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Magnesium in PDB 6evw: Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin

Magnesium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin (pdb code 6evw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin, PDB code: 6evw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6evw

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Magnesium binding site 1 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:0.4
occ:1.00
 O2B E:GTP501 2.1 0.3 1.0
O1G E:GTP501 2.1 0.3 1.0
O3A E:GTP501 2.2 0.3 1.0
OE1 E:GLN11 2.5 94.8 1.0
PB E:GTP501 2.5 0.3 1.0
O2A E:GTP501 3.0 0.3 1.0
CB E:GLN11 3.1 94.8 1.0
PA E:GTP501 3.1 0.3 1.0
O3B E:GTP501 3.1 0.3 1.0
PG E:GTP501 3.2 0.3 1.0
OE2 E:GLU71 3.4 0.3 1.0
CD E:GLN11 3.5 94.8 1.0
O1A E:GTP501 3.8 0.3 1.0
CG E:GLN11 3.9 94.8 1.0
O1B E:GTP501 3.9 0.3 1.0
O3G E:GTP501 4.2 0.3 1.0
N E:GLN11 4.2 94.8 1.0
O2G E:GTP501 4.2 0.3 1.0
CA E:GLN11 4.3 94.8 1.0
CD E:GLU71 4.4 0.3 1.0
O5' E:GTP501 4.5 0.3 1.0
NE2 E:GLN11 4.7 94.8 1.0
NZ G:LYS252 4.8 94.3 1.0

Magnesium binding site 2 out of 12 in 6evw

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Magnesium binding site 2 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg502

b:0.4
occ:1.00
 O2B J:GTP501 2.1 0.5 1.0
O1G J:GTP501 2.1 0.5 1.0
OE1 J:GLN11 2.4 89.0 1.0
O3A J:GTP501 2.6 0.5 1.0
PB J:GTP501 2.7 0.5 1.0
OE2 J:GLU71 2.9 0.6 1.0
CB J:GLN11 3.0 89.0 1.0
PG J:GTP501 3.3 0.5 1.0
O3B J:GTP501 3.3 0.5 1.0
CD J:GLN11 3.4 89.0 1.0
O2A J:GTP501 3.4 0.5 1.0
PA J:GTP501 3.5 0.5 1.0
CG J:GLN11 3.8 89.0 1.0
CD J:GLU71 3.9 0.6 1.0
O1A J:GTP501 4.1 0.5 1.0
O1B J:GTP501 4.1 0.5 1.0
N J:GLN11 4.2 89.0 1.0
O2G J:GTP501 4.2 0.5 1.0
CA J:GLN11 4.2 89.0 1.0
O3G J:GTP501 4.4 0.5 1.0
OE1 J:GLU71 4.5 0.6 1.0
NE2 J:GLN11 4.6 89.0 1.0
NZ F:LYS252 4.6 88.7 1.0
CG J:GLU71 4.7 0.6 1.0
O5' J:GTP501 4.9 0.5 1.0

Magnesium binding site 3 out of 12 in 6evw

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Magnesium binding site 3 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:0.2
occ:1.00
 O2B C:GTP501 2.1 0.6 1.0
O1G C:GTP501 2.1 0.6 1.0
OE1 C:GLN11 2.4 91.9 1.0
O3A C:GTP501 2.4 0.6 1.0
PB C:GTP501 2.6 0.6 1.0
CB C:GLN11 2.9 91.9 1.0
O2A C:GTP501 3.1 0.6 1.0
PG C:GTP501 3.1 0.6 1.0
O3B C:GTP501 3.2 0.6 1.0
OE2 C:GLU71 3.2 0.2 1.0
PA C:GTP501 3.3 0.6 1.0
CD C:GLN11 3.3 91.9 1.0
CG C:GLN11 3.7 91.9 1.0
O1A C:GTP501 3.8 0.6 1.0
O1B C:GTP501 4.0 0.6 1.0
O2G C:GTP501 4.0 0.6 1.0
N C:GLN11 4.0 91.9 1.0
CA C:GLN11 4.1 91.9 1.0
CD C:GLU71 4.1 0.2 1.0
O3G C:GTP501 4.4 0.6 1.0
NE2 C:GLN11 4.6 91.9 1.0
O5' C:GTP501 4.7 0.6 1.0
OE1 C:GLU71 4.8 0.2 1.0
CG C:GLU71 4.9 0.2 1.0

