Fluorine in PDB 5sup: Structure of Mrna Export Factors

Enzymatic activity of Structure of Mrna Export Factors

All present enzymatic activity of Structure of Mrna Export Factors:
3.6.4.13;

Protein crystallography data

The structure of Structure of Mrna Export Factors, PDB code: 5sup was solved by Y.Ren, P.Schmiege, G.Blobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.67 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.346, 99.346, 247.469, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 26.8

Other elements in 5sup:

The structure of Structure of Mrna Export Factors also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Mrna Export Factors (pdb code 5sup). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Structure of Mrna Export Factors, PDB code: 5sup:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5sup

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Fluorine binding site 1 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:41.8
occ:1.00
 F1 A:BEF1001 0.0 41.8 1.0
BE A:BEF1001 1.5 34.6 1.0
NH2 A:ARG396 2.4 35.8 1.0
F3 A:BEF1001 2.5 38.3 1.0
F2 A:BEF1001 2.6 34.4 1.0
NH1 A:ARG396 2.7 35.8 1.0
O2B A:ADP1000 2.7 38.8 1.0
NH2 A:ARG399 2.8 35.4 1.0
CZ A:ARG396 3.0 35.8 1.0
O A:HOH1109 3.2 33.8 1.0
CZ A:ARG399 3.7 37.1 1.0
NH1 A:ARG399 3.7 36.5 1.0
N A:GLY109 3.8 31.1 1.0
CB A:SER108 3.9 37.2 1.0
CA A:SER108 4.0 36.0 1.0
PB A:ADP1000 4.2 30.9 1.0
N A:GLY369 4.2 29.4 1.0
NE A:ARG396 4.3 36.3 1.0
C A:SER108 4.3 35.8 1.0
OG A:SER108 4.4 45.0 1.0
CA A:GLY369 4.4 36.3 1.0
MG A:MG1002 4.5 24.6 1.0
CA A:GLY109 4.6 28.5 1.0
O A:HOH1112 4.6 35.8 1.0
O A:GLY395 4.8 35.9 1.0
O A:HOH1107 4.8 35.5 1.0
C A:GLY369 4.9 31.6 1.0
O3B A:ADP1000 4.9 37.5 1.0
NE A:ARG399 4.9 41.0 1.0
OE2 A:GLU216 4.9 42.9 1.0
O A:GLY369 5.0 37.5 1.0
O1B A:ADP1000 5.0 30.5 1.0

Fluorine binding site 2 out of 9 in 5sup

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Fluorine binding site 2 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:34.4
occ:1.00
 F2 A:BEF1001 0.0 34.4 1.0
BE A:BEF1001 1.6 34.6 1.0
F3 A:BEF1001 2.5 38.3 1.0
F1 A:BEF1001 2.6 41.8 1.0
O2B A:ADP1000 2.6 38.8 1.0
NZ A:LYS112 2.6 32.3 1.0
O A:HOH1112 3.1 35.8 1.0
CA A:SER108 3.3 36.0 1.0
O3B A:ADP1000 3.4 37.5 1.0
PB A:ADP1000 3.4 30.9 1.0
CE A:LYS112 3.4 36.2 1.0
N A:GLY109 3.5 31.1 1.0
CB A:ALA248 3.9 43.5 1.0
C A:SER108 3.9 35.8 1.0
O A:LYS107 4.0 41.1 1.0
CB A:SER108 4.0 37.2 1.0
MG A:MG1002 4.1 24.6 1.0
N A:SER108 4.1 42.3 1.0
O A:HOH1111 4.1 30.4 1.0
O A:HOH1109 4.1 33.8 1.0
O1B A:ADP1000 4.2 30.5 1.0
OG A:SER108 4.3 45.0 1.0
C A:LYS107 4.3 42.8 1.0
NH2 A:ARG396 4.5 35.8 1.0
NH2 A:ARG399 4.6 35.4 1.0
O A:ALA106 4.6 45.9 1.0
CA A:GLY109 4.7 28.5 1.0
O3A A:ADP1000 4.7 29.0 1.0
N A:ALA248 4.7 46.4 1.0
CA A:ALA248 4.8 49.6 1.0
CD A:LYS112 4.8 41.5 1.0

