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Magnesium in PDB 6mti: Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ (pdb code 6mti). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+, PDB code: 6mti:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6mti

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Magnesium binding site 1 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg301

b:0.2
occ:1.00
 O 1:PHE231 2.3 0.2 1.0
OD2 1:ASP172 2.9 0.3 1.0
OD2 1:ASP178 2.9 0.1 1.0
OD1 1:ASP232 3.0 0.2 1.0
CG 1:ASP172 3.3 0.6 1.0
OD1 1:ASP172 3.3 0.2 1.0
C 1:PHE231 3.4 0.4 1.0
CG 1:ASP232 3.4 0.0 1.0
CA 1:ASP232 3.5 0.5 1.0
CG 1:ASP178 3.9 0.4 1.0
N 1:ASP232 3.9 0.5 1.0
CB 1:ASP232 4.0 0.1 1.0
OD2 1:ASP232 4.0 0.0 1.0
CB 1:ASP178 4.3 0.2 1.0
OD1 1:ASP230 4.4 0.5 1.0
CB 1:ASP172 4.6 0.8 1.0
C 1:ASP232 4.7 0.8 1.0
N 1:ARG233 4.7 0.8 1.0
CA 1:PHE231 4.7 0.1 1.0
CD2 1:PHE231 4.7 0.0 1.0
N 1:ASP178 4.9 0.7 1.0
OD2 1:ASP230 4.9 0.7 1.0
OD1 1:ASP178 5.0 0.2 1.0

Magnesium binding site 2 out of 10 in 6mti

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Magnesium binding site 2 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg801

b:0.2
occ:1.00
 O 2:PHE231 2.3 0.2 1.0
OD2 2:ASP172 2.9 0.3 1.0
OD2 2:ASP178 2.9 0.1 1.0
OD1 2:ASP232 3.0 0.2 1.0
CG 2:ASP172 3.3 0.6 1.0
OD1 2:ASP172 3.3 0.2 1.0
C 2:PHE231 3.4 0.4 1.0
CG 2:ASP232 3.4 0.0 1.0
CA 2:ASP232 3.5 0.5 1.0
CG 2:ASP178 3.9 0.4 1.0
N 2:ASP232 3.9 0.5 1.0
CB 2:ASP232 4.0 0.1 1.0
OD2 2:ASP232 4.0 0.0 1.0
CB 2:ASP178 4.3 0.2 1.0
OD1 2:ASP230 4.4 0.5 1.0
CB 2:ASP172 4.6 0.8 1.0
C 2:ASP232 4.7 0.8 1.0
N 2:ARG233 4.7 0.8 1.0
CA 2:PHE231 4.7 0.1 1.0
CD2 2:PHE231 4.7 0.0 1.0
N 2:ASP178 4.9 0.7 1.0
OD2 2:ASP230 4.9 0.7 1.0
OD1 2:ASP178 5.0 0.2 1.0

Magnesium binding site 3 out of 10 in 6mti

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Magnesium binding site 3 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg802

b:0.0
occ:1.00
 OD2 2:ASP584 2.2 0.4 1.0
OD1 2:ASP646 2.3 0.8 1.0
OD1 2:ASP584 2.6 0.1 1.0
CG 2:ASP584 2.7 0.8 1.0
OD2 2:ASP644 2.7 0.5 1.0
OD2 2:ASP590 3.0 0.3 1.0
O 2:TYR645 3.2 0.4 1.0
OD1 2:ASP644 3.2 0.7 1.0
CG 2:ASP644 3.4 0.8 1.0
CG 2:ASP646 3.4 0.1 1.0
CG 2:ASP590 3.5 0.1 1.0
CB 2:ASP590 3.8 0.4 1.0
C 2:TYR645 3.9 0.8 1.0
OD2 2:ASP646 3.9 0.8 1.0
N 2:ASP590 4.2 0.5 1.0
CB 2:ASP584 4.2 0.7 1.0
N 2:ASP646 4.4 0.5 1.0
OD1 2:ASP590 4.4 0.3 1.0
N 2:TYR645 4.4 0.2 1.0
CA 2:ASP646 4.6 0.1 1.0
CB 2:ASP646 4.6 0.7 1.0
CA 2:ASP590 4.6 0.4 1.0
CA 2:TYR645 4.8 0.1 1.0
CB 2:ASP644 4.8 0.8 1.0
CA 2:ASP584 4.9 0.9 1.0

Magnesium binding site 4 out of 10 in 6mti

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Magnesium binding site 4 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg801

b:0.2
occ:1.00
 O 3:PHE231 2.3 0.2 1.0
OD2 3:ASP172 2.9 0.3 1.0
OD2 3:ASP178 2.9 0.1 1.0
OD1 3:ASP232 3.0 0.2 1.0
CG 3:ASP172 3.3 0.6 1.0
OD1 3:ASP172 3.3 0.2 1.0
C 3:PHE231 3.4 0.4 1.0
CG 3:ASP232 3.4 0.0 1.0
CA 3:ASP232 3.5 0.5 1.0
CG 3:ASP178 3.9 0.4 1.0
N 3:ASP232 3.9 0.5 1.0
CB 3:ASP232 4.0 0.1 1.0
OD2 3:ASP232 4.0 0.0 1.0
CB 3:ASP178 4.3 0.2 1.0
OD1 3:ASP230 4.4 0.5 1.0
CB 3:ASP172 4.6 0.8 1.0
C 3:ASP232 4.7 0.8 1.0
N 3:ARG233 4.7 0.8 1.0
CA 3:PHE231 4.7 0.1 1.0
CD2 3:PHE231 4.7 0.0 1.0
N 3:ASP178 4.9 0.7 1.0
OD2 3:ASP230 4.9 0.7 1.0
OD1 3:ASP178 5.0 0.2 1.0