Magnesium binding site 4 out of 12 in 6evw

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Magnesium binding site 4 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg502

b:0.8
occ:1.00
 O2B L:GTP501 2.1 0.8 1.0
O1G L:GTP501 2.1 0.8 1.0
OE1 L:GLN11 2.3 96.6 1.0
O3A L:GTP501 2.4 0.8 1.0
PB L:GTP501 2.6 0.8 1.0
CB L:GLN11 2.8 96.6 1.0
O2A L:GTP501 3.1 0.8 1.0
OE2 L:GLU71 3.1 0.3 1.0
O3B L:GTP501 3.3 0.8 1.0
PA L:GTP501 3.3 0.8 1.0
PG L:GTP501 3.3 0.8 1.0
CD L:GLN11 3.3 96.6 1.0
CG L:GLN11 3.6 96.6 1.0
O1A L:GTP501 3.8 0.8 1.0
O2G L:GTP501 4.0 0.8 1.0
O1B L:GTP501 4.0 0.8 1.0
N L:GLN11 4.0 96.6 1.0
CA L:GLN11 4.1 96.6 1.0
CD L:GLU71 4.1 0.3 1.0
O3G L:GTP501 4.4 0.8 1.0
NE2 L:GLN11 4.5 96.6 1.0
O5' L:GTP501 4.7 0.8 1.0
OE1 L:GLU71 4.8 0.3 1.0
CG L:GLU71 4.9 0.3 1.0
NZ D:LYS252 5.0 91.7 1.0

Magnesium binding site 5 out of 12 in 6evw

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Magnesium binding site 5 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:0.1
occ:1.00
 O2B A:GTP501 2.1 0.1 1.0
O1G A:GTP501 2.1 0.1 1.0
OE1 A:GLN11 2.4 95.4 1.0
O3A A:GTP501 2.5 0.1 1.0
PB A:GTP501 2.6 0.1 1.0
CB A:GLN11 2.9 95.4 1.0
OE2 A:GLU71 3.0 0.1 1.0
PG A:GTP501 3.1 0.1 1.0
O3B A:GTP501 3.2 0.1 1.0
O2A A:GTP501 3.3 0.1 1.0
CD A:GLN11 3.4 95.4 1.0
PA A:GTP501 3.5 0.1 1.0
CG A:GLN11 3.7 95.4 1.0
O2G A:GTP501 3.9 0.1 1.0
CD A:GLU71 4.0 0.1 1.0
O1A A:GTP501 4.0 0.1 1.0
N A:GLN11 4.1 95.4 1.0
O1B A:GTP501 4.1 0.1 1.0
CA A:GLN11 4.1 95.4 1.0
O3G A:GTP501 4.4 0.1 1.0
NE2 A:GLN11 4.6 95.4 1.0
OE1 A:GLU71 4.6 0.1 1.0
CG A:GLU71 4.8 0.1 1.0
O5' A:GTP501 4.9 0.1 1.0

Magnesium binding site 6 out of 12 in 6evw

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Magnesium binding site 6 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg502

b:0.1
occ:1.00
 O2B K:GTP501 2.1 0.8 1.0
O1G K:GTP501 2.1 0.8 1.0
OE1 K:GLN11 2.3 89.3 1.0
O3A K:GTP501 2.6 0.8 1.0
PB K:GTP501 2.7 0.8 1.0
CB K:GLN11 2.9 89.3 1.0
OE2 K:GLU71 2.9 0.4 1.0
PG K:GTP501 3.2 0.8 1.0
O3B K:GTP501 3.3 0.8 1.0
CD K:GLN11 3.3 89.3 1.0
O2A K:GTP501 3.4 0.8 1.0
PA K:GTP501 3.5 0.8 1.0
CG K:GLN11 3.7 89.3 1.0
O2G K:GTP501 3.8 0.8 1.0
CD K:GLU71 3.8 0.4 1.0
O1A K:GTP501 4.0 0.8 1.0
N K:GLN11 4.0 89.3 1.0
CA K:GLN11 4.1 89.3 1.0
O1B K:GTP501 4.1 0.8 1.0
O3G K:GTP501 4.5 0.8 1.0
NE2 K:GLN11 4.5 89.3 1.0
OE1 K:GLU71 4.5 0.4 1.0
CG K:GLU71 4.6 0.4 1.0
O5' K:GTP501 5.0 0.8 1.0
OD1 K:ASP69 5.0 0.5 1.0

Magnesium binding site 7 out of 12 in 6evw

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Magnesium binding site 7 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:0.5
occ:1.00
 OE1 B:GLN11 2.1 0.1 1.0
O1B B:G2P501 2.1 0.4 1.0
O2G B:G2P501 2.2 0.4 1.0
PB B:G2P501 2.5 0.4 1.0
C3A B:G2P501 2.5 0.4 1.0
CB B:GLN11 2.8 0.1 1.0
O3B B:G2P501 3.1 0.4 1.0
CD B:GLN11 3.1 0.1 1.0
PG B:G2P501 3.2 0.4 1.0
CG B:GLN11 3.5 0.1 1.0
PA B:G2P501 3.8 0.4 1.0
OE2 B:GLU69 3.9 0.3 1.0
O2B B:G2P501 3.9 0.4 1.0
CA B:GLN11 4.0 0.1 1.0
N B:GLN11 4.1 0.1 1.0
O1G B:G2P501 4.1 0.4 1.0
O1A B:G2P501 4.2 0.4 1.0
O2A B:G2P501 4.3 0.4 1.0
NE2 B:GLN11 4.3 0.1 1.0
O3G B:G2P501 4.3 0.4 1.0
C B:GLY10 4.7 0.6 1.0
CD B:GLU69 5.0 0.3 1.0