Fluorine binding site 3 out of 9 in 5sup

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Fluorine binding site 3 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:38.3
occ:1.00
 F3 A:BEF1001 0.0 38.3 1.0
BE A:BEF1001 1.5 34.6 1.0
MG A:MG1002 2.2 24.6 1.0
O2B A:ADP1000 2.5 38.8 1.0
F2 A:BEF1001 2.5 34.4 1.0
F1 A:BEF1001 2.5 41.8 1.0
O A:HOH1111 2.9 30.4 1.0
O A:HOH1104 3.0 27.9 1.0
O A:HOH1109 3.2 33.8 1.0
O A:HOH1107 3.3 35.5 1.0
O A:HOH1112 3.3 35.8 1.0
OE2 A:GLU216 3.3 42.9 1.0
PB A:ADP1000 3.4 30.9 1.0
O1B A:ADP1000 3.4 30.5 1.0
CA A:GLY369 3.7 36.3 1.0
N A:GLY369 4.0 29.4 1.0
NZ A:LYS112 4.2 32.3 1.0
O3B A:ADP1000 4.2 37.5 1.0
NH1 A:ARG396 4.3 35.8 1.0
O A:HOH1102 4.3 32.6 1.0
CE A:LYS112 4.4 36.2 1.0
CD A:GLU216 4.4 41.1 1.0
NH2 A:ARG396 4.4 35.8 1.0
O A:GLY369 4.6 37.5 1.0
C A:GLY369 4.6 31.6 1.0
O3A A:ADP1000 4.7 29.0 1.0
OE1 A:GLU216 4.8 35.5 1.0
CZ A:ARG396 4.8 35.8 1.0
O1A A:ADP1000 4.9 35.0 1.0
NH1 A:ARG399 4.9 36.5 1.0
NH2 A:ARG399 5.0 35.4 1.0

Fluorine binding site 4 out of 9 in 5sup

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Fluorine binding site 4 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2001

b:41.2
occ:1.00
 F1 B:BEF2001 0.0 41.2 1.0
BE B:BEF2001 1.5 40.9 1.0
O3B B:ADP2000 2.3 46.1 1.0
F3 B:BEF2001 2.5 42.0 1.0
NH1 B:ARG399 2.5 42.8 1.0
F2 B:BEF2001 2.6 31.6 1.0
NH1 B:ARG396 2.7 40.4 1.0
NH2 B:ARG396 2.7 42.9 1.0
NH2 B:ARG399 3.1 34.7 1.0
CZ B:ARG396 3.1 34.2 1.0
CZ B:ARG399 3.2 47.5 1.0
N B:GLY109 3.8 48.4 1.0
PB B:ADP2000 3.8 36.5 1.0
N B:GLY369 4.0 39.4 1.0
CA B:GLY369 4.0 38.5 1.0
O B:HOH2106 4.1 28.1 1.0
MG B:MG2002 4.2 37.6 1.0
CA B:GLY109 4.4 40.3 1.0
O B:GLY369 4.4 37.2 1.0
C B:GLY369 4.4 33.4 1.0
NE B:ARG396 4.4 39.8 1.0
CA B:SER108 4.5 42.9 1.0
O2B B:ADP2000 4.5 41.0 1.0
NE B:ARG399 4.5 41.7 1.0
CB B:SER108 4.5 39.9 1.0
C B:SER108 4.5 50.0 1.0
NZ B:LYS112 4.6 38.2 1.0
O3A B:ADP2000 4.6 46.9 1.0
O1B B:ADP2000 4.7 37.0 1.0
O B:HOH2109 4.8 35.6 1.0
O2A B:ADP2000 4.8 40.0 1.0
O B:GLY395 4.9 41.7 1.0
OE2 B:GLU216 5.0 36.6 1.0

Fluorine binding site 5 out of 9 in 5sup

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Fluorine binding site 5 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2001

