HD13
|
A:LEU179
|
4.9
|
28.6
|
1.0
|
HZ1
|
A:LYS250
|
4.9
|
48.1
|
1.0
|
HD23
|
A:LEU179
|
4.9
|
28.6
|
1.0
|
CB
|
A:LYS250
|
4.9
|
43.2
|
1.0
|
HB2
|
A:LYS250
|
5.0
|
43.0
|
1.0
|
H3'
|
A:KL2601
|
5.0
|
31.1
|
1.0
|
|
Potassium binding site 3 out
of 3 in 6rvz
Go back to
Potassium Binding Sites List in 6rvz
Potassium binding site 3 out
of 3 in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate
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 ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K606
b:37.4
occ:1.00
|
O
|
A:TRP519
|
2.5
|
27.9
|
1.0
|
O
|
A:HOH930
|
2.5
|
41.4
|
1.0
|
O2'
|
A:ADN603
|
2.7
|
37.3
|
1.0
|
O3'
|
A:ADN603
|
2.8
|
38.0
|
1.0
|
OD1
|
A:ASN522
|
3.0
|
25.9
|
1.0
|
HO2'
|
A:ADN603
|
3.2
|
37.6
|
1.0
|
HO3'
|
A:ADN603
|
3.3
|
36.3
|
0.0
|
HA
|
A:THR520
|
3.5
|
28.0
|
1.0
|
C
|
A:TRP519
|
3.6
|
28.3
|
1.0
|
C3'
|
A:ADN603
|
3.6
|
38.4
|
1.0
|
C2'
|
A:ADN603
|
3.7
|
38.2
|
1.0
|
HA
|
A:ASN522
|
3.8
|
26.6
|
1.0
|
H
|
A:ASN522
|
3.8
|
26.9
|
1.0
|
H3'
|
A:ADN603
|
4.0
|
38.4
|
1.0
|
H1'
|
A:ADN603
|
4.1
|
38.0
|
1.0
|
HB3
|
A:TRP519
|
4.1
|
29.6
|
1.0
|
CA
|
A:THR520
|
4.2
|
27.9
|
1.0
|
CG
|
A:ASN522
|
4.2
|
26.2
|
1.0
|
O
|
A:THR520
|
4.3
|
28.4
|
1.0
|
N
|
A:THR520
|
4.3
|
28.0
|
1.0
|
C
|
A:THR520
|
4.3
|
28.0
|
1.0
|
H2'
|
A:ADN603
|
4.4
|
38.0
|
1.0
|
N
|
A:ASN522
|
4.5
|
26.9
|
1.0
|
C1'
|
A:ADN603
|
4.5
|
37.9
|
1.0
|
HE3
|
A:TRP519
|
4.5
|
30.4
|
1.0
|
CA
|
A:ASN522
|
4.5
|
26.7
|
1.0
|
CA
|
A:TRP519
|
4.7
|
29.1
|
1.0
|
HA
|
A:TRP519
|
4.8
|
29.1
|
1.0
|
O
|
A:HOH735
|
4.8
|
26.0
|
1.0
|
CB
|
A:TRP519
|
4.9
|
29.7
|
1.0
|
CB
|
A:ASN522
|
5.0
|
26.4
|
1.0
|
C4'
|
A:ADN603
|
5.0
|
39.0
|
1.0
|
|
Reference:
P.Pinto,
A.Kroupova,
M.Jinek,
S.Weitzer,
J.Martinez.
ANGEL2, A Member of the CCR4-Not Family of Deadenylases, Is A Mammalian 2,3-Cyclic Phosphatase. To Be Published.
Page generated: Mon Aug 12 17:34:14 2024
|