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Magnesium in PDB 5xxt: Gdp-Microtubule Complexed with Nucleotide-Free KIF5C

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C (pdb code 5xxt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C, PDB code: 5xxt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5xxt

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Magnesium binding site 1 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:0.0
occ:1.00
 O A:HOH601 2.1 0.0 1.0
O A:HOH602 2.3 0.0 1.0
O A:HOH603 2.3 0.0 1.0
O A:HOH604 2.4 0.0 1.0
O1G A:GTP501 2.4 0.0 1.0
O1B A:GTP501 3.2 0.0 1.0
PG A:GTP501 3.7 0.0 1.0
O3B A:GTP501 3.7 0.0 1.0
PB A:GTP501 3.8 0.0 1.0
CG A:GLN11 3.9 0.0 1.0
O3A A:GTP501 4.1 0.0 1.0
OE1 A:GLN11 4.2 0.0 1.0
N A:GLN11 4.3 0.0 1.0
OD2 A:ASP69 4.4 0.0 1.0
O2A A:GTP501 4.4 0.0 1.0
OD1 A:ASP98 4.4 0.0 1.0
OD1 A:ASP69 4.4 0.0 1.0
O2G A:GTP501 4.5 0.0 1.0
CD A:GLN11 4.5 0.0 1.0
CB A:GLN11 4.6 0.0 1.0
PA A:GTP501 4.8 0.0 1.0
CA A:GLN11 4.8 0.0 1.0
CG A:ASP69 4.8 0.0 1.0
O3G A:GTP501 4.9 0.0 1.0
OD2 A:ASP98 4.9 0.0 1.0
CG A:ASP98 5.0 0.0 1.0

Magnesium binding site 2 out of 9 in 5xxt

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Magnesium binding site 2 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:0.0
occ:1.00
 O C:HOH601 2.1 0.0 1.0
O C:HOH602 2.3 0.0 1.0
O C:HOH603 2.3 0.0 1.0
O C:HOH604 2.4 0.0 1.0
O1G C:GTP501 2.5 0.0 1.0
O1B C:GTP501 3.2 0.0 1.0
PG C:GTP501 3.7 0.0 1.0
O3B C:GTP501 3.7 0.0 1.0
PB C:GTP501 3.8 0.0 1.0
CG C:GLN11 3.9 0.0 1.0
O3A C:GTP501 4.1 0.0 1.0
OE1 C:GLN11 4.2 0.0 1.0
N C:GLN11 4.3 0.0 1.0
OD2 C:ASP69 4.4 0.0 1.0
O2A C:GTP501 4.4 0.0 1.0
OD1 C:ASP98 4.4 0.0 1.0
OD1 C:ASP69 4.4 0.0 1.0
O2G C:GTP501 4.5 0.0 1.0
CD C:GLN11 4.5 0.0 1.0
CB C:GLN11 4.6 0.0 1.0
PA C:GTP501 4.8 0.0 1.0
CA C:GLN11 4.8 0.0 1.0
CG C:ASP69 4.8 0.0 1.0
O3G C:GTP501 4.9 0.0 1.0
OD2 C:ASP98 4.9 0.0 1.0
CG C:ASP98 5.0 0.0 1.0

Magnesium binding site 3 out of 9 in 5xxt

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Magnesium binding site 3 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:0.0
occ:1.00
 O E:HOH601 2.1 0.0 1.0
O E:HOH602 2.3 0.0 1.0
O E:HOH603 2.3 0.0 1.0
O E:HOH604 2.4 0.0 1.0
O1G E:GTP501 2.4 0.0 1.0
O1B E:GTP501 3.2 0.0 1.0
PG E:GTP501 3.7 0.0 1.0
O3B E:GTP501 3.7 0.0 1.0
PB E:GTP501 3.8 0.0 1.0
CG E:GLN11 3.9 0.0 1.0
O3A E:GTP501 4.1 0.0 1.0
OE1 E:GLN11 4.2 0.0 1.0
N E:GLN11 4.3 0.0 1.0
OD2 E:ASP69 4.4 0.0 1.0
O2A E:GTP501 4.4 0.0 1.0
OD1 E:ASP98 4.4 0.0 1.0
OD1 E:ASP69 4.4 0.0 1.0
O2G E:GTP501 4.5 0.0 1.0
CD E:GLN11 4.5 0.0 1.0
CB E:GLN11 4.6 0.0 1.0
PA E:GTP501 4.8 0.0 1.0
CA E:GLN11 4.8 0.0 1.0
CG E:ASP69 4.8 0.0 1.0
O3G E:GTP501 4.9 0.0 1.0
OD2 E:ASP98 4.9 0.0 1.0
CG E:ASP98 5.0 0.0 1.0

