Magnesium in PDB 7zcw: Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp

Enzymatic activity of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp

All present enzymatic activity of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp:
3.4.17.17;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp (pdb code 7zcw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp, PDB code: 7zcw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7zcw

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp


Mono view


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-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:39.4
occ:1.00
O1G A:GTP501 1.9 54.9 1.0
O2B A:GTP501 2.3 54.9 1.0
OE1 A:GLU71 3.3 51.7 1.0
PG A:GTP501 3.3 54.9 1.0
HB2 A:GLN11 3.4 46.4 1.0
PB A:GTP501 3.6 54.9 1.0
HZ1 B:LYS252 3.6 47.2 1.0
O3B A:GTP501 3.8 54.9 1.0
H A:GLN11 4.0 46.4 1.0
HB3 A:GLN11 4.0 46.4 1.0
O3G A:GTP501 4.1 54.9 1.0
CB A:GLN11 4.1 46.4 1.0
OE1 A:GLN11 4.3 46.4 1.0
HB3 A:GLU71 4.3 51.7 1.0
HB2 A:ASP98 4.3 49.4 1.0
O2G A:GTP501 4.3 54.9 1.0
CD A:GLU71 4.4 51.7 1.0
NZ B:LYS252 4.4 47.2 1.0
HB2 B:ASN247 4.5 50.4 1.0
O3A A:GTP501 4.5 54.9 1.0
HE3 B:LYS252 4.5 47.2 1.0
HZ2 B:LYS252 4.6 47.2 1.0
O1B A:GTP501 4.6 54.9 1.0
HB2 A:GLU71 4.6 51.7 1.0
N A:GLN11 4.7 46.4 1.0
HG1 A:THR145 4.8 43.3 1.0
OD2 A:ASP69 4.8 45.8 1.0
HD21 B:ASN247 4.8 50.4 1.0
O2A A:GTP501 4.8 54.9 1.0
OD1 A:ASP69 4.8 45.8 1.0
HB3 A:ASP98 4.8 49.4 1.0
CB A:GLU71 4.9 51.7 1.0
CD A:GLN11 4.9 46.4 1.0
CE B:LYS252 5.0 47.2 1.0

Magnesium binding site 2 out of 6 in 7zcw

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp


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-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:48.2
occ:1.00
O3G B:G2P501 2.0 57.7 1.0
O2G B:G2P501 2.0 57.7 1.0
O2B B:G2P501 2.0 57.7 1.0
PG B:G2P501 2.3 57.7 1.0
PB B:G2P501 3.1 57.7 1.0
O3B B:G2P501 3.1 57.7 1.0
O1G B:G2P501 3.7 57.7 1.0
HB2 B:GLN11 3.8 57.9 1.0
H B:GLN11 3.9 57.9 1.0
O2A B:G2P501 3.9 57.7 1.0
HG1 B:THR143 4.0 56.9 1.0
HB B:THR143 4.1 56.9 1.0
C3A B:G2P501 4.2 57.7 1.0
H3A2 B:G2P501 4.2 57.7 1.0
O1B B:G2P501 4.2 57.7 1.0
HB3 B:GLN11 4.4 57.9 1.0
PA B:G2P501 4.4 57.7 1.0
OE1 B:GLU69 4.5 63.5 1.0
O1A B:G2P501 4.5 57.7 1.0
OG1 B:THR143 4.5 56.9 1.0
CB B:GLN11 4.6 57.9 1.0
N B:GLN11 4.7 57.9 1.0
OD2 B:ASP67 4.7 61.2 1.0
HA2 B:GLY10 4.7 56.0 1.0
CB B:THR143 4.8 56.9 1.0
OD1 B:ASP67 4.8 61.2 1.0
HB3 B:GLU69 4.9 63.5 1.0
HD22 B:ASN99 4.9 54.5 1.0
HD21 B:ASN99 4.9 54.5 1.0

Magnesium binding site 3 out of 6 in 7zcw

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp


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-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:44.3
occ:1.00
O1G E:GTP501 1.9 54.9 1.0
O2B E:GTP501 3.0 54.9 1.0
OE1 E:GLU71 3.1 47.7 1.0
PG E:GTP501 3.4 54.9 1.0
HB2 E:GLN11 3.4 44.8 1.0
HE21 E:GLN11 3.6 44.8 1.0
HZ1 F:LYS252 3.7 45.5 1.0
HB2 E:ASP98 4.0 46.2 1.0
HB3 E:GLN11 4.0 44.8 1.0
H E:GLN11 4.1 44.8 1.0
PB E:GTP501 4.1 54.9 1.0
O3G E:GTP501 4.1 54.9 1.0
NE2 E:GLN11 4.1 44.8 1.0
O3B E:GTP501 4.2 54.9 1.0
CB E:GLN11 4.2 44.8 1.0
HB3 E:ASP98 4.2 46.2 1.0
HB3 E:GLU71 4.3 47.7 1.0
CD E:GLU71 4.3 47.7 1.0
O2G E:GTP501 4.3 54.9 1.0
HE22 E:GLN11 4.3 44.8 1.0
HB2 F:ASN247 4.6 49.3 1.0
CB E:ASP98 4.6 46.2 1.0
NZ F:LYS252 4.6 45.5 1.0
HD21 F:ASN247 4.6 49.3 1.0
O3A E:GTP501 4.6 54.9 1.0
OD1 E:ASP69 4.7 42.7 1.0
OD2 E:ASP69 4.7 42.7 1.0
N E:GLN11 4.7 44.8 1.0
HG1 E:THR145 4.8 41.4 1.0
HD2 F:LYS252 4.8 45.5 1.0
HZ3 F:LYS252 4.9 45.5 1.0
HZ2 F:LYS252 4.9 45.5 1.0