b:31.6
occ:1.00
 F2 B:BEF2001 0.0 31.6 1.0
BE B:BEF2001 1.6 40.9 1.0
NZ B:LYS112 2.3 38.2 1.0
F3 B:BEF2001 2.5 42.0 1.0
F1 B:BEF2001 2.6 41.2 1.0
O3B B:ADP2000 2.7 46.1 1.0
O B:HOH2109 2.9 35.6 1.0
PB B:ADP2000 3.5 36.5 1.0
O1B B:ADP2000 3.6 37.0 1.0
CA B:SER108 3.7 42.9 1.0
CE B:LYS112 3.7 39.9 1.0
N B:GLY109 3.8 48.4 1.0
O B:HOH2108 3.8 37.6 1.0
MG B:MG2002 4.0 37.6 1.0
CB B:ALA248 4.1 43.5 1.0
O2B B:ADP2000 4.1 41.0 1.0
NH2 B:ARG396 4.1 42.9 1.0
CB B:SER108 4.2 39.9 1.0
C B:SER108 4.3 50.0 1.0
OG B:SER108 4.5 48.1 1.0
O B:LYS107 4.5 45.5 1.0
N B:SER108 4.6 45.7 1.0
OE2 B:GLU216 4.6 36.6 1.0
CD B:LYS112 4.7 39.4 1.0
NH1 B:ARG399 4.7 42.8 1.0
ND1 B:HIS392 4.8 48.6 1.0
N B:ALA248 4.9 46.1 1.0
C B:LYS107 4.9 44.4 1.0
CA B:GLY109 4.9 40.3 1.0
O3A B:ADP2000 4.9 46.9 1.0
CE1 B:HIS392 5.0 48.7 1.0

Fluorine binding site 6 out of 9 in 5sup

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Fluorine binding site 6 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2001

b:42.0
occ:1.00
 F3 B:BEF2001 0.0 42.0 1.0
BE B:BEF2001 1.5 40.9 1.0
MG B:MG2002 1.9 37.6 1.0
F2 B:BEF2001 2.5 31.6 1.0
F1 B:BEF2001 2.5 41.2 1.0
O3B B:ADP2000 2.6 46.1 1.0
O B:HOH2108 2.7 37.6 1.0
O B:HOH2103 2.8 25.7 1.0
O B:HOH2106 2.9 28.1 1.0
O2B B:ADP2000 3.1 41.0 1.0
OE2 B:GLU216 3.3 36.6 1.0
PB B:ADP2000 3.3 36.5 1.0
CA B:GLY369 3.4 38.5 1.0
O B:HOH2109 3.5 35.6 1.0
N B:GLY369 3.8 39.4 1.0
NZ B:LYS112 3.8 38.2 1.0
O B:HOH2101 4.0 33.7 1.0
O B:GLY369 4.2 37.2 1.0
O1B B:ADP2000 4.3 37.0 1.0
C B:GLY369 4.3 33.4 1.0
NH2 B:ARG399 4.4 34.7 1.0
CD B:GLU216 4.4 46.4 1.0
NH1 B:ARG396 4.4 40.4 1.0
NH2 B:ARG396 4.5 42.9 1.0
O3A B:ADP2000 4.6 46.9 1.0
O2A B:ADP2000 4.7 40.0 1.0
NH1 B:ARG399 4.9 42.8 1.0
OE1 B:GLU216 4.9 37.1 1.0
CZ B:ARG396 4.9 34.2 1.0

Fluorine binding site 7 out of 9 in 5sup

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Fluorine binding site 7 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3001

b:47.9
occ:1.00
 F1 C:BEF3001 0.0 47.9 1.0
BE C:BEF3001 1.5 47.4 1.0
O2B C:ADP3000 2.3 52.9 1.0
F3 C:BEF3001 2.5 53.1 1.0
F2 C:BEF3001 2.6 51.4 1.0
NH1 C:ARG399 2.6 45.6 1.0
NH2 C:ARG396 2.7 53.3 1.0
NH1 C:ARG396 3.0 39.5 1.0
CZ C:ARG396 3.3 42.7 1.0
NH2 C:ARG399 3.3 44.5 1.0
CZ C:ARG399 3.4 47.2 1.0
N C:GLY109 3.6 45.5 1.0
PB C:ADP3000 3.8 47.0 1.0
CA C:SER108 4.0 55.2 1.0
CB C:SER108 4.1 51.9 1.0
C C:SER108 4.3 55.6 1.0
CA C:GLY109 4.3 50.0 1.0
O C:HOH3104 4.3 37.5 1.0
N C:GLY369 4.3 38.0 1.0
CA C:GLY369 4.4 38.2 1.0
MG C:MG3002 4.4 44.8 1.0
O1B C:ADP3000 4.6 47.8 1.0
OG C:SER108 4.6 50.2 1.0
NE C:ARG396 4.6 42.5 1.0
O3A C:ADP3000 4.6 41.1 1.0
O3B C:ADP3000 4.6 46.3 1.0
NE C:ARG399 4.7 38.9 1.0
O C:GLY369 4.8 47.4 1.0
C C:GLY369 4.8 37.2 1.0
NZ C:LYS112 4.9 44.5 1.0
O1A C:ADP3000 4.9 53.2 1.0
OE2 C:GLU216 5.0 42.2 1.0
O C:GLY395 5.0 47.8 1.0
O C:HOH3102 5.0 44.2 1.0

