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Fluorine in PDB 4hna: Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin

Protein crystallography data

The structure of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin, PDB code: 4hna was solved by B.Gigant, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.14 / 3.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.050, 160.540, 174.950, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.1

Other elements in 4hna:

The structure of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin (pdb code 4hna). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin, PDB code: 4hna:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 1 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:99.1
occ:1.00
 F1 B:ALF503 0.0 99.1 1.0
AL B:ALF503 1.8 93.9 1.0
F3 B:ALF503 2.4 98.0 1.0
F4 B:ALF503 2.6 86.8 1.0
O3B B:GDP501 2.7 85.3 1.0
OG1 B:THR145 2.8 73.1 1.0
N B:ALA99 2.9 79.5 1.0
CB B:ALA99 3.4 75.2 1.0
F2 B:ALF503 3.6 96.0 1.0
CA B:ALA99 3.6 77.0 1.0
C B:GLY98 3.9 87.4 1.0
PB B:GDP501 3.9 79.6 1.0
N B:GLY100 4.0 79.2 1.0
CB B:THR145 4.0 71.0 1.0
O2B B:GDP501 4.0 76.2 1.0
N B:THR145 4.1 65.2 1.0
CA B:GLY98 4.1 88.9 1.0
C B:ALA99 4.1 80.8 1.0
OE1 B:GLU71 4.3 0.8 1.0
MG B:MG502 4.4 55.8 1.0
CA B:THR145 4.6 65.6 1.0
OD1 B:ASP69 4.6 86.7 1.0
N B:ASN101 4.8 74.2 1.0
C B:GLY144 4.9 67.7 1.0
N B:GLY144 4.9 67.9 1.0
CA B:GLY144 4.9 67.0 1.0
O3A B:GDP501 4.9 79.9 1.0
CB B:LEU70 5.0 80.5 1.0

Fluorine binding site 2 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 2 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:96.0
occ:1.00
 F2 B:ALF503 0.0 96.0 1.0
AL B:ALF503 1.8 93.9 1.0
F3 B:ALF503 2.5 98.0 1.0
F4 B:ALF503 2.6 86.8 1.0
O3B B:GDP501 2.9 85.3 1.0
O3A B:GDP501 3.0 79.9 1.0
PB B:GDP501 3.3 79.6 1.0
O2B B:GDP501 3.3 76.2 1.0
O1A B:GDP501 3.5 74.7 1.0
F1 B:ALF503 3.6 99.1 1.0
OD1 B:ASN101 3.6 74.8 1.0
MG B:MG502 3.7 55.8 1.0
PA B:GDP501 3.9 73.4 1.0
CG B:ASN101 4.2 87.1 1.0
ND2 B:ASN101 4.5 76.9 1.0
N B:ASN101 4.7 74.2 1.0
O1B B:GDP501 4.7 78.6 1.0
O5' B:GDP501 4.8 67.0 1.0
OE1 B:GLU71 4.9 0.8 1.0
N B:GLY144 4.9 67.9 1.0

Fluorine binding site 3 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 3 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:98.0
occ:1.00
 F3 B:ALF503 0.0 98.0 1.0
AL B:ALF503 1.8 93.9 1.0
MG B:MG502 2.1 55.8 1.0
F1 B:ALF503 2.4 99.1 1.0
F2 B:ALF503 2.5 96.0 1.0
O2B B:GDP501 2.6 76.2 1.0
O3B B:GDP501 3.0 85.3 1.0
OE1 B:GLU71 3.2 0.8 1.0
PB B:GDP501 3.4 79.6 1.0
F4 B:ALF503 3.6 86.8 1.0
CD B:GLU71 4.0 0.2 1.0
O3A B:GDP501 4.1 79.9 1.0
OD1 B:ASP69 4.2 86.7 1.0
OG1 B:THR145 4.3 73.1 1.0
CB B:GLU71 4.4 92.9 1.0
OE2 B:GLU71 4.4 0.9 1.0
O1B B:GDP501 4.8 78.6 1.0
OD2 B:ASP69 4.9 97.5 1.0
CG B:GLU71 4.9 0.1 1.0
O1A B:GDP501 4.9 74.7 1.0
N B:GLN11 4.9 72.2 1.0
N B:ALA99 5.0 79.5 1.0
CB B:GLN11 5.0 75.8 1.0
CG B:ASP69 5.0 87.9 1.0

