Magnesium in PDB 7nvm: Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound

The structure of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound also contains other interesting chemical elements:

Aluminium	(Al)	16 atoms
Fluorine	(F)	48 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound (pdb code 7nvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound, PDB code: 7nvm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:78.9 occ:1.00 OD1 A:ASP88 2.0 67.8 1.0 O3A A:ADP601 2.2 202.8 1.0 F1 A:AF3603 2.5 58.2 1.0 CG A:ASP88 2.7 67.8 1.0 OD2 A:ASP88 2.8 67.8 1.0 O3B A:ADP601 3.0 161.5 1.0 O2A A:ADP601 3.1 200.0 1.0 PB A:ADP601 3.2 189.6 1.0 PA A:ADP601 3.3 210.3 1.0 O2B A:ADP601 3.8 194.1 1.0 AL A:AF3603 3.9 55.7 1.0 O A:SER155 3.9 68.1 1.0 O5' A:ADP601 4.2 184.4 1.0 CB A:ASP88 4.2 67.8 1.0 CE A:LYS159 4.3 68.3 1.0 O1A A:ADP601 4.4 177.2 1.0 O1B A:ADP601 4.5 179.6 1.0 N A:GLY89 4.5 66.4 1.0 CA A:SER155 4.6 68.1 1.0 F2 A:AF3603 4.6 47.6 1.0 OD2 A:ASP394 4.6 69.1 1.0 NZ A:LYS159 4.7 68.3 1.0 CA A:ASP88 4.7 67.8 1.0 C A:SER155 4.7 68.1 1.0 OG A:SER158 4.8 68.3 1.0 CB A:SER155 5.0 68.1 1.0

Magnesium binding site 2 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:78.9 occ:1.00 OD1 B:ASP97 2.0 68.1 1.0 F1 B:AF3603 2.0 58.2 1.0 O1A B:ADP601 2.0 177.2 1.0 CG B:ASP97 3.1 68.1 1.0 O1B B:ADP601 3.4 194.1 1.0 PA B:ADP601 3.4 210.3 1.0 AL B:AF3603 3.5 55.7 1.0 OD2 B:ASP97 3.6 68.1 1.0 CE B:LYS170 3.6 68.5 1.0 O B:THR166 3.7 68.4 1.0 O2B B:ADP601 4.0 179.6 1.0 OD2 B:ASP392 4.1 69.5 1.0 NZ B:LYS170 4.1 68.5 1.0 PB B:ADP601 4.1 189.6 1.0 O2A B:ADP601 4.1 200.0 1.0 O3A B:ADP601 4.2 202.8 1.0 CB B:ASP97 4.3 68.1 1.0 F2 B:AF3603 4.4 47.6 1.0 F3 B:AF3603 4.5 62.6 1.0 O5' B:ADP601 4.5 184.4 1.0 CA B:THR166 4.5 68.4 1.0 C B:THR166 4.5 68.4 1.0 CD B:LYS170 4.8 68.5 1.0 CB B:SER169 4.8 68.8 1.0 CA B:ASP97 4.8 68.1 1.0 CB B:THR166 4.8 68.4 1.0 CG B:ASP392 4.9 69.5 1.0 C5' B:ADP601 4.9 239.2 1.0 CG B:LYS170 5.0 68.5 1.0

Magnesium binding site 3 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:78.9 occ:1.00 F2 D:AF3603 1.9 47.6 1.0 O1A D:ADP601 2.2 177.2 1.0 OD1 D:ASP104 3.1 70.1 1.0 NZ D:LYS174 3.2 68.4 1.0 O2B D:ADP601 3.3 194.1 1.0 AL D:AF3603 3.5 55.7 1.0 O D:SER170 3.5 68.9 1.0 PA D:ADP601 3.6 210.3 1.0 CG D:ASP104 3.7 70.1 1.0 OD2 D:ASP104 3.7 70.1 1.0 OG D:SER170 4.1 68.9 1.0 PB D:ADP601 4.2 189.6 1.0 O3A D:ADP601 4.2 202.8 1.0 CB D:SER173 4.3 67.7 1.0 O3B D:ADP601 4.3 179.6 1.0 F1 D:AF3603 4.3 58.2 1.0 C D:SER170 4.3 68.9 1.0 CA D:SER170 4.3 68.9 1.0 OD2 D:ASP407 4.4 71.0 1.0 CE D:LYS174 4.5 68.4 1.0 O2A D:ADP601 4.6 200.0 1.0 O5' D:ADP601 4.6 184.4 1.0 OG D:SER173 4.7 67.7 1.0 F3 D:AF3603 4.7 62.6 1.0 CB D:SER170 4.9 68.9 1.0