Magnesium binding site 5 out of 10 in 6mti

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Magnesium binding site 5 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg802

b:0.0
occ:1.00
 OD2 3:ASP584 2.2 0.4 1.0
OD1 3:ASP646 2.3 0.8 1.0
OD1 3:ASP584 2.6 0.1 1.0
CG 3:ASP584 2.7 0.8 1.0
OD2 3:ASP644 2.7 0.5 1.0
OD2 3:ASP590 3.0 0.3 1.0
O 3:TYR645 3.2 0.4 1.0
OD1 3:ASP644 3.2 0.7 1.0
CG 3:ASP644 3.4 0.8 1.0
CG 3:ASP646 3.4 0.1 1.0
CG 3:ASP590 3.5 0.1 1.0
CB 3:ASP590 3.8 0.4 1.0
C 3:TYR645 3.9 0.8 1.0
OD2 3:ASP646 3.9 0.8 1.0
N 3:ASP590 4.2 0.5 1.0
CB 3:ASP584 4.2 0.7 1.0
N 3:ASP646 4.4 0.5 1.0
OD1 3:ASP590 4.4 0.3 1.0
N 3:TYR645 4.4 0.2 1.0
CA 3:ASP646 4.6 0.1 1.0
CB 3:ASP646 4.6 0.7 1.0
CA 3:ASP590 4.6 0.4 1.0
CA 3:TYR645 4.8 0.1 1.0
CB 3:ASP644 4.9 0.8 1.0
CA 3:ASP584 4.9 0.9 1.0

Magnesium binding site 6 out of 10 in 6mti

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Magnesium binding site 6 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg801

b:0.2
occ:1.00
 O 4:PHE231 2.3 0.2 1.0
OD2 4:ASP172 2.9 0.3 1.0
OD2 4:ASP178 2.9 0.1 1.0
OD1 4:ASP232 3.0 0.2 1.0
CG 4:ASP172 3.3 0.6 1.0
OD1 4:ASP172 3.3 0.2 1.0
C 4:PHE231 3.4 0.4 1.0
CG 4:ASP232 3.4 0.0 1.0
CA 4:ASP232 3.5 0.5 1.0
CG 4:ASP178 3.9 0.4 1.0
N 4:ASP232 3.9 0.5 1.0
CB 4:ASP232 4.0 0.1 1.0
OD2 4:ASP232 4.0 0.0 1.0
CB 4:ASP178 4.3 0.2 1.0
OD1 4:ASP230 4.4 0.5 1.0
CB 4:ASP172 4.6 0.8 1.0
C 4:ASP232 4.7 0.8 1.0
N 4:ARG233 4.7 0.8 1.0
CA 4:PHE231 4.7 0.1 1.0
CD2 4:PHE231 4.7 0.0 1.0
N 4:ASP178 4.9 0.7 1.0
OD2 4:ASP230 4.9 0.7 1.0
OD1 4:ASP178 5.0 0.2 1.0

Magnesium binding site 7 out of 10 in 6mti

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Magnesium binding site 7 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg802

b:0.0
occ:1.00
 OD2 4:ASP584 2.2 0.4 1.0
OD1 4:ASP646 2.3 0.8 1.0
OD1 4:ASP584 2.6 0.1 1.0
CG 4:ASP584 2.7 0.8 1.0
OD2 4:ASP644 2.7 0.5 1.0
OD2 4:ASP590 3.0 0.3 1.0
O 4:TYR645 3.2 0.4 1.0
OD1 4:ASP644 3.2 0.7 1.0
CG 4:ASP644 3.4 0.8 1.0
CG 4:ASP646 3.4 0.1 1.0
CG 4:ASP590 3.5 0.1 1.0
CB 4:ASP590 3.8 0.4 1.0
C 4:TYR645 3.9 0.8 1.0
OD2 4:ASP646 3.9 0.8 1.0
N 4:ASP590 4.2 0.5 1.0
CB 4:ASP584 4.2 0.7 1.0
N 4:ASP646 4.4 0.5 1.0
OD1 4:ASP590 4.4 0.3 1.0
N 4:TYR645 4.4 0.2 1.0
CA 4:ASP646 4.6 0.1 1.0
CB 4:ASP646 4.6 0.7 1.0
CA 4:ASP590 4.6 0.4 1.0
CA 4:TYR645 4.8 0.1 1.0
CB 4:ASP644 4.9 0.8 1.0
CA 4:ASP584 4.9 0.9 1.0