Fluorine binding site 4 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 4 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:86.8
occ:1.00
 F4 B:ALF503 0.0 86.8 1.0
AL B:ALF503 1.8 93.9 1.0
O3B B:GDP501 2.5 85.3 1.0
F2 B:ALF503 2.6 96.0 1.0
F1 B:ALF503 2.6 99.1 1.0
N B:ASN101 2.7 74.2 1.0
CA B:ASN101 3.2 71.6 1.0
N B:GLY144 3.3 67.9 1.0
OD1 B:ASN101 3.6 74.8 1.0
F3 B:ALF503 3.6 98.0 1.0
N B:GLY100 3.6 79.2 1.0
C B:GLY100 3.8 80.3 1.0
CA B:GLY144 3.8 67.0 1.0
PB B:GDP501 3.8 79.6 1.0
CG B:ASN101 3.8 87.1 1.0
C B:ALA99 4.0 80.8 1.0
O3A B:GDP501 4.0 79.9 1.0
CA B:GLY100 4.0 79.1 1.0
CB B:ALA99 4.1 75.2 1.0
CB B:ASN101 4.1 73.2 1.0
N B:THR145 4.2 65.2 1.0
C B:GLY143 4.3 71.0 1.0
CA B:ALA99 4.3 77.0 1.0
N B:ALA99 4.4 79.5 1.0
C B:ASN101 4.4 72.8 1.0
CA B:GLY143 4.5 67.6 1.0
ND2 B:ASN101 4.5 76.9 1.0
O B:ALA99 4.5 78.6 1.0
C B:GLY144 4.6 67.7 1.0
O2B B:GDP501 4.6 76.2 1.0
N B:ASN102 4.6 70.7 1.0
OG1 B:THR145 4.7 73.1 1.0
O B:GLY100 4.9 80.2 1.0
O1B B:GDP501 5.0 78.6 1.0

Fluorine binding site 5 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 5 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F403

b:50.3
occ:1.00
 F1 K:ALF403 0.0 50.3 1.0
AL K:ALF403 1.8 52.8 1.0
F3 K:ALF403 2.5 51.4 1.0
O K:HOH502 2.5 17.7 1.0
F4 K:ALF403 2.6 55.5 1.0
O3B K:ADP401 2.6 55.7 1.0
O2B K:ADP401 3.1 59.2 1.0
N K:GLY234 3.1 48.9 1.0
MG K:MG402 3.3 27.4 1.0
CE K:LYS91 3.3 37.0 1.0
CA K:ALA233 3.3 46.7 1.0
PB K:ADP401 3.4 59.4 1.0
F2 K:ALF403 3.5 54.5 1.0
C K:ALA233 3.6 50.8 1.0
CB K:SER202 3.6 60.2 1.0
NZ K:LYS91 3.7 42.2 1.0
O K:LEU232 3.8 47.6 1.0
O K:SER202 4.1 65.5 1.0
CA K:GLY234 4.1 49.6 1.0
N K:SER202 4.1 62.5 1.0
CB K:ALA233 4.1 48.4 1.0
OG K:SER202 4.2 64.2 1.0
O1B K:ADP401 4.3 60.3 1.0
CA K:SER202 4.3 60.3 1.0
N K:ALA233 4.3 46.4 1.0
C K:LEU232 4.5 48.5 1.0
C K:SER202 4.6 64.7 1.0
OG1 K:THR92 4.7 63.3 1.0
O K:ALA233 4.7 49.4 1.0
CD K:LYS91 4.7 33.3 1.0
O3A K:ADP401 4.7 57.6 1.0
O K:HOH501 4.8 0.8 1.0
CB K:LYS91 4.9 46.3 1.0

Fluorine binding site 6 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 6 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F403

b:54.5
occ:1.00
 F2 K:ALF403 0.0 54.5 1.0
AL K:ALF403 1.8 52.8 1.0
O3B K:ADP401 2.5 55.7 1.0
F3 K:ALF403 2.5 51.4 1.0
F4 K:ALF403 2.5 55.5 1.0
OG K:SER201 2.9 85.0 1.0
OG1 K:THR87 3.0 54.6 1.0
ND2 K:ASN198 3.0 61.1 1.0
N K:SER88 3.3 59.8 1.0
CB K:SER201 3.5 74.0 1.0
CA K:SER201 3.5 69.0 1.0
F1 K:ALF403 3.5 50.3 1.0
CB K:ASN198 3.6 52.7 1.0
CG K:ASN198 3.8 70.7 1.0
PB K:ADP401 3.8 59.4 1.0
CB K:THR87 3.9 62.6 1.0
CA K:THR87 3.9 55.5 1.0
N K:SER202 4.0 62.5 1.0
C K:THR87 4.0 62.6 1.0
CA K:SER88 4.1 60.5 1.0
O3A K:ADP401 4.2 57.6 1.0
C K:SER201 4.2 70.9 1.0
CB K:SER88 4.5 65.6 1.0
O2B K:ADP401 4.6 59.2 1.0
N K:SER201 4.6 71.2 1.0
MG K:MG402 4.7 27.4 1.0
O K:SER202 4.8 65.5 1.0
O1B K:ADP401 4.9 60.3 1.0
OD1 K:ASN198 5.0 66.1 1.0

