Fluorine in PDB 6zm2: Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna
Protein crystallography data
The structure of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna, PDB code: 6zm2
was solved by
F.Hamann,
R.Ficner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
81.78 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.66,
100.41,
140.95,
90,
90,
90
|
R / Rfree (%)
|
18.5 /
23.3
|
Other elements in 6zm2:
The structure of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna
(pdb code 6zm2). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna, PDB code: 6zm2:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6zm2
Go back to
Fluorine Binding Sites List in 6zm2
Fluorine binding site 1 out
of 3 in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1101
b:32.7
occ:1.00
|
F1
|
A:BEF1101
|
0.0
|
32.7
|
1.0
|
BE
|
A:BEF1101
|
1.5
|
30.8
|
1.0
|
F2
|
A:BEF1101
|
2.4
|
32.8
|
1.0
|
F3
|
A:BEF1101
|
2.5
|
33.9
|
1.0
|
O3B
|
A:ADP1102
|
2.5
|
33.0
|
1.0
|
NH2
|
A:ARG628
|
2.7
|
30.1
|
1.0
|
NH2
|
A:ARG625
|
2.8
|
30.4
|
1.0
|
NH1
|
A:ARG625
|
3.1
|
26.1
|
1.0
|
O
|
A:HOH1233
|
3.1
|
28.5
|
1.0
|
NH1
|
A:ARG628
|
3.2
|
27.0
|
1.0
|
CZ
|
A:ARG628
|
3.3
|
30.3
|
1.0
|
CB
|
A:THR322
|
3.3
|
33.3
|
1.0
|
CZ
|
A:ARG625
|
3.4
|
30.9
|
1.0
|
CA
|
A:THR322
|
3.4
|
33.5
|
1.0
|
N
|
A:GLY323
|
3.5
|
31.9
|
1.0
|
CG2
|
A:THR322
|
3.6
|
29.1
|
1.0
|
C
|
A:THR322
|
3.9
|
31.0
|
1.0
|
PB
|
A:ADP1102
|
4.0
|
33.7
|
1.0
|
MG
|
A:MG1103
|
4.5
|
34.2
|
1.0
|
N
|
A:SER578
|
4.5
|
28.2
|
1.0
|
O
|
A:GLY624
|
4.5
|
34.6
|
1.0
|
OE1
|
A:GLN621
|
4.5
|
30.1
|
1.0
|
NE
|
A:ARG628
|
4.6
|
31.9
|
1.0
|
OG1
|
A:THR322
|
4.6
|
32.7
|
1.0
|
CA
|
A:GLY323
|
4.6
|
28.7
|
1.0
|
O2B
|
A:ADP1102
|
4.7
|
34.5
|
1.0
|
NE
|
A:ARG625
|
4.7
|
33.3
|
1.0
|
CA
|
A:SER578
|
4.7
|
26.9
|
1.0
|
O3A
|
A:ADP1102
|
4.8
|
34.2
|
1.0
|
O
|
A:HOH1242
|
4.8
|
29.2
|
1.0
|
N
|
A:THR322
|
4.8
|
35.9
|
1.0
|
O
|
A:HOH1213
|
4.8
|
29.6
|
1.0
|
O
|
A:SER578
|
4.8
|
28.8
|
1.0
|
C
|
A:SER578
|
4.8
|
29.2
|
1.0
|
O1B
|
A:ADP1102
|
4.9
|
29.3
|
1.0
|
NZ
|
A:LYS326
|
4.9
|
26.3
|
1.0
|
OE2
|
A:GLU419
|
5.0
|
30.9
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6zm2
Go back to
Fluorine Binding Sites List in 6zm2
Fluorine binding site 2 out
of 3 in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1101
b:32.8
occ:1.00
|
F2
|
A:BEF1101
|
0.0
|
32.8
|
1.0
|
BE
|
A:BEF1101
|
1.5
|
30.8
|
1.0
|
MG
|
A:MG1103
|
2.2
|
34.2
|
1.0
|
F1
|
A:BEF1101
|
2.4
|
32.7
|
1.0
|
F3
|
A:BEF1101
|
2.5
|
33.9
|
1.0
|
O3B
|
A:ADP1102
|
2.6
|
33.0
|
1.0
|
O
|
A:HOH1233
|
2.8
|
28.5
|
1.0
|
O
|
A:HOH1255
|
3.0
|
26.8
|
1.0
|
O
|
A:HOH1213
|
3.1
|
29.6
|
1.0
|
OE2
|
