Magnesium in PDB 7yly: Yeast Tric-PLP2 Complex at S5 Closed Tric State

The structure of Yeast Tric-PLP2 Complex at S5 Closed Tric State also contains other interesting chemical elements:

Aluminium	(Al)	14 atoms
Fluorine	(F)	42 atoms

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Yeast Tric-PLP2 Complex at S5 Closed Tric State (pdb code 7yly). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Yeast Tric-PLP2 Complex at S5 Closed Tric State, PDB code: 7yly:
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 Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:88.2 occ:1.00 O3A A:ADP601 2.1 93.1 1.0 O1A A:ADP601 2.4 93.1 1.0 PA A:ADP601 2.7 93.1 1.0 PB A:ADP601 3.0 93.1 1.0 O3B A:ADP601 3.0 93.1 1.0 F1 A:AF3603 3.1 102.0 1.0 O1B A:ADP601 3.3 93.1 1.0 OD1 A:ASP96 3.6 96.7 1.0 O2A A:ADP601 3.7 93.1 1.0 AL A:AF3603 3.8 102.0 1.0 O5' A:ADP601 4.0 93.1 1.0 NZ A:LYS167 4.1 95.4 1.0 O2B A:ADP601 4.3 93.1 1.0 F2 A:AF3603 4.3 102.0 1.0 OG A:SER166 4.5 94.7 1.0 O A:SER163 4.6 97.6 1.0 CG A:ASP96 4.6 96.7 1.0 N A:GLY97 4.8 96.9 1.0 C5' A:ADP601 4.9 93.1 1.0 CA A:SER163 4.9 97.6 1.0

Magnesium binding site 2 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:95.2 occ:1.00 O2B B:ADP601 2.1 96.3 1.0 O2A B:ADP601 2.1 96.3 1.0 OD1 B:ASP90 2.5 96.4 1.0 O1B B:ADP601 2.5 96.3 1.0 F1 B:AF3603 2.5 98.5 1.0 PB B:ADP601 2.6 96.3 1.0 PA B:ADP601 2.9 96.3 1.0 O3A B:ADP601 3.1 96.3 1.0 CG B:ASP90 3.2 96.4 1.0 AL B:AF3603 3.3 98.5 1.0 OD2 B:ASP90 3.3 96.4 1.0 NZ B:LYS164 3.5 95.2 1.0 O1A B:ADP601 3.5 96.3 1.0 O3B B:ADP601 4.1 96.3 1.0 OG B:SER163 4.1 95.3 1.0 F3 B:AF3603 4.2 98.5 1.0 F2 B:AF3603 4.3 98.5 1.0 CB B:SER163 4.3 95.3 1.0 N B:GLY91 4.4 95.7 1.0 O5' B:ADP601 4.4 96.3 1.0 CB B:ASP90 4.6 96.4 1.0 O B:THR160 4.6 94.8 1.0 CG2 B:THR160 4.8 94.8 1.0 CE B:LYS164 4.9 95.2 1.0 CA B:ASP90 4.9 96.4 1.0

Magnesium binding site 3 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:98.6 occ:1.00 O2A D:ADP601 2.1 93.1 1.0 O2B D:ADP601 2.3 93.1 1.0 OD1 D:ASP91 2.5 96.4 1.0 OG D:SER157 2.7 95.3 1.0 PB D:ADP601 3.3 93.1 1.0 PA D:ADP601 3.3 93.1 1.0 CG D:ASP91 3.6 96.4 1.0 O3A D:ADP601 3.6 93.1 1.0 O1B D:ADP601 3.6 93.1 1.0 CB D:SER157 3.8 95.3 1.0 OG D:SER160 3.9 94.1 1.0 O D:SER157 4.0 95.3 1.0 CA D:SER157 4.2 95.3 1.0 OD2 D:ASP91 4.2 96.4 1.0 N D:GLY92 4.3 93.8 1.0 O1A D:ADP601 4.3 93.1 1.0 O5' D:ADP601 4.5 93.1 1.0 C D:SER157 4.5 95.3 1.0 CB D:ASP396 4.6 98.0 1.0 CB D:ASP91 4.6 96.4 1.0 CA D:ASP91 4.7 96.4 1.0 O3B D:ADP601 4.7 93.1 1.0 OD2 D:ASP396 4.8 98.0 1.0 NZ D:LYS161 4.8 94.5 1.0 CE D:LYS161 4.9 94.5 1.0

