Sodium in PDB 7p8p: Crystal Structure of Fhit Covalently Bound to A Nucleotide
Enzymatic activity of Crystal Structure of Fhit Covalently Bound to A Nucleotide
All present enzymatic activity of Crystal Structure of Fhit Covalently Bound to A Nucleotide:
3.6.1.29;
Protein crystallography data
The structure of Crystal Structure of Fhit Covalently Bound to A Nucleotide, PDB code: 7p8p
was solved by
D.Herzog,
M.Missun,
K.Diederichs,
A.Marx,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.33 /
2.34
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.422,
61.736,
198.009,
90,
90,
90
|
R / Rfree (%)
|
19.3 /
24.6
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Fhit Covalently Bound to A Nucleotide
(pdb code 7p8p). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Crystal Structure of Fhit Covalently Bound to A Nucleotide, PDB code: 7p8p:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 7p8p
Go back to
Sodium Binding Sites List in 7p8p
Sodium binding site 1 out
of 3 in the Crystal Structure of Fhit Covalently Bound to A Nucleotide
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 Fhit Covalently Bound to A Nucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:57.4
occ:1.00
|
OD1
|
A:ASN96
|
2.2
|
46.3
|
1.0
|
HG3
|
A:GLN90
|
2.5
|
56.8
|
1.0
|
HE21
|
A:GLN90
|
2.7
|
56.3
|
1.0
|
O11
|
A:6BI201
|
2.7
|
49.4
|
1.0
|
O
|
A:VAL92
|
2.9
|
42.7
|
1.0
|
O
|
A:HIS94
|
2.9
|
41.8
|
1.0
|
HG2
|
A:GLN90
|
3.1
|
56.8
|
1.0
|
CG
|
A:GLN90
|
3.2
|
47.3
|
1.0
|
O3
|
A:6BI201
|
3.3
|
41.5
|
1.0
|
CG
|
A:ASN96
|
3.4
|
46.4
|
1.0
|
P
|
A:6BI201
|
3.4
|
53.8
|
1.0
|
NE2
|
A:GLN90
|
3.4
|
46.9
|
1.0
|
HB
|
A:VAL92
|
3.6
|
61.5
|
1.0
|
O
|
A:HOH311
|
3.6
|
38.6
|
1.0
|
H
|
A:HIS94
|
3.7
|
53.3
|
1.0
|
CD
|
A:GLN90
|
3.8
|
48.7
|
1.0
|
H
|
A:VAL92
|
3.8
|
64.2
|
1.0
|
H
|
A:ASN96
|
3.9
|
43.1
|
1.0
|
O2
|
A:6BI201
|
4.0
|
60.3
|
1.0
|
HD21
|
A:ASN96
|
4.0
|
53.0
|
1.0
|
C
|
A:VAL92
|
4.0
|
47.9
|
1.0
|
HA
|
A:GLN90
|
4.1
|
56.3
|
1.0
|
C
|
A:HIS94
|
4.1
|
41.5
|
1.0
|
HE22
|
A:GLN90
|
4.1
|
56.3
|
1.0
|
ND2
|
A:ASN96
|
4.2
|
44.1
|
1.0
|
N
|
A:ASN96
|
4.3
|
35.9
|
1.0
|
HB3
|
A:ASN96
|
4.3
|
52.5
|
1.0
|
O
|
A:GLN83
|
4.4
|
42.4
|
1.0
|
HA
|
A:VAL95
|
4.4
|
47.8
|
1.0
|
H
|
A:THR91
|
4.4
|
67.8
|
1.0
|
N
|
A:VAL92
|
4.4
|
53.4
|
1.0
|
CB
|
A:ASN96
|
4.4
|
43.7
|
1.0
|
CB
|
A:VAL92
|
4.4
|
51.2
|
1.0
|
CB
|
A:GLN90
|
4.4
|
41.0
|
1.0
|
N
|
A:HIS94
|
4.5
|
44.4
|
1.0
|
HZ
|
A:PHE5
|
4.5
|
50.8
|
1.0
|
CA
|
A:VAL92
|
4.5
|
53.3
|
1.0
|
HE2
|
A:HIS98
|
4.6
|
48.9
|
1.0
|
HB2
|
A:GLN83