Magnesium binding site 8 out of 10 in 6mti

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Magnesium binding site 8 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Mg801

b:0.2
occ:1.00
 O 5:PHE231 2.3 0.2 1.0
OD2 5:ASP172 2.9 0.3 1.0
OD2 5:ASP178 2.9 0.1 1.0
OD1 5:ASP232 3.0 0.2 1.0
CG 5:ASP172 3.3 0.6 1.0
OD1 5:ASP172 3.3 0.2 1.0
C 5:PHE231 3.4 0.4 1.0
CG 5:ASP232 3.4 0.0 1.0
CA 5:ASP232 3.5 0.5 1.0
CG 5:ASP178 3.9 0.4 1.0
N 5:ASP232 3.9 0.5 1.0
CB 5:ASP232 4.0 0.1 1.0
OD2 5:ASP232 4.0 0.0 1.0
CB 5:ASP178 4.3 0.2 1.0
OD1 5:ASP230 4.4 0.5 1.0
CB 5:ASP172 4.6 0.8 1.0
C 5:ASP232 4.7 0.8 1.0
N 5:ARG233 4.7 0.8 1.0
CA 5:PHE231 4.7 0.1 1.0
CD2 5:PHE231 4.7 0.0 1.0
N 5:ASP178 4.9 0.7 1.0
OD2 5:ASP230 4.9 0.7 1.0
OD1 5:ASP178 5.0 0.2 1.0

Magnesium binding site 9 out of 10 in 6mti

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Magnesium binding site 9 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Mg802

b:0.0
occ:1.00
 OD2 5:ASP584 2.2 0.4 1.0
OD1 5:ASP646 2.3 0.8 1.0
OD1 5:ASP584 2.6 0.1 1.0
CG 5:ASP584 2.7 0.8 1.0
OD2 5:ASP644 2.7 0.5 1.0
OD2 5:ASP590 3.0 0.3 1.0
O 5:TYR645 3.2 0.4 1.0
OD1 5:ASP644 3.2 0.7 1.0
CG 5:ASP644 3.4 0.8 1.0
CG 5:ASP646 3.4 0.1 1.0
CG 5:ASP590 3.5 0.1 1.0
CB 5:ASP590 3.8 0.4 1.0
C 5:TYR645 3.9 0.8 1.0
OD2 5:ASP646 3.9 0.8 1.0
N 5:ASP590 4.2 0.5 1.0
CB 5:ASP584 4.2 0.7 1.0
N 5:ASP646 4.4 0.5 1.0
OD1 5:ASP590 4.4 0.3 1.0
N 5:TYR645 4.4 0.2 1.0
CA 5:ASP646 4.6 0.1 1.0
CB 5:ASP646 4.6 0.7 1.0
CA 5:ASP590 4.6 0.4 1.0
CA 5:TYR645 4.8 0.1 1.0
CB 5:ASP644 4.8 0.8 1.0
CA 5:ASP584 4.9 0.9 1.0

Magnesium binding site 10 out of 10 in 6mti

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Magnesium binding site 10 out of 10 in the Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Synaptotagmin-1 C2A, C2B Domains and Snare-Pin Proteins (5CCI) Individually Docked Into Cryo-Em Map of C2AB-Snare Complexes Helically Organized on Lipid Nanotube Surface in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg301

b:0.2
occ:1.00
 O 6:PHE231 2.3 0.2 1.0
OD2 6:ASP172 2.9 0.3 1.0
OD2 6:ASP178 2.9 0.1 1.0
OD1 6:ASP232 3.0 0.2 1.0
CG 6:ASP172 3.3 0.6 1.0
OD1 6:ASP172 3.3 0.2 1.0
C 6:PHE231 3.4 0.4 1.0
CG 6:ASP232 3.4 0.0 1.0
CA 6:ASP232 3.5 0.5 1.0
CG 6:ASP178 3.9 0.4 1.0
N 6:ASP232 3.9 0.5 1.0
CB 6:ASP232 4.0 0.1 1.0
OD2 6:ASP232 4.0 0.0 1.0
CB 6:ASP178 4.3 0.2 1.0
OD1 6:ASP230 4.4 0.5 1.0
CB 6:ASP172 4.6 0.8 1.0
C 6:ASP232 4.7 0.8 1.0
N 6:ARG233 4.7 0.8 1.0
CA 6:PHE231 4.7 0.1 1.0
CD2 6:PHE231 4.7 0.0 1.0
N 6:ASP178 4.9 0.7 1.0
OD2 6:ASP230 4.9 0.7 1.0
OD1 6:ASP178 5.0 0.2 1.0

Reference:

K.Grushin, J.Wang, J.Coleman, J.E.Rothman, C.V.Sindelar, S.S.Krishnakumar. Structural Basis For the Clamping and CA2+Activation of Snare-Mediated Fusion By Synaptotagmin. Nat Commun V. 10 2413 2019.
ISSN: ESSN 2041-1723
PubMed: 31160571
DOI: 10.1038/S41467-019-10391-X
Page generated: Tue Oct 1 12:02:37 2024

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