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

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 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 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 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 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 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 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 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 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 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

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