Magnesium in PDB 2ynj: Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography

The structure of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography also contains other interesting chemical elements:

Thallium

(Tl)

56 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography (pdb code 2ynj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography, PDB code: 2ynj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg553 b:0.2 occ:1.00 O2A A:AGS549 2.1 0.2 1.0 O2G A:AGS549 2.1 0.2 1.0 O1B A:AGS549 2.2 0.2 1.0 OD1 A:ASP87 2.3 0.2 1.0 PB A:AGS549 3.3 0.2 1.0 PG A:AGS549 3.4 0.2 1.0 PA A:AGS549 3.4 0.2 1.0 CG A:ASP87 3.5 0.2 1.0 O3B A:AGS549 3.7 0.2 1.0 O3A A:AGS549 3.8 0.2 1.0 OD2 A:ASP87 4.1 0.2 1.0 C5' A:AGS549 4.2 0.2 1.0 O5' A:AGS549 4.3 0.2 1.0 O3G A:AGS549 4.5 0.2 1.0 N A:GLY88 4.5 0.2 1.0 O1A A:AGS549 4.5 0.2 1.0 S1G A:AGS549 4.6 0.2 1.0 CB A:ASP87 4.7 0.2 1.0 O2B A:AGS549 4.7 0.2 1.0 CA A:ASP87 4.8 0.2 1.0

Magnesium binding site 2 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg553 b:0.2 occ:1.00 O2A B:AGS549 2.1 0.2 1.0 O2G B:AGS549 2.1 0.2 1.0 O1B B:AGS549 2.2 0.2 1.0 OD1 B:ASP87 2.3 0.2 1.0 PB B:AGS549 3.3 0.2 1.0 PG B:AGS549 3.4 0.2 1.0 PA B:AGS549 3.4 0.2 1.0 CG B:ASP87 3.5 0.2 1.0 O3B B:AGS549 3.7 0.2 1.0 O3A B:AGS549 3.8 0.2 1.0 OD2 B:ASP87 4.1 0.2 1.0 C5' B:AGS549 4.2 0.2 1.0 O5' B:AGS549 4.3 0.2 1.0 O3G B:AGS549 4.5 0.2 1.0 N B:GLY88 4.5 0.2 1.0 O1A B:AGS549 4.5 0.2 1.0 S1G B:AGS549 4.6 0.2 1.0 CB B:ASP87 4.7 0.2 1.0 O2B B:AGS549 4.7 0.2 1.0 CA B:ASP87 4.8 0.2 1.0

Magnesium binding site 3 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg553 b:0.2 occ:1.00 O2A C:AGS549 2.1 0.2 1.0 O2G C:AGS549 2.1 0.2 1.0 O1B C:AGS549 2.2 0.2 1.0 OD1 C:ASP87 2.3 0.2 1.0 PB C:AGS549 3.3 0.2 1.0 PG C:AGS549 3.4 0.2 1.0 PA C:AGS549 3.4 0.2 1.0 CG C:ASP87 3.5 0.2 1.0 O3B C:AGS549 3.7 0.2 1.0 O3A C:AGS549 3.8 0.2 1.0 OD2 C:ASP87 4.1 0.2 1.0 C5' C:AGS549 4.2 0.2 1.0 O5' C:AGS549 4.3 0.2 1.0 O3G C:AGS549 4.5 0.2 1.0 N C:GLY88 4.5 0.2 1.0 O1A C:AGS549 4.5 0.2 1.0 S1G C:AGS549 4.6 0.2 1.0 CB C:ASP87 4.7 0.2 1.0 O2B C:AGS549 4.7 0.2 1.0 CA C:ASP87 4.8 0.2 1.0