Fluorine binding site 8 out of 9 in 5sup

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Fluorine binding site 8 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3001

b:51.4
occ:1.00
 F2 C:BEF3001 0.0 51.4 1.0
BE C:BEF3001 1.6 47.4 1.0
F3 C:BEF3001 2.5 53.1 1.0
F1 C:BEF3001 2.6 47.9 1.0
O2B C:ADP3000 2.9 52.9 1.0
NZ C:LYS112 3.0 44.5 1.0
CE C:LYS112 3.5 47.4 1.0
CB C:ALA248 3.5 50.9 1.0
CA C:SER108 3.7 55.2 1.0
PB C:ADP3000 3.8 47.0 1.0
O C:HOH3105 3.8 44.1 1.0
O3B C:ADP3000 3.9 46.3 1.0
N C:GLY109 4.1 45.5 1.0
MG C:MG3002 4.1 44.8 1.0
NH2 C:ARG396 4.2 53.3 1.0
CB C:SER108 4.2 51.9 1.0
OG C:SER108 4.3 50.2 1.0
N C:ALA248 4.4 64.7 1.0
O1B C:ADP3000 4.4 47.8 1.0
OE2 C:GLU216 4.5 42.2 1.0
CA C:ALA248 4.5 51.4 1.0
ND1 C:HIS392 4.5 40.1 1.0
N C:SER108 4.5 63.4 1.0
C C:SER108 4.5 55.6 1.0
CE1 C:HIS392 4.6 54.0 1.0
O C:LYS107 4.6 59.5 1.0
O C:ALA106 4.8 58.4 1.0
C C:LYS107 4.8 67.6 1.0
O C:HOH3102 4.9 44.2 1.0
CD C:LYS112 5.0 55.2 1.0
NH1 C:ARG399 5.0 45.6 1.0

Fluorine binding site 9 out of 9 in 5sup

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Fluorine binding site 9 out of 9 in the Structure of Mrna Export Factors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Mrna Export Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3001

b:53.1
occ:1.00
 F3 C:BEF3001 0.0 53.1 1.0
BE C:BEF3001 1.5 47.4 1.0
MG C:MG3002 2.1 44.8 1.0
O2B C:ADP3000 2.4 52.9 1.0
F2 C:BEF3001 2.5 51.4 1.0
F1 C:BEF3001 2.5 47.9 1.0
O C:HOH3102 2.7 44.2 1.0
O C:HOH3105 2.7 44.1 1.0
O C:HOH3104 2.8 37.5 1.0
O1B C:ADP3000 3.1 47.8 1.0
PB C:ADP3000 3.2 47.0 1.0
OE2 C:GLU216 3.3 42.2 1.0
CA C:GLY369 3.7 38.2 1.0
O3B C:ADP3000 4.1 46.3 1.0
N C:GLY369 4.1 38.0 1.0
NZ C:LYS112 4.3 44.5 1.0
O C:HOH3101 4.3 42.2 1.0
CE C:LYS112 4.4 47.4 1.0
NH2 C:ARG399 4.4 44.5 1.0
CD C:GLU216 4.4 40.8 1.0
O3A C:ADP3000 4.5 41.1 1.0
O C:GLY369 4.5 47.4 1.0
NH2 C:ARG396 4.5 53.3 1.0
NH1 C:ARG396 4.6 39.5 1.0
C C:GLY369 4.6 37.2 1.0
O1A C:ADP3000 4.6 53.2 1.0
NH1 C:ARG399 4.9 45.6 1.0
OE1 C:GLU216 5.0 44.6 1.0

Reference:

Y.Ren, P.Schmiege, G.Blobel. Structural and Biochemical Analyses of the Dead-Box Atpase SUB2 in Association with Tho or YRA1. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28059701
DOI: 10.7554/ELIFE.20070
Page generated: Sun Dec 13 12:37:29 2020

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