Magnesium binding site 4 out of 6 in 7zcw

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp


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-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:51.5
occ:1.00
O3G F:G2P501 1.9 56.6 1.0
O2B F:G2P501 2.7 56.6 1.0
PG F:G2P501 3.3 56.6 1.0
HG1 F:THR143 3.5 55.8 1.0
O2G F:G2P501 3.7 56.6 1.0
HB2 F:GLN11 3.7 54.4 1.0
PB F:G2P501 3.9 56.6 1.0
O3B F:G2P501 4.0 56.6 1.0
OG1 F:THR143 4.2 55.8 1.0
OD2 F:ASP67 4.3 57.8 1.0
HB F:THR143 4.3 55.8 1.0
OD1 F:ASP67 4.3 57.8 1.0
O1G F:G2P501 4.4 56.6 1.0
H F:GLN11 4.4 54.4 1.0
HA2 F:GLY10 4.5 52.3 1.0
HB2 F:GLU69 4.5 62.8 1.0
HG21 F:THR72 4.7 61.7 1.0
CB F:GLN11 4.7 54.4 1.0
CB F:THR143 4.8 55.8 1.0
N F:GLN11 4.8 54.4 1.0
CG F:ASP67 4.8 57.8 1.0
O2A F:G2P501 4.8 56.6 1.0
HG21 F:THR143 4.8 55.8 1.0
O1B F:G2P501 4.8 56.6 1.0
HG3 F:GLN11 4.9 54.4 1.0
HG23 F:THR72 4.9 61.7 1.0
HA3 F:GLY96 5.0 61.8 1.0

Magnesium binding site 5 out of 6 in 7zcw

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp


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-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:38.4
occ:1.00
O3G G:G2P501 1.9 52.8 1.0
OE2 G:GLU69 2.4 59.6 1.0
O2B G:G2P501 2.5 52.8 1.0
PG G:G2P501 3.1 52.8 1.0
O2G G:G2P501 3.2 52.8 1.0
CD G:GLU69 3.4 59.6 1.0
HB2 G:GLN11 3.5 53.3 1.0
PB G:G2P501 3.8 52.8 1.0
O3B G:G2P501 3.9 52.8 1.0
H G:GLN11 3.9 53.3 1.0
HG2 G:GLU69 4.1 59.6 1.0
OE1 G:GLU69 4.2 59.6 1.0
O1G G:G2P501 4.2 52.8 1.0
CG G:GLU69 4.3 59.6 1.0
CB G:GLN11 4.4 53.3 1.0
HB3 G:GLN11 4.4 53.3 1.0
OE1 G:GLN11 4.5 53.3 1.0
HG3 G:GLU69 4.5 59.6 1.0
OD2 G:ASP67 4.6 57.6 1.0
O2A G:G2P501 4.7 52.8 1.0
N G:GLN11 4.7 53.3 1.0
O1B G:G2P501 4.8 52.8 1.0
O1A G:G2P501 4.8 52.8 1.0
HA2 G:GLY10 4.9 52.0 1.0
OD1 G:ASP67 4.9 57.6 1.0
C3A G:G2P501 5.0 52.8 1.0
HB G:THR143 5.0 52.4 1.0

Magnesium binding site 6 out of 6 in 7zcw

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp


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-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:50.5
occ:1.00
O3G H:G2P501 2.0 54.1 1.0
O2B H:G2P501 2.6 54.1 1.0
PG H:G2P501 3.2 54.1 1.0
O2G H:G2P501 3.4 54.1 1.0
HB2 H:GLN11 3.6 53.3 1.0
PB H:G2P501 3.8 54.1 1.0
O3B H:G2P501 4.0 54.1 1.0
H H:GLN11 4.0 53.3 1.0
O1G H:G2P501 4.3 54.1 1.0
CB H:GLN11 4.5 53.3 1.0
HB2 H:GLU69 4.5 61.7 1.0
HB3 H:GLN11 4.5 53.3 1.0
O2A H:G2P501 4.6 54.1 1.0
OD2 H:ASP67 4.6 57.1 1.0
HG1 H:THR143 4.7 53.0 1.0
HB H:THR143 4.7 53.0 1.0
N H:GLN11 4.7 53.3 1.0
OD1 H:ASP67 4.7 57.1 1.0
OE1 H:GLN11 4.7 53.3 1.0
O1A H:G2P501 4.8 54.1 1.0
HA2 H:GLY10 4.8 53.4 1.0
O1B H:G2P501 4.8 54.1 1.0
HG1 H:THR72 4.8 60.7 1.0
HA3 H:GLY96 4.9 56.9 1.0

Reference:

S.R.Choi, T.Blum, M.O.Steinmetz. Structural and Functional Comparison of Vash-Svbp Microtubule-Detyrosinating Enzyme Complexes To Be Published.
Page generated: Thu Oct 3 16:23:18 2024

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