Magnesium binding site 4 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:95.4 occ:1.00 O3A E:ADP601 2.3 95.1 1.0 O2B E:ADP601 2.4 95.1 1.0 PB E:ADP601 2.8 95.1 1.0 OD1 E:ASP117 3.1 97.8 1.0 O3B E:ADP601 3.4 95.1 1.0 F1 E:AF3603 3.4 99.0 1.0 PA E:ADP601 3.7 95.1 1.0 O2A E:ADP601 3.9 95.1 1.0 AL E:AF3603 4.0 99.0 1.0 CG E:ASP117 4.1 97.8 1.0 O1B E:ADP601 4.2 95.1 1.0 O5' E:ADP601 4.3 95.1 1.0 OG E:SER190 4.5 98.6 1.0 F2 E:AF3603 4.6 99.0 1.0 CE E:LYS191 4.7 98.8 1.0 N E:GLY118 4.7 97.1 1.0 O E:SER187 4.7 102.8 1.0 OD2 E:ASP117 4.8 97.8 1.0 O1A E:ADP601 4.8 95.1 1.0 F3 E:AF3603 4.8 99.0 1.0 OG E:SER187 4.8 102.8 1.0 CA E:SER187 4.9 102.8 1.0

Magnesium binding site 5 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:97.2 occ:1.00 O3A G:ADP601 2.1 93.3 1.0 O1A G:ADP601 2.1 93.3 1.0 OD1 G:ASP91 2.2 94.7 1.0 PA G:ADP601 2.5 93.3 1.0 F2 G:AF3603 2.7 96.2 1.0 PB G:ADP601 2.9 93.3 1.0 O1B G:ADP601 3.1 93.3 1.0 O3B G:ADP601 3.1 93.3 1.0 CG G:ASP91 3.2 94.7 1.0 O2A G:ADP601 3.4 93.3 1.0 OD2 G:ASP91 3.6 94.7 1.0 AL G:AF3603 3.6 96.2 1.0 OG G:SER158 3.8 99.8 1.0 O5' G:ADP601 3.8 93.3 1.0 CB G:SER158 3.9 99.8 1.0 N G:GLY92 4.1 93.0 1.0 OG1 G:THR161 4.2 95.7 1.0 O2B G:ADP601 4.3 93.3 1.0 F1 G:AF3603 4.4 96.2 1.0 CA G:SER158 4.4 99.8 1.0 CB G:ASP91 4.5 94.7 1.0 F3 G:AF3603 4.5 96.2 1.0 O G:SER158 4.6 99.8 1.0 C5' G:ADP601 4.7 93.3 1.0 CA G:ASP91 4.8 94.7 1.0 CA G:GLY92 4.8 93.0 1.0 C G:ASP91 4.9 94.7 1.0 C G:SER158 5.0 99.8 1.0

Magnesium binding site 6 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg602 b:89.9 occ:1.00 O3A H:ADP601 2.1 94.5 1.0 OD1 H:ASP96 2.4 92.3 1.0 O1A H:ADP601 2.6 94.5 1.0 PA H:ADP601 2.7 94.5 1.0 F1 H:AF3603 2.9 101.4 1.0 O2B H:ADP601 3.1 94.5 1.0 AL H:AF3603 3.1 101.4 1.0 PB H:ADP601 3.2 94.5 1.0 O2A H:ADP601 3.5 94.5 1.0 CG H:ASP96 3.6 92.3 1.0 F2 H:AF3603 3.6 101.4 1.0 O3B H:ADP601 4.0 94.5 1.0 N H:GLY97 4.0 93.1 1.0 O H:ALA165 4.0 98.2 1.0 F3 H:AF3603 4.1 101.4 1.0 OG H:SER168 4.1 99.8 1.0 O5' H:ADP601 4.1 94.5 1.0 OD2 H:ASP96 4.2 92.3 1.0 O1B H:ADP601 4.3 94.5 1.0 O H:SER167 4.4 99.8 1.0 CA H:ASP96 4.7 92.3 1.0 CB H:ASP96 4.7 92.3 1.0 CA H:GLY97 4.8 93.1 1.0 C H:ASP96 4.9 92.3 1.0 OG H:SER167 4.9 99.8 1.0 C H:ALA165 5.0 98.2 1.0

Magnesium binding site 7 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg601 b:98.0 occ:1.00 O3B Q:ADP602 2.1 92.6 1.0 O3A Q:ADP602 2.7 92.6 1.0 PB Q:ADP602 2.8 92.6 1.0 OD1 Q:ASP98 3.0 93.3 1.0 O1B Q:ADP602 3.4 92.6 1.0 O Q:VAL166 3.5 94.8 1.0 CA Q:VAL166 3.6 94.8 1.0 CG Q:ASP98 3.9 93.3 1.0 CG1 Q:VAL166 4.0 94.8 1.0 C Q:VAL166 4.0 94.8 1.0 O Q:PRO165 4.1 96.2 1.0 CB Q:VAL166 4.2 94.8 1.0 O2B Q:ADP602 4.2 92.6 1.0 OD2 Q:ASP98 4.2 93.3 1.0 PA Q:ADP602 4.2 92.6 1.0 CG2 Q:VAL166 4.3 94.8 1.0 OG Q:SER169 4.4 92.7 1.0 O5' Q:ADP602 4.5 92.6 1.0 N Q:VAL166 4.6 94.8 1.0 C Q:PRO165 4.8 96.2 1.0 O2A Q:ADP602 4.9 92.6 1.0 CB Q:SER169 5.0 92.7 1.0