Magnesium binding site 8 out of 12 in 6evw

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Magnesium binding site 8 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:1.0
occ:1.00
 O1B F:G2P501 2.1 0.4 1.0
O2G F:G2P501 2.2 0.4 1.0
OE1 F:GLN11 2.2 95.2 1.0
PB F:G2P501 2.5 0.4 1.0
C3A F:G2P501 2.5 0.4 1.0
CB F:GLN11 2.9 95.2 1.0
O3B F:G2P501 3.1 0.4 1.0
CD F:GLN11 3.1 95.2 1.0
PG F:G2P501 3.2 0.4 1.0
CG F:GLN11 3.6 95.2 1.0
OE2 F:GLU69 3.8 0.7 1.0
PA F:G2P501 3.8 0.4 1.0
O2B F:G2P501 4.0 0.4 1.0
CA F:GLN11 4.1 95.2 1.0
O1G F:G2P501 4.1 0.4 1.0
N F:GLN11 4.1 95.2 1.0
O1A F:G2P501 4.2 0.4 1.0
O3G F:G2P501 4.3 0.4 1.0
O2A F:G2P501 4.3 0.4 1.0
NE2 F:GLN11 4.3 95.2 1.0
C F:GLY10 4.7 93.1 1.0
CD F:GLU69 4.9 0.7 1.0
OG1 F:THR143 5.0 0.5 1.0

Magnesium binding site 9 out of 12 in 6evw

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Magnesium binding site 9 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:0.9
occ:1.00
 OE1 G:GLN11 2.1 0.4 1.0
O1B G:G2P501 2.1 0.9 1.0
O2G G:G2P501 2.1 0.9 1.0
PB G:G2P501 2.5 0.9 1.0
C3A G:G2P501 2.5 0.9 1.0
CB G:GLN11 2.8 0.4 1.0
CD G:GLN11 3.1 0.4 1.0
O3B G:G2P501 3.1 0.9 1.0
PG G:G2P501 3.2 0.9 1.0
CG G:GLN11 3.5 0.4 1.0
PA G:G2P501 3.8 0.9 1.0
OE2 G:GLU69 3.9 0.2 1.0
O2B G:G2P501 3.9 0.9 1.0
CA G:GLN11 4.1 0.4 1.0
O1G G:G2P501 4.1 0.9 1.0
N G:GLN11 4.2 0.4 1.0
O1A G:G2P501 4.2 0.9 1.0
O3G G:G2P501 4.3 0.9 1.0
O2A G:G2P501 4.3 0.9 1.0
NE2 G:GLN11 4.3 0.4 1.0
C G:GLY10 4.8 0.1 1.0
CD G:GLU69 5.0 0.2 1.0

Magnesium binding site 10 out of 12 in 6evw

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Magnesium binding site 10 out of 12 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerised with Doublecortin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:0.3
occ:1.00
 O1B D:G2P501 2.1 0.2 1.0
OE1 D:GLN11 2.1 0.5 1.0
O2G D:G2P501 2.2 0.2 1.0
PB D:G2P501 2.5 0.2 1.0
C3A D:G2P501 2.5 0.2 1.0
CB D:GLN11 2.9 0.5 1.0
O3B D:G2P501 3.1 0.2 1.0
CD D:GLN11 3.1 0.5 1.0
PG D:G2P501 3.2 0.2 1.0
CG D:GLN11 3.6 0.5 1.0
OE2 D:GLU69 3.8 0.4 1.0
PA D:G2P501 3.8 0.2 1.0
O2B D:G2P501 4.0 0.2 1.0
O1G D:G2P501 4.1 0.2 1.0
CA D:GLN11 4.1 0.5 1.0
N D:GLN11 4.2 0.5 1.0
O1A D:G2P501 4.2 0.2 1.0
O2A D:G2P501 4.3 0.2 1.0
NE2 D:GLN11 4.3 0.5 1.0
O3G D:G2P501 4.3 0.2 1.0
C D:GLY10 4.8 0.2 1.0
CD D:GLU69 4.9 0.4 1.0
OG1 D:THR143 5.0 0.1 1.0

Reference:

S.W.Manka, C.A.Moores. The Role of Tubulin-Tubulin Lattice Contacts in the Mechanism of Microtubule Dynamic Instability. Nat. Struct. Mol. Biol. V. 25 607 2018.
ISSN: ESSN 1545-9985
PubMed: 29967541
DOI: 10.1038/S41594-018-0087-8
Page generated: Tue Oct 1 00:02:41 2024

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