Magnesium binding site 4 out of 9 in 5xxt

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Magnesium binding site 4 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:0.0
occ:1.00
 O G:HOH601 2.1 0.0 1.0
O G:HOH602 2.3 0.0 1.0
O G:HOH603 2.3 0.0 1.0
O G:HOH604 2.4 0.0 1.0
O1G G:GTP501 2.5 0.0 1.0
O1B G:GTP501 3.2 0.0 1.0
PG G:GTP501 3.7 0.0 1.0
O3B G:GTP501 3.7 0.0 1.0
PB G:GTP501 3.8 0.0 1.0
CG G:GLN11 3.9 0.0 1.0
O3A G:GTP501 4.1 0.0 1.0
OE1 G:GLN11 4.2 0.0 1.0
N G:GLN11 4.3 0.0 1.0
OD2 G:ASP69 4.4 0.0 1.0
O2A G:GTP501 4.4 0.0 1.0
OD1 G:ASP98 4.4 0.0 1.0
OD1 G:ASP69 4.4 0.0 1.0
O2G G:GTP501 4.5 0.0 1.0
CD G:GLN11 4.5 0.0 1.0
CB G:GLN11 4.6 0.0 1.0
PA G:GTP501 4.8 0.0 1.0
CA G:GLN11 4.8 0.0 1.0
CG G:ASP69 4.8 0.0 1.0
O3G G:GTP501 4.9 0.0 1.0
OD2 G:ASP98 4.9 0.0 1.0
CG G:ASP98 5.0 0.0 1.0

Magnesium binding site 5 out of 9 in 5xxt

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Magnesium binding site 5 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg502

b:0.0
occ:1.00
 O I:HOH601 2.1 0.0 1.0
O I:HOH602 2.3 0.0 1.0
O I:HOH603 2.3 0.0 1.0
O I:HOH604 2.4 0.0 1.0
O1G I:GTP501 2.4 0.0 1.0
O1B I:GTP501 3.2 0.0 1.0
PG I:GTP501 3.7 0.0 1.0
O3B I:GTP501 3.7 0.0 1.0
PB I:GTP501 3.8 0.0 1.0
CG I:GLN11 3.9 0.0 1.0
O3A I:GTP501 4.1 0.0 1.0
OE1 I:GLN11 4.2 0.0 1.0
N I:GLN11 4.3 0.0 1.0
OD2 I:ASP69 4.4 0.0 1.0
O2A I:GTP501 4.4 0.0 1.0
OD1 I:ASP98 4.4 0.0 1.0
OD1 I:ASP69 4.4 0.0 1.0
O2G I:GTP501 4.5 0.0 1.0
CD I:GLN11 4.5 0.0 1.0
CB I:GLN11 4.6 0.0 1.0
PA I:GTP501 4.8 0.0 1.0
CA I:GLN11 4.8 0.0 1.0
CG I:ASP69 4.8 0.0 1.0
O3G I:GTP501 4.9 0.0 1.0
OD2 I:ASP98 4.9 0.0 1.0
CG I:ASP98 5.0 0.0 1.0

Magnesium binding site 6 out of 9 in 5xxt

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Magnesium binding site 6 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg502

b:0.0
occ:1.00
 O K:HOH601 2.1 0.0 1.0
O K:HOH602 2.3 0.0 1.0
O K:HOH603 2.3 0.0 1.0
O K:HOH604 2.4 0.0 1.0
O1G K:GTP501 2.5 0.0 1.0
O1B K:GTP501 3.2 0.0 1.0
PG K:GTP501 3.7 0.0 1.0
O3B K:GTP501 3.7 0.0 1.0
PB K:GTP501 3.8 0.0 1.0
CG K:GLN11 3.9 0.0 1.0
O3A K:GTP501 4.1 0.0 1.0
OE1 K:GLN11 4.2 0.0 1.0
N K:GLN11 4.3 0.0 1.0
OD2 K:ASP69 4.4 0.0 1.0
O2A K:GTP501 4.4 0.0 1.0
OD1 K:ASP98 4.4 0.0 1.0
OD1 K:ASP69 4.4 0.0 1.0
O2G K:GTP501 4.5 0.0 1.0
CD K:GLN11 4.5 0.0 1.0
CB K:GLN11 4.6 0.0 1.0
PA K:GTP501 4.8 0.0 1.0
CA K:GLN11 4.8 0.0 1.0
CG K:ASP69 4.8 0.0 1.0
O3G K:GTP501 4.9 0.0 1.0
OD2 K:ASP98 4.9 0.0 1.0
CG K:ASP98 5.0 0.0 1.0
CA L:ASN249 5.0 0.0 1.0

