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

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 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 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 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 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 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 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 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 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 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

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