A:GLU419
|
3.1
|
30.9
|
1.0
|
O
|
A:HOH1211
|
3.2
|
28.2
|
1.0
|
O2B
|
A:ADP1102
|
3.2
|
34.5
|
1.0
|
PB
|
A:ADP1102
|
3.4
|
33.7
|
1.0
|
CA
|
A:SER578
|
3.6
|
26.9
|
1.0
|
N
|
A:SER578
|
3.8
|
28.2
|
1.0
|
NH1
|
A:ARG628
|
4.1
|
27.0
|
1.0
|
O
|
A:SER578
|
4.1
|
28.8
|
1.0
|
C
|
A:SER578
|
4.2
|
29.2
|
1.0
|
O
|
A:HOH1242
|
4.2
|
29.2
|
1.0
|
CD
|
A:GLU419
|
4.2
|
34.6
|
1.0
|
OG1
|
A:THR327
|
4.3
|
29.2
|
1.0
|
NH1
|
A:ARG625
|
4.3
|
26.1
|
1.0
|
NH2
|
A:ARG625
|
4.4
|
30.4
|
1.0
|
NZ
|
A:LYS326
|
4.5
|
26.3
|
1.0
|
O1B
|
A:ADP1102
|
4.5
|
29.3
|
1.0
|
O2A
|
A:ADP1102
|
4.5
|
34.5
|
1.0
|
O3A
|
A:ADP1102
|
4.6
|
34.2
|
1.0
|
CB
|
A:SER578
|
4.7
|
29.1
|
1.0
|
OE1
|
A:GLU419
|
4.7
|
30.0
|
1.0
|
NH2
|
A:ARG628
|
4.7
|
30.1
|
1.0
|
OG
|
A:SER578
|
4.8
|
29.9
|
1.0
|
CZ
|
A:ARG625
|
4.8
|
30.9
|
1.0
|
CZ
|
A:ARG628
|
4.9
|
30.3
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6zm2
Go back to
Fluorine Binding Sites List in 6zm2
Fluorine binding site 3 out
of 3 in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1101
b:33.9
occ:1.00
|
F3
|
A:BEF1101
|
0.0
|
33.9
|
1.0
|
BE
|
A:BEF1101
|
1.5
|
30.8
|
1.0
|
F2
|
A:BEF1101
|
2.5
|
32.8
|
1.0
|
F1
|
A:BEF1101
|
2.5
|
32.7
|
1.0
|
O3B
|
A:ADP1102
|
2.6
|
33.0
|
1.0
|
NZ
|
A:LYS326
|
2.7
|
26.3
|
1.0
|
O
|
A:HOH1242
|
2.9
|
29.2
|
1.0
|
CA
|
A:THR322
|
3.3
|
33.5
|
1.0
|
O
|
A:HOH1233
|
3.4
|
28.5
|
1.0
|
PB
|
A:ADP1102
|
3.5
|
33.7
|
1.0
|
O
|
A:HOH1255
|
3.5
|
26.8
|
1.0
|
CE
|
A:LYS326
|
3.6
|
27.2
|
1.0
|
CG2
|
A:THR322
|
3.7
|
29.1
|
1.0
|
CB
|
A:THR322
|
3.8
|
33.3
|
1.0
|
O1B
|
A:ADP1102
|
3.8
|
29.3
|
1.0
|
MG
|
A:MG1103
|
3.9
|
34.2
|
1.0
|
CB
|
A:ALA451
|
4.0
|
27.3
|
1.0
|
O2B
|
A:ADP1102
|
4.0
|
34.5
|
1.0
|
N
|
A:GLY323
|
4.0
|
31.9
|
1.0
|
N
|
A:THR322
|
4.1
|
35.9
|
1.0
|
OE2
|
A:GLU419
|
4.1
|
30.9
|
1.0
|
O
|
A:GLU321
|
4.1
|
30.6
|
1.0
|
C
|
A:THR322
|
4.2
|
31.0
|
1.0
|
C
|
A:GLU321
|
4.4
|
32.5
|
1.0
|
NH2
|
A:ARG625
|
4.5
|
30.4
|
1.0
|
OE1
|
A:GLN621
|
4.6
|
30.1
|
1.0
|
N
|
A:ALA451
|
4.7
|
32.6
|
1.0
|
O
|
A:GLY320
|
4.7
|
34.1
|
1.0
|
OE1
|
A:GLU419
|
4.8
|
30.0
|
1.0
|
NH2
|
A:ARG628
|
4.9
|
30.1
|
1.0
|
CD
|
A:GLU419
|
4.9
|
34.6
|
1.0
|
O3A
|
A:ADP1102
|
4.9
|
34.2
|
1.0
|
NH1
|
A:ARG628
|
5.0
|
27.0
|
1.0
|
CA
|
A:ALA451
|
5.0
|
34.6
|
1.0
|
|
Reference:
F.Hamann,
L.C.Zimmerningkat,
R.A.Becker,
T.B.Garbers,
P.Neumann,
J.S.Hub,
R.Ficner.
The Structure of PRP2 Bound to Rna and Adp-Bef 3 - Reveals Structural Features Important For Rna Unwinding By Deah-Box Atpases. Acta Crystallogr D Struct V. 77 496 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 33825710
DOI: 10.1107/S2059798321001194
Page generated: Fri Aug 2 05:18:10 2024
|