Magnesium binding site 8 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg602 b:94.3 occ:1.00 O1A Z:ADP601 2.1 92.0 1.0 OD1 Z:ASP89 2.5 94.0 1.0 PA Z:ADP601 2.5 92.0 1.0 O2A Z:ADP601 2.7 92.0 1.0 O3A Z:ADP601 2.9 92.0 1.0 O2B Z:ADP601 3.1 92.0 1.0 F1 Z:AF3603 3.1 97.8 1.0 CG Z:ASP89 3.2 94.0 1.0 F2 Z:AF3603 3.4 97.8 1.0 OD2 Z:ASP89 3.5 94.0 1.0 AL Z:AF3603 3.6 97.8 1.0 PB Z:ADP601 3.7 92.0 1.0 O5' Z:ADP601 4.1 92.0 1.0 CB Z:ASP89 4.3 94.0 1.0 CE Z:LYS161 4.5 95.0 1.0 O3B Z:ADP601 4.5 92.0 1.0 CA Z:ASP89 4.6 94.0 1.0 N Z:GLY90 4.7 92.2 1.0 CB Z:SER157 4.7 94.5 1.0 NZ Z:LYS161 4.8 95.0 1.0 O1B Z:ADP601 4.8 92.0 1.0

Magnesium binding site 9 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg602 b:102.2 occ:1.00 OD1 a:ASP96 2.2 95.5 1.0 O1A a:ADP601 2.4 97.1 1.0 O2A a:ADP601 2.5 97.1 1.0 O1B a:ADP601 2.6 97.1 1.0 PA a:ADP601 2.7 97.1 1.0 CG a:ASP96 2.8 95.5 1.0 OD2 a:ASP96 2.9 95.5 1.0 F1 a:AF3603 2.9 100.0 1.0 O3B a:ADP601 3.2 97.1 1.0 PB a:ADP601 3.3 97.1 1.0 O3A a:ADP601 3.4 97.1 1.0 AL a:AF3603 4.0 100.0 1.0 O a:SER163 4.1 97.8 1.0 CA a:SER163 4.1 97.8 1.0 CB a:ASP96 4.2 95.5 1.0 O5' a:ADP601 4.3 97.1 1.0 O a:THR162 4.4 97.9 1.0 N a:GLY97 4.6 92.7 1.0 F3 a:AF3603 4.6 100.0 1.0 C a:SER163 4.6 97.8 1.0 O2B a:ADP601 4.7 97.1 1.0 CA a:ASP96 4.8 95.5 1.0 CB a:SER163 4.8 97.8 1.0 NZ a:LYS167 4.8 96.9 1.0

Magnesium binding site 10 out of 16 in the Yeast Tric-PLP2 Complex at S5 Closed Tric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast Tric-PLP2 Complex at S5 Closed Tric State within 5.0Å range: probe atom residue distance (Å) B Occ b:Mg602 b:93.5 occ:1.00 O3B b:ADP601 2.1 92.8 1.0 O2A b:ADP601 2.1 92.8 1.0 OD1 b:ASP90 2.2 94.4 1.0 NZ b:LYS164 2.6 94.0 1.0 CG b:ASP90 2.9 94.4 1.0 PA b:ADP601 2.9 92.8 1.0 OD2 b:ASP90 3.0 94.4 1.0 O3A b:ADP601 3.1 92.8 1.0 PB b:ADP601 3.2 92.8 1.0 F1 b:AF3603 3.3 95.5 1.0 O1A b:ADP601 3.6 92.8 1.0 OG b:SER163 3.6 94.5 1.0 O b:THR160 3.7 93.0 1.0 AL b:AF3603 3.9 95.5 1.0 CE b:LYS164 4.0 94.0 1.0 O1B b:ADP601 4.1 92.8 1.0 F3 b:AF3603 4.2 95.5 1.0 CG2 b:THR160 4.3 93.0 1.0 O2B b:ADP601 4.3 92.8 1.0 O5' b:ADP601 4.4 92.8 1.0 CB b:ASP90 4.4 94.4 1.0 CA b:THR160 4.5 93.0 1.0 C b:THR160 4.5 93.0 1.0 N b:GLY91 4.8 93.9 1.0 CB b:SER163 4.8 94.5 1.0 CB b:THR160 5.0 93.0 1.0

W.Han, M.Jin, C.Liu, Q.Zhao, S.Wang, Y.Wang, Y.Yin, C.Peng, Y.Wang, Y.Cong. Structural Basis of PLP2-Mediated Cytoskeletal Protein Folding By Tric/Cct. Sci Adv V. 9 E1207 2023.
ISSN: ESSN 2375-2548
PubMed: 36921056
DOI: 10.1126/SCIADV.ADE1207