Magnesium binding site 7 out of 9 in 5xxt

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Magnesium binding site 7 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg502

b:0.0
occ:1.00
 O M:HOH601 2.1 0.0 1.0
O M:HOH602 2.3 0.0 1.0
O M:HOH603 2.3 0.0 1.0
O M:HOH604 2.4 0.0 1.0
O1G M:GTP501 2.4 0.0 1.0
O1B M:GTP501 3.2 0.0 1.0
PG M:GTP501 3.7 0.0 1.0
O3B M:GTP501 3.7 0.0 1.0
PB M:GTP501 3.8 0.0 1.0
CG M:GLN11 3.9 0.0 1.0
O3A M:GTP501 4.1 0.0 1.0
OE1 M:GLN11 4.2 0.0 1.0
N M:GLN11 4.3 0.0 1.0
OD2 M:ASP69 4.4 0.0 1.0
O2A M:GTP501 4.4 0.0 1.0
OD1 M:ASP98 4.4 0.0 1.0
OD1 M:ASP69 4.4 0.0 1.0
O2G M:GTP501 4.5 0.0 1.0
CD M:GLN11 4.5 0.0 1.0
CB M:GLN11 4.6 0.0 1.0
PA M:GTP501 4.8 0.0 1.0
CA M:GLN11 4.8 0.0 1.0
CG M:ASP69 4.8 0.0 1.0
O3G M:GTP501 4.9 0.0 1.0
OD2 M:ASP98 4.9 0.0 1.0
CG M:ASP98 5.0 0.0 1.0

Magnesium binding site 8 out of 9 in 5xxt

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Magnesium binding site 8 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg502

b:0.0
occ:1.00
 O O:HOH601 2.1 0.0 1.0
O O:HOH602 2.3 0.0 1.0
O O:HOH603 2.3 0.0 1.0
O O:HOH604 2.4 0.0 1.0
O1G O:GTP501 2.5 0.0 1.0
O1B O:GTP501 3.2 0.0 1.0
PG O:GTP501 3.7 0.0 1.0
O3B O:GTP501 3.7 0.0 1.0
PB O:GTP501 3.8 0.0 1.0
CG O:GLN11 3.9 0.0 1.0
O3A O:GTP501 4.1 0.0 1.0
OE1 O:GLN11 4.2 0.0 1.0
N O:GLN11 4.3 0.0 1.0
OD2 O:ASP69 4.4 0.0 1.0
O2A O:GTP501 4.4 0.0 1.0
OD1 O:ASP98 4.4 0.0 1.0
OD1 O:ASP69 4.4 0.0 1.0
O2G O:GTP501 4.5 0.0 1.0
CD O:GLN11 4.5 0.0 1.0
CB O:GLN11 4.6 0.0 1.0
PA O:GTP501 4.8 0.0 1.0
CA O:GLN11 4.8 0.0 1.0
CG O:ASP69 4.8 0.0 1.0
O3G O:GTP501 4.9 0.0 1.0
OD2 O:ASP98 4.9 0.0 1.0
CG O:ASP98 5.0 0.0 1.0

Magnesium binding site 9 out of 9 in 5xxt

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Magnesium binding site 9 out of 9 in the Gdp-Microtubule Complexed with Nucleotide-Free KIF5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Gdp-Microtubule Complexed with Nucleotide-Free KIF5C within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg502

b:0.0
occ:1.00
 O Q:HOH601 2.1 0.0 1.0
O Q:HOH602 2.3 0.0 1.0
O Q:HOH603 2.3 0.0 1.0
O Q:HOH604 2.4 0.0 1.0
O1G Q:GTP501 2.4 0.0 1.0
O1B Q:GTP501 3.2 0.0 1.0
PG Q:GTP501 3.7 0.0 1.0
O3B Q:GTP501 3.7 0.0 1.0
PB Q:GTP501 3.8 0.0 1.0
CG Q:GLN11 3.9 0.0 1.0
O3A Q:GTP501 4.1 0.0 1.0
OE1 Q:GLN11 4.2 0.0 1.0
N Q:GLN11 4.3 0.0 1.0
OD2 Q:ASP69 4.4 0.0 1.0
O2A Q:GTP501 4.4 0.0 1.0
OD1 Q:ASP98 4.4 0.0 1.0
OD1 Q:ASP69 4.4 0.0 1.0
O2G Q:GTP501 4.5 0.0 1.0
CD Q:GLN11 4.5 0.0 1.0
CB Q:GLN11 4.6 0.0 1.0
PA Q:GTP501 4.8 0.0 1.0
CA Q:GLN11 4.8 0.0 1.0
CG Q:ASP69 4.8 0.0 1.0
O3G Q:GTP501 4.9 0.0 1.0
OD2 Q:ASP98 4.9 0.0 1.0
CG Q:ASP98 5.0 0.0 1.0

Reference:

T.Shima, M.Morikawa, J.Kaneshiro, T.Kambara, S.Kamimura, T.Yagi, H.Iwamoto, S.Uemura, H.Shigematsu, M.Shirouzu, T.Ichimura, T.M.Watanabe, R.Nitta, Y.Okada, N.Hirokawa. Kinesin-Binding-Triggered Conformation Switching of Microtubules Contributes to Polarized Transport J. Cell Biol. V. 217 4164 2018.
ISSN: ESSN 1540-8140
PubMed: 30297389
DOI: 10.1083/JCB.201711178
Page generated: Mon Sep 30 10:38:50 2024

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