|
4.6
|
51.9
|
1.0
|
C3
|
A:6BI201
|
4.6
|
51.0
|
1.0
|
CA
|
A:GLN90
|
4.7
|
46.9
|
1.0
|
HE1
|
A:PHE5
|
4.8
|
54.5
|
1.0
|
HB2
|
A:GLN90
|
4.8
|
49.2
|
1.0
|
HG12
|
A:VAL92
|
4.8
|
56.3
|
1.0
|
C
|
A:VAL95
|
4.8
|
40.9
|
1.0
|
O
|
A:ASN96
|
4.9
|
35.7
|
1.0
|
HB3
|
A:HIS94
|
4.9
|
52.5
|
1.0
|
O4
|
A:6BI201
|
4.9
|
53.0
|
1.0
|
CA
|
A:ASN96
|
4.9
|
31.4
|
1.0
|
CA
|
A:HIS94
|
4.9
|
42.6
|
1.0
|
N
|
A:THR91
|
4.9
|
56.5
|
1.0
|
CA
|
A:VAL95
|
4.9
|
39.8
|
1.0
|
N
|
A:VAL95
|
5.0
|
38.2
|
1.0
|
HD22
|
A:ASN96
|
5.0
|
53.0
|
1.0
|
|
Sodium binding site 2 out
of 3 in 7p8p
Go back to
Sodium Binding Sites List in 7p8p
Sodium binding site 2 out
of 3 in the Crystal Structure of Fhit Covalently Bound to A Nucleotide
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 Fhit Covalently Bound to A Nucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na203
b:52.6
occ:1.00
|
HG3
|
B:GLN90
|
2.2
|
56.4
|
1.0
|
HE21
|
B:GLN90
|
2.4
|
51.8
|
1.0
|
OD1
|
B:ASN96
|
2.6
|
42.8
|
1.0
|
O
|
B:HIS94
|
2.9
|
39.4
|
1.0
|
NA
|
B:NA204
|
2.9
|
52.8
|
1.0
|
NE2
|
B:GLN90
|
3.0
|
43.1
|
1.0
|
CG
|
B:GLN90
|
3.1
|
46.9
|
1.0
|
H
|
B:ASN96
|
3.4
|
55.5
|
1.0
|
O
|
B:HOH308
|
3.4
|
35.1
|
1.0
|
CD
|
B:GLN90
|
3.4
|
42.5
|
1.0
|
HG2
|
B:GLN90
|
3.5
|
56.4
|
1.0
|
CG
|
B:ASN96
|
3.6
|
45.1
|
1.0
|
HE22
|
B:GLN90
|
3.6
|
51.8
|
1.0
|
O
|
B:GLN83
|
3.6
|
38.8
|
1.0
|
HA
|
B:VAL95
|
3.7
|
49.0
|
1.0
|
O11
|
B:6BI201
|
3.7
|
51.5
|
1.0
|
O
|
B:VAL92
|
3.7
|
44.5
|
1.0
|
N
|
B:ASN96
|
3.9
|
46.2
|
1.0
|
H
|
B:HIS94
|
3.9
|
46.3
|
1.0
|
C
|
B:HIS94
|
3.9
|
38.4
|
1.0
|
HA
|
B:GLN90
|
4.1
|
52.9
|
1.0
|
CB
|
B:GLN90
|
4.2
|
41.7
|
1.0
|
HB2
|
B:GLN90
|
4.3
|
50.1
|
1.0
|
HD21
|
B:ASN96
|
4.3
|
51.2
|
1.0
|
O3
|
B:6BI201
|
4.3
|
46.8
|
1.0
|
ND2
|
B:ASN96
|
4.3
|
42.6
|
1.0
|
CA
|
B:VAL95
|
4.3
|
40.8
|
1.0
|
C
|
B:VAL95
|
4.4
|
42.1
|
1.0
|
HB3
|
B:ASN96
|
4.4
|
52.8
|
1.0
|
CB
|
B:ASN96
|
4.5
|
43.9
|
1.0
|
HB2
|
B:GLN83
|
4.5
|
52.4
|
1.0
|
P
|
B:6BI201
|
4.5
|
49.3
|
1.0
|
O
|
B:ASN96
|
4.5
|
45.0
|
1.0
|
OE1
|
B:GLN90
|
4.5
|
53.9
|
1.0
|
N
|
B:VAL95
|
4.6
|
40.2
|
1.0
|
CA
|
B:ASN96
|
4.6
|
44.4
|
1.0
|
C
|
B:GLN83
|
4.7
|
36.2
|
1.0
|
H
|
B:GLN83
|
4.7
|
48.7
|
1.0
|
N
|
B:HIS94
|
4.7
|
38.8
|
1.0
|
CA
|
B:GLN90
|
4.7
|
44.0
|
1.0
|
HB
|
B:VAL92
|
4.9
|
64.0
|
1.0
|
HE2
|
B:HIS98
|
4.9
|
54.3
|
1.0
|
H
|
B:THR91
|
4.9
|
57.4
|
1.0
|
HA
|
B:ASP84
|
4.9
|
49.7
|
1.0
|
C
|
B:VAL92
|
4.9
|
46.1
|
1.0
|
H
|
B:GLY85
|
5.0
|
44.4
|
1.0
|
CA
|
B:HIS94
|
5.0
|
38.7
|
1.0
|
O2
|
B:6BI201
|
5.0
|
49.5
|
1.0
|
