Magnesium in PDB 7zcw: 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;

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 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 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 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 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 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 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

S.R.Choi, T.Blum, M.O.Steinmetz. Structural and Functional Comparison of Vash-Svbp Microtubule-Detyrosinating Enzyme Complexes To Be Published.