Magnesium binding site 4 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg553 b:0.2 occ:1.00 O2A D:AGS549 2.1 0.2 1.0 O2G D:AGS549 2.1 0.2 1.0 O1B D:AGS549 2.2 0.2 1.0 OD1 D:ASP87 2.3 0.2 1.0 PB D:AGS549 3.3 0.2 1.0 PG D:AGS549 3.4 0.2 1.0 PA D:AGS549 3.4 0.2 1.0 CG D:ASP87 3.5 0.2 1.0 O3B D:AGS549 3.7 0.2 1.0 O3A D:AGS549 3.8 0.2 1.0 OD2 D:ASP87 4.1 0.2 1.0 C5' D:AGS549 4.2 0.2 1.0 O5' D:AGS549 4.3 0.2 1.0 O3G D:AGS549 4.5 0.2 1.0 N D:GLY88 4.5 0.2 1.0 O1A D:AGS549 4.5 0.2 1.0 S1G D:AGS549 4.6 0.2 1.0 CB D:ASP87 4.7 0.2 1.0 O2B D:AGS549 4.7 0.2 1.0 CA D:ASP87 4.8 0.2 1.0

Magnesium binding site 5 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg553 b:0.2 occ:1.00 O2A E:AGS549 2.1 0.2 1.0 O2G E:AGS549 2.1 0.2 1.0 O1B E:AGS549 2.2 0.2 1.0 OD1 E:ASP87 2.3 0.2 1.0 PB E:AGS549 3.3 0.2 1.0 PG E:AGS549 3.4 0.2 1.0 PA E:AGS549 3.4 0.2 1.0 CG E:ASP87 3.5 0.2 1.0 O3B E:AGS549 3.7 0.2 1.0 O3A E:AGS549 3.8 0.2 1.0 OD2 E:ASP87 4.1 0.2 1.0 C5' E:AGS549 4.2 0.2 1.0 O5' E:AGS549 4.3 0.2 1.0 O3G E:AGS549 4.5 0.2 1.0 N E:GLY88 4.5 0.2 1.0 O1A E:AGS549 4.5 0.2 1.0 S1G E:AGS549 4.6 0.2 1.0 CB E:ASP87 4.7 0.2 1.0 O2B E:AGS549 4.7 0.2 1.0 CA E:ASP87 4.8 0.2 1.0

Magnesium binding site 6 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg553 b:0.2 occ:1.00 O2A F:AGS549 2.1 0.2 1.0 O2G F:AGS549 2.1 0.2 1.0 O1B F:AGS549 2.2 0.2 1.0 OD1 F:ASP87 2.3 0.2 1.0 PB F:AGS549 3.3 0.2 1.0 PG F:AGS549 3.4 0.2 1.0 PA F:AGS549 3.4 0.2 1.0 CG F:ASP87 3.5 0.2 1.0 O3B F:AGS549 3.7 0.2 1.0 O3A F:AGS549 3.8 0.2 1.0 OD2 F:ASP87 4.1 0.2 1.0 C5' F:AGS549 4.2 0.2 1.0 O5' F:AGS549 4.3 0.2 1.0 O3G F:AGS549 4.5 0.2 1.0 N F:GLY88 4.5 0.2 1.0 O1A F:AGS549 4.5 0.2 1.0 S1G F:AGS549 4.6 0.2 1.0 CB F:ASP87 4.7 0.2 1.0 O2B F:AGS549 4.7 0.2 1.0 CA F:ASP87 4.8 0.2 1.0

Magnesium binding site 7 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg553 b:0.2 occ:1.00 O2A G:AGS549 2.1 0.2 1.0 O2G G:AGS549 2.1 0.2 1.0 O1B G:AGS549 2.2 0.2 1.0 OD1 G:ASP87 2.3 0.2 1.0 PB G:AGS549 3.3 0.2 1.0 PG G:AGS549 3.4 0.2 1.0 PA G:AGS549 3.4 0.2 1.0 CG G:ASP87 3.5 0.2 1.0 O3B G:AGS549 3.7 0.2 1.0 O3A G:AGS549 3.8 0.2 1.0 OD2 G:ASP87 4.1 0.2 1.0 C5' G:AGS549 4.2 0.2 1.0 O5' G:AGS549 4.3 0.2 1.0 O3G G:AGS549 4.5 0.2 1.0 N G:GLY88 4.5 0.2 1.0 O1A G:AGS549 4.5 0.2 1.0 S1G G:AGS549 4.6 0.2 1.0 CB G:ASP87 4.7 0.2 1.0 O2B G:AGS549 4.7 0.2 1.0 CA G:ASP87 4.8 0.2 1.0