H
|
B:VAL92
|
5.0
|
61.8
|
1.0
|
|
Sodium binding site 3 out
of 3 in 7p8p
Go back to
Sodium Binding Sites List in 7p8p
Sodium binding site 3 out
of 3 in the Crystal Structure of Fhit Covalently Bound to A Nucleotide
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 Fhit Covalently Bound to A Nucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na204
b:52.8
occ:1.00
|
O3
|
B:6BI201
|
2.3
|
46.8
|
1.0
|
HB
|
B:VAL92
|
2.6
|
64.0
|
1.0
|
H
|
B:VAL92
|
2.7
|
61.8
|
1.0
|
OD1
|
B:ASN96
|
2.8
|
42.8
|
1.0
|
NA
|
B:NA203
|
2.9
|
52.6
|
1.0
|
P
|
B:6BI201
|
3.0
|
49.3
|
1.0
|
C3
|
B:6BI201
|
3.0
|
45.6
|
1.0
|
O
|
B:VAL92
|
3.1
|
44.5
|
1.0
|
O2
|
B:6BI201
|
3.1
|
49.5
|
1.0
|
O11
|
B:6BI201
|
3.3
|
51.5
|
1.0
|
N
|
B:VAL92
|
3.3
|
51.4
|
1.0
|
HG3
|
B:GLN90
|
3.4
|
56.4
|
1.0
|
HZ
|
B:PHE5
|
3.4
|
59.7
|
1.0
|
H
|
B:THR91
|
3.4
|
57.4
|
1.0
|
CB
|
B:VAL92
|
3.5
|
53.3
|
1.0
|
HG1
|
B:THR91
|
3.7
|
70.2
|
1.0
|
HG2
|
B:GLN90
|
3.7
|
56.4
|
1.0
|
CA
|
B:VAL92
|
3.7
|
52.1
|
1.0
|
C
|
B:VAL92
|
3.8
|
46.1
|
1.0
|
CG
|
B:ASN96
|
3.9
|
45.1
|
1.0
|
HE21
|
B:GLN90
|
4.0
|
51.8
|
1.0
|
HG23
|
B:VAL92
|
4.0
|
53.2
|
1.0
|
CG
|
B:GLN90
|
4.0
|
46.9
|
1.0
|
OG1
|
B:THR91
|
4.0
|
58.4
|
1.0
|
O
|
B:HIS94
|
4.1
|
39.4
|
1.0
|
HA
|
B:GLN90
|
4.1
|
52.9
|
1.0
|
N
|
B:THR91
|
4.1
|
47.8
|
1.0
|
CZ
|
B:PHE5
|
4.1
|
50.0
|
1.0
|
CG2
|
B:VAL92
|
4.2
|
44.3
|
1.0
|
HD21
|
B:ASN96
|
4.3
|
51.2
|
1.0
|
HE1
|
B:PHE5
|
4.3
|
60.0
|
1.0
|
C
|
B:THR91
|
4.4
|
49.8
|
1.0
|
H
|
B:HIS94
|
4.4
|
46.3
|
1.0
|
HG12
|
B:VAL92
|
4.4
|
53.2
|
1.0
|
C2
|
B:6BI201
|
4.5
|
42.7
|
1.0
|
HG21
|
B:VAL92
|
4.5
|
53.2
|
1.0
|
O4
|
B:6BI201
|
4.5
|
39.6
|
1.0
|
CG1
|
B:VAL92
|
4.5
|
44.2
|
1.0
|
ND2
|
B:ASN96
|
4.6
|
42.6
|
1.0
|
CE1
|
B:PHE5
|
4.6
|
50.3
|
1.0
|
CA
|
B:THR91
|
4.7
|
48.6
|
1.0
|
HA
|
B:VAL92
|
4.7
|
62.6
|
1.0
|
NE2
|
B:GLN90
|
4.7
|
43.1
|
1.0
|
HG11
|
B:VAL92
|
4.7
|
53.2
|
1.0
|
HE2
|
B:HIS98
|
4.8
|
54.3
|
1.0
|
CA
|
B:GLN90
|
4.8
|
44.0
|
1.0
|
HB3
|
B:ASN96
|
4.9
|
52.8
|
1.0
|
C
|
B:GLN90
|
4.9
|
42.1
|
1.0
|
O12
|
B:6BI201
|
4.9
|
47.7
|
1.0
|
CD
|
B:GLN90
|
4.9
|
42.5
|
1.0
|
HB3
|
B:HIS94
|
5.0
|
47.4
|
1.0
|
CB
|
B:THR91
|
5.0
|
43.5
|
1.0
|
|
Reference:
D.Herzog,
J.Jansen,
M.Missun,
K.Diederichs,
F.Stengel,
A.Marx.
Chemical Proteomics of the Tumor Suppressor Fhit Covalently Bound to the Cofactor Ap 3 A Elucidates Its Inhibitory Action on Translation. J.Am.Chem.Soc. V. 144 8613 2022.
ISSN: ESSN 1520-5126
PubMed: 35522782
DOI: 10.1021/JACS.2C00815
Page generated: Tue Oct 8 18:28:09 2024
|