Magnesium binding site 4 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:78.9 occ:1.00 O3A E:ADP601 2.1 202.8 1.0 OD1 E:ASP104 2.3 68.7 1.0 O1A E:ADP601 2.7 200.0 1.0 OD2 E:ASP104 2.8 68.7 1.0 CG E:ASP104 2.8 68.7 1.0 PA E:ADP601 3.0 210.3 1.0 PB E:ADP601 3.3 189.6 1.0 F1 E:AF3603 3.3 58.2 1.0 O3B E:ADP601 3.4 194.1 1.0 O1B E:ADP601 3.7 161.5 1.0 O5' E:ADP601 3.8 184.4 1.0 AL E:AF3603 3.9 55.7 1.0 O E:THR172 4.0 68.7 1.0 CB E:ASP104 4.3 68.7 1.0 OG E:SER175 4.3 69.5 1.0 O2A E:ADP601 4.3 177.2 1.0 CG2 E:THR172 4.3 68.7 1.0 NZ E:LYS176 4.3 69.3 1.0 O2B E:ADP601 4.5 179.6 1.0 N E:GLY105 4.5 67.4 1.0 CA E:THR172 4.7 68.7 1.0 F2 E:AF3603 4.7 47.6 1.0 F3 E:AF3603 4.7 62.6 1.0 CA E:ASP104 4.8 68.7 1.0 OD2 E:ASP404 4.8 69.8 1.0 C E:THR172 4.8 68.7 1.0

Magnesium binding site 5 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:78.9 occ:1.00 OD1 G:ASP93 2.0 68.1 1.0 OD2 G:ASP93 2.2 68.1 1.0 CG G:ASP93 2.4 68.1 1.0 O2A G:ADP601 2.7 200.0 1.0 O3B G:ADP601 2.8 161.5 1.0 F2 G:AF3603 2.8 47.6 1.0 O G:SER159 3.4 68.3 1.0 PB G:ADP601 3.8 189.6 1.0 CB G:ASP93 3.9 68.1 1.0 O1B G:ADP601 3.9 194.1 1.0 OG1 G:THR162 4.0 67.3 1.0 PA G:ADP601 4.1 210.3 1.0 OG G:SER159 4.2 68.3 1.0 AL G:AF3603 4.3 55.7 1.0 O3A G:ADP601 4.3 202.8 1.0 C G:SER159 4.4 68.3 1.0 N G:GLY94 4.5 67.0 1.0 C5' G:ADP601 4.5 239.2 1.0 OD2 G:ASP393 4.5 69.1 1.0 CA G:SER159 4.5 68.3 1.0 CA G:ASP93 4.6 68.1 1.0 CE G:LYS163 4.7 67.6 1.0 CB G:SER159 4.8 68.3 1.0 O5' G:ADP601 4.8 184.4 1.0