Magnesium binding site 8 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg553 b:0.2 occ:1.00 O2A H:AGS549 2.1 0.2 1.0 O2G H:AGS549 2.1 0.2 1.0 O1B H:AGS549 2.2 0.2 1.0 OD1 H:ASP87 2.3 0.2 1.0 PB H:AGS549 3.3 0.2 1.0 PG H:AGS549 3.4 0.2 1.0 PA H:AGS549 3.4 0.2 1.0 CG H:ASP87 3.5 0.2 1.0 O3B H:AGS549 3.7 0.2 1.0 O3A H:AGS549 3.8 0.2 1.0 OD2 H:ASP87 4.1 0.2 1.0 C5' H:AGS549 4.2 0.2 1.0 O5' H:AGS549 4.3 0.2 1.0 O3G H:AGS549 4.5 0.2 1.0 N H:GLY88 4.5 0.2 1.0 O1A H:AGS549 4.5 0.2 1.0 S1G H:AGS549 4.6 0.2 1.0 CB H:ASP87 4.7 0.2 1.0 O2B H:AGS549 4.7 0.2 1.0 CA H:ASP87 4.8 0.2 1.0

Magnesium binding site 9 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg553 b:0.2 occ:1.00 O2A I:AGS549 2.1 0.2 1.0 O2G I:AGS549 2.1 0.2 1.0 O1B I:AGS549 2.2 0.2 1.0 OD1 I:ASP87 2.3 0.2 1.0 PB I:AGS549 3.3 0.2 1.0 PG I:AGS549 3.4 0.2 1.0 PA I:AGS549 3.4 0.2 1.0 CG I:ASP87 3.5 0.2 1.0 O3B I:AGS549 3.7 0.2 1.0 O3A I:AGS549 3.8 0.2 1.0 OD2 I:ASP87 4.1 0.2 1.0 C5' I:AGS549 4.2 0.2 1.0 O5' I:AGS549 4.3 0.2 1.0 O3G I:AGS549 4.5 0.2 1.0 N I:GLY88 4.5 0.2 1.0 O1A I:AGS549 4.5 0.2 1.0 S1G I:AGS549 4.6 0.2 1.0 CB I:ASP87 4.7 0.2 1.0 O2B I:AGS549 4.7 0.2 1.0 CA I:ASP87 4.8 0.2 1.0

Magnesium binding site 10 out of 14 in the Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Groel at Sub-Nanometer Resolution By Constrained Single Particle Tomography within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg553 b:0.2 occ:1.00 O2A J:AGS549 2.1 0.2 1.0 O2G J:AGS549 2.1 0.2 1.0 O1B J:AGS549 2.2 0.2 1.0 OD1 J:ASP87 2.3 0.2 1.0 PB J:AGS549 3.3 0.2 1.0 PG J:AGS549 3.4 0.2 1.0 PA J:AGS549 3.4 0.2 1.0 CG J:ASP87 3.5 0.2 1.0 O3B J:AGS549 3.7 0.2 1.0 O3A J:AGS549 3.8 0.2 1.0 OD2 J:ASP87 4.1 0.2 1.0 C5' J:AGS549 4.2 0.2 1.0 O5' J:AGS549 4.3 0.2 1.0 O3G J:AGS549 4.5 0.2 1.0 N J:GLY88 4.5 0.2 1.0 O1A J:AGS549 4.5 0.2 1.0 S1G J:AGS549 4.6 0.2 1.0 CB J:ASP87 4.7 0.2 1.0 O2B J:AGS549 4.7 0.2 1.0 CA J:ASP87 4.8 0.2 1.0

A.Bartesaghi, F.Lecumberry, G.Sapiro, S.Subramaniam. Protein Secondary Structure Determination By Constrained Single-Particle Cryo-Electron Tomography Structure V. 20 2003 2012.
ISSN: ISSN 0969-2126
PubMed: 23217682
DOI: 10.1016/J.STR.2012.10.016