Phosphorus in PDB 1afk: Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
Enzymatic activity of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
All present enzymatic activity of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate:
3.1.27.5;
Protein crystallography data
The structure of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate, PDB code: 1afk
was solved by
D.D.Leonidas,
K.R.Acharya,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.70
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.540,
33.360,
73.250,
90.00,
90.09,
90.00
|
R / Rfree (%)
|
21.1 /
26.6
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
(pdb code 1afk). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the
Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate, PDB code: 1afk:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
Phosphorus binding site 1 out
of 6 in 1afk
Go back to
Phosphorus Binding Sites List in 1afk
Phosphorus binding site 1 out
of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P125
b:26.9
occ:1.00
|
PB
|
A:PAP125
|
0.0
|
26.9
|
1.0
|
O1B
|
A:PAP125
|
1.5
|
24.2
|
1.0
|
O3B
|
A:PAP125
|
1.5
|
28.2
|
1.0
|
O2B
|
A:PAP125
|
1.5
|
26.9
|
1.0
|
O3A
|
A:PAP125
|
1.6
|
29.9
|
1.0
|
PA
|
A:PAP125
|
3.1
|
31.2
|
1.0
|
O
|
A:HOH197
|
3.4
|
62.1
|
1.0
|
NE2
|
A:HIS12
|
3.6
|
10.6
|
1.0
|
O
|
A:HOH200
|
3.6
|
15.8
|
1.0
|
O2A
|
A:PAP125
|
3.6
|
32.6
|
1.0
|
ND1
|
A:HIS119
|
3.7
|
16.3
|
1.0
|
C5'
|
A:PAP125
|
3.8
|
29.1
|
1.0
|
O5'
|
A:PAP125
|
3.8
|
30.1
|
1.0
|
NE2
|
A:GLN11
|
3.9
|
19.5
|
1.0
|
N
|
A:PHE120
|
4.1
|
9.7
|
1.0
|
O1A
|
A:PAP125
|
4.2
|
32.4
|
1.0
|
NZ
|
A:LYS41
|
4.2
|
21.9
|
1.0
|
CE1
|
A:HIS12
|
4.3
|
10.0
|
1.0
|
CA
|
A:HIS119
|
4.4
|
11.2
|
1.0
|
CE1
|
A:HIS119
|
4.5
|
16.9
|
1.0
|
O
|
A:PHE120
|
4.5
|
8.7
|
1.0
|
CG
|
A:HIS119
|
4.6
|
14.6
|
1.0
|
CD2
|
A:HIS12
|
4.6
|
10.1
|
1.0
|
CB
|
A:HIS119
|
4.7
|
12.2
|
1.0
|
O
|
A:HOH196
|
4.8
|
36.1
|
1.0
|
C
|
A:HIS119
|
4.8
|
10.4
|
1.0
|
|
Phosphorus binding site 2 out
of 6 in 1afk
Go back to
Phosphorus Binding Sites List in 1afk
Phosphorus binding site 2 out
of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P125
b:31.2
occ:1.00
|
PA
|
A:PAP125
|
0.0
|
31.2
|
1.0
|
O2A
|
A:PAP125
|
1.5
|
32.6
|
1.0
|
O1A
|
A:PAP125
|
1.5
|
32.4
|
1.0
|
O5'
|
A:PAP125
|
1.6
|
30.1
|
1.0
|
O3A
|
A:PAP125
|
1.7
|
29.9
|
1.0
|
C5'
|
A:PAP125
|
2.6
|
29.1
|
1.0
|
PB
|
A:PAP125
|
3.1
|
26.9
|
1.0
|
O3B
|
A:PAP125
|
3.3