Magnesium binding site 6 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg602 b:78.9 occ:1.00 OD1 H:ASP92 2.0 67.8 1.0 OD2 H:ASP92 2.3 67.8 1.0 O3A H:ADP601 2.3 202.8 1.0 CG H:ASP92 2.4 67.8 1.0 O1B H:ADP601 2.9 161.5 1.0 PB H:ADP601 3.1 189.6 1.0 O3B H:ADP601 3.5 194.1 1.0 F2 H:AF3603 3.5 47.6 1.0 PA H:ADP601 3.6 210.3 1.0 O1A H:ADP601 3.6 200.0 1.0 O H:ALA162 3.9 67.2 1.0 CB H:ASP92 4.0 67.8 1.0 C5' H:ADP601 4.2 239.2 1.0 O5' H:ADP601 4.3 184.4 1.0 AL H:AF3603 4.3 55.7 1.0 NZ H:LYS166 4.4 67.3 1.0 CA H:ALA162 4.4 67.2 1.0 O2B H:ADP601 4.5 179.6 1.0 N H:GLY93 4.5 65.8 1.0 F1 H:AF3603 4.5 58.2 1.0 C H:ALA162 4.6 67.2 1.0 CA H:ASP92 4.7 67.8 1.0 O2A H:ADP601 4.7 177.2 1.0 OD2 H:ASP391 4.8 68.5 1.0 CB H:ALA162 4.9 67.2 1.0

Magnesium binding site 7 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg602 b:78.9 occ:1.00 OD1 Q:ASP99 1.9 72.2 1.0 O3B Q:ADP601 2.1 161.5 1.0 OD2 Q:ASP99 2.2 72.2 1.0 CG Q:ASP99 2.3 72.2 1.0 O2A Q:ADP601 2.4 177.2 1.0 PB Q:ADP601 3.3 189.6 1.0 F3 Q:AF3603 3.5 62.6 1.0 O1B Q:ADP601 3.6 179.6 1.0 PA Q:ADP601 3.6 210.3 1.0 CB Q:ASP99 3.8 72.2 1.0 O3A Q:ADP601 3.9 202.8 1.0 O5' Q:ADP601 4.2 184.4 1.0 C5' Q:ADP601 4.2 239.2 1.0 OG Q:SER170 4.2 70.7 1.0 OD2 Q:ASP394 4.2 71.8 1.0 O Q:SER167 4.3 71.0 1.0 AL Q:AF3603 4.4 55.7 1.0 N Q:GLY100 4.4 71.1 1.0 CB Q:SER170 4.4 70.7 1.0 O2B Q:ADP601 4.6 194.1 1.0 CA Q:ASP99 4.6 72.2 1.0 F1 Q:AF3603 4.8 58.2 1.0 CA Q:SER167 4.9 71.0 1.0 O1A Q:ADP601 4.9 200.0 1.0 CG Q:ASP394 4.9 71.8 1.0 F2 Q:AF3603 4.9 47.6 1.0 C Q:ASP99 4.9 72.2 1.0 CE Q:LYS171 5.0 70.4 1.0

Magnesium binding site 8 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg602 b:78.9 occ:1.00 OD2 Z:ASP90 2.0 69.6 1.0 O2A Z:ADP601 2.2 200.0 1.0 CG Z:ASP90 2.4 69.6 1.0 OD1 Z:ASP90 2.4 69.6 1.0 NZ Z:LYS159 2.9 69.1 1.0 O3A Z:ADP601 3.3 202.8 1.0 PA Z:ADP601 3.3 210.3 1.0 O1B Z:ADP601 3.4 194.1 1.0 CB Z:ASP90 3.7 69.6 1.0 OG1 Z:THR158 3.8 69.2 1.0 PB Z:ADP601 3.9 189.6 1.0 AL Z:AF3603 4.1 55.7 1.0 OD2 Z:ASP393 4.2 70.8 1.0 O3B Z:ADP601 4.2 161.5 1.0 CE Z:LYS159 4.3 69.1 1.0 F1 Z:AF3603 4.3 58.2 1.0 O1A Z:ADP601 4.3 177.2 1.0 F2 Z:AF3603 4.4 47.6 1.0 O5' Z:ADP601 4.5 184.4 1.0 CA Z:ASP90 4.6 69.6 1.0 OG Z:SER155 4.7 70.4 1.0 CB Z:SER155 4.7 70.4 1.0 CA Z:SER155 4.7 70.4 1.0 F3 Z:AF3603 4.7 62.6 1.0 O Z:SER155 4.8 70.4 1.0 N Z:GLY91 4.8 67.6 1.0 CB Z:THR158 4.9 69.2 1.0 CG Z:LYS159 5.0 69.1 1.0