Fluorine binding site 7 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 7 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F403

b:51.4
occ:1.00
 F3 K:ALF403 0.0 51.4 1.0
AL K:ALF403 1.8 52.8 1.0
F1 K:ALF403 2.5 50.3 1.0
F2 K:ALF403 2.5 54.5 1.0
N K:GLY234 2.8 48.9 1.0
O3B K:ADP401 2.8 55.7 1.0
CA K:GLY234 3.1 49.6 1.0
CA K:THR87 3.4 55.5 1.0
OG1 K:THR87 3.5 54.6 1.0
CB K:THR87 3.5 62.6 1.0
F4 K:ALF403 3.6 55.5 1.0
O K:GLY234 3.8 57.2 1.0
C K:GLY234 3.9 55.7 1.0
NZ K:LYS91 3.9 42.2 1.0
OG K:SER201 3.9 85.0 1.0
C K:ALA233 3.9 50.8 1.0
N K:SER88 4.1 59.8 1.0
CE K:LYS91 4.2 37.0 1.0
N K:THR87 4.2 54.1 1.0
OE1 K:GLU236 4.2 87.0 1.0
C K:THR87 4.3 62.6 1.0
O K:SER202 4.3 65.5 1.0
PB K:ADP401 4.3 59.4 1.0
CA K:ALA233 4.4 46.7 1.0
CB K:ALA233 4.8 48.4 1.0
O2B K:ADP401 4.8 59.2 1.0
N K:SER202 4.8 62.5 1.0
C K:GLN86 4.9 54.8 1.0
O K:GLN86 4.9 54.5 1.0
O K:HOH502 4.9 17.7 1.0
O1B K:ADP401 5.0 60.3 1.0
O K:ALA233 5.0 49.4 1.0

Fluorine binding site 8 out of 8 in 4hna

Go back to Fluorine Binding Sites List in 4hna
Fluorine binding site 8 out of 8 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F403

b:55.5
occ:1.00
 F4 K:ALF403 0.0 55.5 1.0
AL K:ALF403 1.8 52.8 1.0
MG K:MG402 2.2 27.4 1.0
O3B K:ADP401 2.5 55.7 1.0
F2 K:ALF403 2.5 54.5 1.0
F1 K:ALF403 2.6 50.3 1.0
N K:SER202 2.7 62.5 1.0
O K:HOH501 2.7 0.8 1.0
O2B K:ADP401 2.9 59.2 1.0
PB K:ADP401 3.1 59.4 1.0
ND2 K:ASN198 3.3 61.1 1.0
CB K:SER202 3.4 60.2 1.0
O K:HOH502 3.4 17.7 1.0
O3A K:ADP401 3.4 57.6 1.0
OG K:SER202 3.5 64.2 1.0
CA K:SER201 3.5 69.0 1.0
F3 K:ALF403 3.6 51.4 1.0
C K:SER201 3.6 70.9 1.0
CA K:SER202 3.6 60.3 1.0
O K:HIS200 3.9 72.7 1.0
O1A K:ADP401 4.1 57.6 1.0
OG K:SER201 4.2 85.0 1.0
OG1 K:THR92 4.2 63.3 1.0
O K:SER202 4.3 65.5 1.0
PA K:ADP401 4.4 56.3 1.0
CB K:SER201 4.4 74.0 1.0
O1B K:ADP401 4.5 60.3 1.0
C K:SER202 4.5 64.7 1.0
CG K:ASN198 4.5 70.7 1.0
N K:SER201 4.5 71.2 1.0
C K:HIS200 4.6 74.5 1.0
O K:SER201 4.8 73.0 1.0
N K:SER88 4.9 59.8 1.0

Reference:

B.Gigant, W.Wang, B.Dreier, Q.Jiang, L.Pecqueur, A.Pluckthun, C.Wang, M.Knossow. Structure of A Kinesin-Tubulin Complex and Implications For Kinesin Motility. Nat.Struct.Mol.Biol. V. 20 1001 2013.
ISSN: ISSN 1545-9993
PubMed: 23872990
DOI: 10.1038/NSMB.2624
Page generated: Thu Aug 1 02:06:08 2024

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