|
28.2
|
1.0
|
NE2
|
A:GLN11
|
3.7
|
19.5
|
1.0
|
C4'
|
A:PAP125
|
3.9
|
30.7
|
1.0
|
O2B
|
A:PAP125
|
4.0
|
26.9
|
1.0
|
CE
|
A:LYS7
|
4.0
|
24.1
|
1.0
|
O1B
|
A:PAP125
|
4.0
|
24.2
|
1.0
|
NZ
|
A:LYS7
|
4.2
|
26.1
|
1.0
|
O
|
A:HOH200
|
4.3
|
15.8
|
1.0
|
C3'
|
A:PAP125
|
4.3
|
32.0
|
1.0
|
O3
|
A:PAP125
|
4.6
|
40.6
|
1.0
|
O
|
A:HOH201
|
4.6
|
21.6
|
1.0
|
CD
|
A:GLN11
|
4.7
|
20.0
|
1.0
|
OE1
|
A:GLN11
|
4.8
|
23.8
|
1.0
|
O
|
A:HOH197
|
4.9
|
62.1
|
1.0
|
O4'
|
A:PAP125
|
5.0
|
30.6
|
1.0
|
|
Phosphorus binding site 3 out
of 6 in 1afk
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Phosphorus Binding Sites List in 1afk
Phosphorus binding site 3 out
of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P125
b:39.7
occ:1.00
|
P
|
A:PAP125
|
0.0
|
39.7
|
1.0
|
O1
|
A:PAP125
|
1.5
|
40.5
|
1.0
|
O2
|
A:PAP125
|
1.5
|
39.4
|
1.0
|
O3
|
A:PAP125
|
1.5
|
40.6
|
1.0
|
O3'
|
A:PAP125
|
1.7
|
36.2
|
1.0
|
C3'
|
A:PAP125
|
2.8
|
32.0
|
1.0
|
NZ
|
A:LYS7
|
3.5
|
26.1
|
1.0
|
C4'
|
A:PAP125
|
3.7
|
30.7
|
1.0
|
C2'
|
A:PAP125
|
4.0
|
31.0
|
1.0
|
O2'
|
A:PAP125
|
4.0
|
29.1
|
1.0
|
O5'
|
A:PAP125
|
4.3
|
30.1
|
1.0
|
CE
|
A:LYS7
|
4.4
|
24.1
|
1.0
|
C1'
|
A:PAP125
|
4.5
|
29.6
|
1.0
|
C5'
|
A:PAP125
|
4.7
|
29.1
|
1.0
|
CB
|
A:ALA4
|
4.7
|
20.7
|
1.0
|
O4'
|
A:PAP125
|
4.7
|
30.6
|
1.0
|
|
Phosphorus binding site 4 out
of 6 in 1afk
Go back to
Phosphorus Binding Sites List in 1afk
Phosphorus binding site 4 out
of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P125
b:42.7
occ:1.00
|
PB
|
B:PAP125
|
0.0
|
42.7
|
1.0
|
O1B
|
B:PAP125
|
1.5
|
41.5
|
1.0
|
O3B
|
B:PAP125
|
1.5
|
42.4
|
1.0
|
O2B
|
B:PAP125
|
1.5
|
44.0
|
1.0
|
O3A
|
B:PAP125
|
1.7
|
43.6
|
1.0
|
PA
|
B:PAP125
|
3.2
|
45.4
|
1.0
|
O
|
B:HOH161
|
3.3
|
23.1
|
1.0
|
O5'
|
B:PAP125
|
3.3
|
41.4
|
1.0
|
C5'
|
B:PAP125
|
3.3
|
37.6
|
1.0
|
NE2
|
B:HIS12
|
3.5
|
9.9
|
1.0
|
ND1
|
B:HIS119
|
3.6
|
22.2
|
1.0
|
O1A
|
B:PAP125
|
3.7
|
44.6
|
1.0
|
N
|
B:PHE120
|
3.7
|
10.3
|
1.0
|
NE2
|
B:GLN11
|
3.8
|
18.3
|
1.0
|
CA
|
B:HIS119
|
4.2
|
12.1
|
1.0
|
O
|
B:PHE120
|
4.2
|
12.5
|
1.0
|
CE1
|
B:HIS119
|
4.3
|
21.9
|
1.0
|
O2A
|
B:PAP125
|
4.4
|
45.2
|
1.0
|
CG
|
B:HIS119
|
4.4
|
20.1
|
1.0
|
CE1
|
B:HIS12
|
4.4
|
8.0
|
1.0
|
CD2
|
B:HIS12
|
4.4
|
9.1
|
1.0
|
C
|
B:HIS119
|
4.5
|
12.2
|
1.0
|
CB
|
B:HIS119
|
4.6
|
15.7
|
1.0
|
CB
|
B:PHE120
|
4.7
|
9.9
|
1.0
|
CA
|
B:PHE120
|
4.7
|
10.5
|
1.0
|
C4'
|
B:PAP125
|
4.8
|
37.6
|
1.0
|
C
|