Magnesium binding site 9 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg602 b:78.9 occ:1.00 F1 a:AF3603 2.0 58.2 1.0 OD1 a:ASP88 2.1 67.8 1.0 O3A a:ADP601 2.8 202.8 1.0 CG a:ASP88 2.8 67.8 1.0 OD2 a:ASP88 2.8 67.8 1.0 O2A a:ADP601 3.2 200.0 1.0 O3B a:ADP601 3.5 161.5 1.0 O a:SER155 3.6 67.8 1.0 AL a:AF3603 3.6 55.7 1.0 PA a:ADP601 3.7 210.3 1.0 PB a:ADP601 3.7 189.6 1.0 O2B a:ADP601 4.1 194.1 1.0 CE a:LYS159 4.3 67.9 1.0 CB a:ASP88 4.3 67.8 1.0 CA a:SER155 4.3 67.8 1.0 C a:SER155 4.4 67.8 1.0 F2 a:AF3603 4.4 47.6 1.0 O5' a:ADP601 4.6 184.4 1.0 CB a:SER155 4.6 67.8 1.0 NZ a:LYS159 4.7 67.9 1.0 OD2 a:ASP394 4.7 68.5 1.0 OG a:SER158 4.7 68.0 1.0 N a:GLY89 4.8 66.2 1.0 O1A a:ADP601 4.8 177.2 1.0 F3 a:AF3603 4.8 62.6 1.0 CA a:ASP88 4.8 67.8 1.0 O1B a:ADP601 5.0 179.6 1.0

Magnesium binding site 10 out of 16 in the Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human Tric Complex in Closed State with Nanobody NB18, Actin and PHLP2A Bound within 5.0Å range: probe atom residue distance (Å) B Occ b:Mg602 b:78.9 occ:1.00 OD1 b:ASP97 1.9 67.1 1.0 O1A b:ADP601 2.0 0.0 1.0 CG b:ASP97 2.7 67.1 1.0 F1 b:AF3603 2.9 58.2 1.0 OD2 b:ASP97 2.9 67.1 1.0 O b:THR166 3.4 67.5 1.0 PA b:ADP601 3.5 10.3 1.0 O1B b:ADP601 3.7 94.1 1.0 CA b:THR166 3.9 67.5 1.0 CE b:LYS170 3.9 67.6 1.0 C b:THR166 4.1 67.5 1.0 CB b:ASP97 4.1 67.1 1.0 CB b:THR166 4.3 67.5 1.0 O5' b:ADP601 4.3 84.4 1.0 O2A b:ADP601 4.4 77.2 1.0 O3A b:ADP601 4.4 2.8 1.0 AL b:AF3603 4.4 55.7 1.0 NZ b:LYS170 4.5 67.6 1.0 CG2 b:THR166 4.5 67.5 1.0 PB b:ADP601 4.5 89.6 1.0 C5' b:ADP601 4.6 39.2 1.0 O2B b:ADP601 4.6 61.5 1.0 OD2 b:ASP392 4.6 67.9 1.0 CB b:SER169 4.7 67.4 1.0 O b:THR165 4.8 68.0 1.0 CA b:ASP97 5.0 67.1 1.0 CD b:LYS170 5.0 67.6 1.0

J.J.Kelly, D.Tranter, E.Pardon, G.Chi, H.Kramer, L.Happonen, K.M.Knee, J.M.Janz, J.Steyaert, C.Bulawa, V.O.Paavilainen, J.T.Huiskonen, W.W.Yue. Snapshots of Actin and Tubulin Folding Inside the Tric Chaperonin. Nat.Struct.Mol.Biol. V. 29 420 2022.
ISSN: ESSN 1545-9985
PubMed: 35449234
DOI: 10.1038/S41594-022-00755-1