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Magnesium in PDB 5xxv: Gdp-Microtubule Complexed with KIF5C in Amppnp State

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gdp-Microtubule Complexed with KIF5C in Amppnp State (pdb code 5xxv). 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 KIF5C in Amppnp State, PDB code: 5xxv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5xxv

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Magnesium binding site 1 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

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 B:HOH601 2.4 0.0 1.0
O1G B:GTP501 2.4 0.0 1.0
O1B B:GTP501 3.2 0.0 1.0
PG B:GTP501 3.7 0.0 1.0
O3B B:GTP501 3.7 0.0 1.0
PB B:GTP501 3.8 0.0 1.0
CG A:GLN11 3.9 0.0 1.0
O3A B: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 B: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 B:GTP501 4.5 0.0 1.0
CA B:ASN249 4.5 0.0 1.0
CD A:GLN11 4.5 0.0 1.0
CB A:GLN11 4.6 0.0 1.0
CB B:ASN249 4.8 0.0 1.0
PA B: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 B: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 5xxv

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Magnesium binding site 2 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

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 D:HOH601 2.4 0.0 1.0
O1G D:GTP501 2.5 0.0 1.0
O1B D:GTP501 3.2 0.0 1.0
PG D:GTP501 3.7 0.0 1.0
O3B D:GTP501 3.7 0.0 1.0
PB D:GTP501 3.8 0.0 1.0
CG C:GLN11 3.9 0.0 1.0
O3A D: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 D: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 D:GTP501 4.5 0.0 1.0
CA D:ASN249 4.5 0.0 1.0
CD C:GLN11 4.5 0.0 1.0
CB C:GLN11 4.6 0.0 1.0
CB D:ASN249 4.8 0.0 1.0
PA D: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 D: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 5xxv

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Magnesium binding site 3 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

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 F:HOH601 2.4 0.0 1.0
O1G F:GTP501 2.4 0.0 1.0
O1B F:GTP501 3.2 0.0 1.0
PG F:GTP501 3.7 0.0 1.0
O3B F:GTP501 3.7 0.0 1.0
PB F:GTP501 3.8 0.0 1.0
CG E:GLN11 3.9 0.0 1.0
O3A F: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 F: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 F:GTP501 4.5 0.0 1.0
CA F:ASN249 4.5 0.0 1.0
CD E:GLN11 4.5 0.0 1.0
CB E:GLN11 4.6 0.0 1.0
CB F:ASN249 4.7 0.0 1.0
PA F: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 F: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 5xxv

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Magnesium binding site 4 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

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 H:HOH601 2.4 0.0 1.0
O1G H:GTP501 2.5 0.0 1.0
O1B H:GTP501 3.2 0.0 1.0
PG H:GTP501 3.7 0.0 1.0
O3B H:GTP501 3.7 0.0 1.0
PB H:GTP501 3.8 0.0 1.0
CG G:GLN11 3.9 0.0 1.0
O3A H: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
CA H:ASN249 4.4 0.0 1.0
O2A H: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 H: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
CB H:ASN249 4.6 0.0 1.0
PA H: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 H: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
N H:ALA250 5.0 0.0 1.0

Magnesium binding site 5 out of 9 in 5xxv

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Magnesium binding site 5 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg501

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 J:HOH601 2.4 0.0 1.0
O1G J:GTP501 2.4 0.0 1.0
O1B J:GTP501 3.2 0.0 1.0
PG J:GTP501 3.7 0.0 1.0
O3B J:GTP501 3.7 0.0 1.0
PB J:GTP501 3.8 0.0 1.0
CG I:GLN11 3.9 0.0 1.0
O3A J: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
CA J:ASN249 4.4 0.0 1.0
O2A J: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 J: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
CB J:ASN249 4.6 0.0 1.0
PA J: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 J: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
N J:ALA250 5.0 0.0 1.0

Magnesium binding site 6 out of 9 in 5xxv

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Magnesium binding site 6 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg501

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 L:HOH601 2.4 0.0 1.0
O1G L:GTP501 2.5 0.0 1.0
O1B L:GTP501 3.2 0.0 1.0
PG L:GTP501 3.7 0.0 1.0
O3B L:GTP501 3.7 0.0 1.0
PB L:GTP501 3.8 0.0 1.0
CG K:GLN11 3.9 0.0 1.0
O3A L: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
CA L:ASN249 4.4 0.0 1.0
OD2 K:ASP69 4.4 0.0 1.0
O2A L: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 L: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
CB L:ASN249 4.6 0.0 1.0
PA L: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 L: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
N L:ALA250 5.0 0.0 1.0

Magnesium binding site 7 out of 9 in 5xxv

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Magnesium binding site 7 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg501

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 N:HOH601 2.4 0.0 1.0
O1G N:GTP501 2.4 0.0 1.0
O1B N:GTP501 3.2 0.0 1.0
PG N:GTP501 3.7 0.0 1.0
O3B N:GTP501 3.7 0.0 1.0
PB N:GTP501 3.8 0.0 1.0
CG M:GLN11 3.9 0.0 1.0
O3A N: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 N:GTP501 4.4 0.0 1.0
OD1 M:ASP98 4.4 0.0 1.0
CA N:ASN249 4.4 0.0 1.0
OD1 M:ASP69 4.4 0.0 1.0
O2G N: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
CB N:ASN249 4.7 0.0 1.0
PA N: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 N:GTP501 4.9 0.0 1.0
OD2 M:ASP98 4.9 0.0 1.0
N N:ALA250 4.9 0.0 1.0
CG M:ASP98 4.9 0.0 1.0

Magnesium binding site 8 out of 9 in 5xxv

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Magnesium binding site 8 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg501

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 P:HOH601 2.4 0.0 1.0
O1G P:GTP501 2.5 0.0 1.0
O1B P:GTP501 3.2 0.0 1.0
PG P:GTP501 3.7 0.0 1.0
O3B P:GTP501 3.7 0.0 1.0
PB P:GTP501 3.8 0.0 1.0
CG O:GLN11 3.9 0.0 1.0
O3A P: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 P: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
CA P:ASN249 4.4 0.0 1.0
O2G P: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
CB P:ASN249 4.7 0.0 1.0
PA P: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 P:GTP501 4.9 0.0 1.0
OD2 O:ASP98 4.9 0.0 1.0
N P:ALA250 4.9 0.0 1.0
CG O:ASP98 5.0 0.0 1.0

Magnesium binding site 9 out of 9 in 5xxv

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Magnesium binding site 9 out of 9 in the Gdp-Microtubule Complexed with KIF5C in Amppnp State


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 KIF5C in Amppnp State within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg501

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 R:HOH601 2.4 0.0 1.0
O1G R:GTP501 2.4 0.0 1.0
O1B R:GTP501 3.2 0.0 1.0
PG R:GTP501 3.7 0.0 1.0
O3B R:GTP501 3.7 0.0 1.0
PB R:GTP501 3.8 0.0 1.0
CG Q:GLN11 3.9 0.0 1.0
O3A R: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 R:GTP501 4.4 0.0 1.0
OD1 Q:ASP98 4.4 0.0 1.0
CA R:ASN249 4.4 0.0 1.0
OD1 Q:ASP69 4.4 0.0 1.0
O2G R: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
CB R:ASN249 4.7 0.0 1.0
PA R: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 R:GTP501 4.9 0.0 1.0
OD2 Q:ASP98 4.9 0.0 1.0
N R:ALA250 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: Wed Aug 13 00:29:19 2025

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