B:PHE120
|
4.9
|
11.0
|
1.0
|
CD
|
B:GLN11
|
5.0
|
17.8
|
1.0
|
|
Phosphorus binding site 5 out
of 6 in 1afk
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Phosphorus Binding Sites List in 1afk
Phosphorus binding site 5 out
of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P125
b:45.4
occ:1.00
|
PA
|
B:PAP125
|
0.0
|
45.4
|
1.0
|
O1A
|
B:PAP125
|
1.5
|
44.6
|
1.0
|
O2A
|
B:PAP125
|
1.5
|
45.2
|
1.0
|
O5'
|
B:PAP125
|
1.7
|
41.4
|
1.0
|
O3A
|
B:PAP125
|
1.7
|
43.6
|
1.0
|
C5'
|
B:PAP125
|
2.6
|
37.6
|
1.0
|
NZ
|
B:LYS7
|
3.0
|
35.2
|
1.0
|
PB
|
B:PAP125
|
3.2
|
42.7
|
1.0
|
C3'
|
B:PAP125
|
3.6
|
38.8
|
1.0
|
C4'
|
B:PAP125
|
3.7
|
37.6
|
1.0
|
NE2
|
B:GLN11
|
3.8
|
18.3
|
1.0
|
O1B
|
B:PAP125
|
3.8
|
41.5
|
1.0
|
O2B
|
B:PAP125
|
3.8
|
44.0
|
1.0
|
O3B
|
B:PAP125
|
3.8
|
42.4
|
1.0
|
O
|
B:HOH161
|
4.1
|
23.1
|
1.0
|
O
|
B:HOH160
|
4.2
|
18.9
|
1.0
|
CE
|
B:LYS7
|
4.3
|
29.2
|
1.0
|
C2'
|
B:PAP125
|
4.3
|
37.5
|
1.0
|
CD
|
B:LYS7
|
4.5
|
25.1
|
1.0
|
O2'
|
B:PAP125
|
4.6
|
37.8
|
1.0
|
O3'
|
B:PAP125
|
4.7
|
45.3
|
1.0
|
CD
|
B:GLN11
|
4.7
|
17.8
|
1.0
|
CG
|
B:LYS7
|
4.8
|
18.0
|
1.0
|
O4'
|
B:PAP125
|
4.9
|
36.2
|
1.0
|
OE1
|
B:GLN11
|
4.9
|
22.2
|
1.0
|
ND1
|
B:HIS119
|
5.0
|
22.2
|
1.0
|
|
Phosphorus binding site 6 out
of 6 in 1afk
Go back to
Phosphorus Binding Sites List in 1afk
Phosphorus binding site 6 out
of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P125
b:50.9
occ:1.00
|
P
|
B:PAP125
|
0.0
|
50.9
|
1.0
|
O3
|
B:PAP125
|
1.5
|
48.8
|
1.0
|
O1
|
B:PAP125
|
1.5
|
47.8
|
1.0
|
O2
|
B:PAP125
|
1.5
|
48.9
|
1.0
|
O3'
|
B:PAP125
|
1.7
|
45.3
|
1.0
|
C3'
|
B:PAP125
|
3.0
|
38.8
|
1.0
|
CB
|
B:ALA4
|
3.5
|
13.5
|
1.0
|
NZ
|
B:LYS7
|
3.8
|
35.2
|
1.0
|
C4'
|
B:PAP125
|
3.8
|
37.6
|
1.0
|
O2'
|
B:PAP125
|
4.2
|
37.8
|
1.0
|
C1'
|
B:PAP125
|
4.2
|
36.0
|
1.0
|
C2'
|
B:PAP125
|
4.2
|
37.5
|
1.0
|
CA
|
B:ALA4
|
4.2
|
14.4
|
1.0
|
CE
|
B:LYS7
|
4.5
|
29.2
|
1.0
|
O4'
|
B:PAP125
|
4.6
|
36.2
|
1.0
|
O
|
B:HOH160
|
4.6
|
18.9
|
1.0
|
O5'
|
B:PAP125
|
4.7
|
41.4
|
1.0
|
C5'
|
B:PAP125
|
4.9
|
37.6
|
1.0
|
N
|
B:ALA4
|
5.0
|
16.6
|
1.0
|
|
Reference:
D.D.Leonidas,
R.Shapiro,
L.I.Irons,
N.Russo,
K.R.Acharya.
Crystal Structures of Ribonuclease A Complexes with 5'-Diphosphoadenosine 3'-Phosphate and 5'-Diphosphoadenosine 2'-Phosphate at 1.7 A Resolution. Biochemistry V. 36 5578 1997.
ISSN: ISSN 0006-2960
PubMed: 9154942
DOI: 10.1021/BI9700330
Page generated: Fri Sep 25 12:47:23 2020
|