Magnesium in PDB 6kpj: 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd (pdb code 6kpj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd, PDB code: 6kpj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:0.7 occ:1.00 MG A:MG404 1.2 0.8 1.0 OE2 A:GLU227 2.1 0.6 1.0 CD A:GLU227 2.8 0.6 1.0 OE1 A:GLU227 2.8 0.6 1.0 O01 B:9TY404 3.0 0.6 1.0 OE1 A:GLU233 3.1 0.7 1.0 OD1 B:ASP191 3.4 0.8 1.0 O09 B:9TY404 3.5 0.6 1.0 HH11 B:ARG130 3.5 0.6 1.0 HG B:SER194 3.5 0.5 1.0 OE2 A:GLU233 3.7 0.7 1.0 C02 B:9TY404 3.7 0.6 1.0 HH12 B:ARG130 3.7 0.6 1.0 HA B:ASP191 3.7 0.8 1.0 CD A:GLU233 3.8 0.7 1.0 NH1 B:ARG130 3.8 0.6 1.0 HB2 B:SER194 3.9 0.5 1.0 OG B:SER194 4.1 0.5 1.0 CG A:GLU227 4.2 0.6 1.0 HB3 B:SER194 4.3 0.5 1.0 CB B:SER194 4.3 0.5 1.0 CG B:ASP191 4.4 0.8 1.0 HD3 B:ARG130 4.4 0.6 1.0 HG3 A:GLU227 4.5 0.6 1.0 O A:GLU227 4.5 0.6 1.0 HG2 A:GLU227 4.6 0.6 1.0 CA B:ASP191 4.7 0.8 1.0 HA A:GLU227 4.7 0.6 1.0 CZ B:ARG130 4.9 0.6 1.0 O B:ASP191 5.0 0.8 1.0

Magnesium binding site 2 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:0.8 occ:1.00 MG A:MG401 1.2 0.7 1.0 O01 B:9TY404 2.2 0.6 1.0 O09 B:9TY404 2.3 0.6 1.0 C02 B:9TY404 2.6 0.6 1.0 OD1 B:ASP191 2.9 0.8 1.0 OE2 A:GLU227 3.1 0.6 1.0 OE2 A:GLU233 3.4 0.7 1.0 OE1 A:GLU233 3.5 0.7 1.0 HA B:ASP191 3.7 0.8 1.0 CG B:ASP191 3.8 0.8 1.0 CD A:GLU227 3.9 0.6 1.0 HB2 B:SER194 3.9 0.5 1.0 CD A:GLU233 3.9 0.7 1.0 OE1 A:GLU227 3.9 0.6 1.0 HH12 B:ARG130 3.9 0.6 1.0 MG B:MG402 3.9 0.8 1.0 C03 B:9TY404 4.1 0.6 1.0 HH11 B:ARG130 4.1 0.6 1.0 HG B:SER194 4.1 0.5 1.0 NH1 B:ARG130 4.3 0.6 1.0 OD2 B:ASP191 4.4 0.8 1.0 O B:ASP191 4.4 0.8 1.0 HG3 B:GLU195 4.5 0.5 1.0 CA B:ASP191 4.5 0.8 1.0 CB B:SER194 4.5 0.5 1.0 H2 B:9TY404 4.6 0.6 1.0 H3 B:9TY404 4.6 0.6 1.0 HB3 B:SER194 4.6 0.5 1.0 OG B:SER194 4.6 0.5 1.0 OE2 B:GLU195 4.6 0.5 1.0 CB B:ASP191 4.7 0.8 1.0 C07 B:9TY404 4.9 0.6 1.0 C08 B:9TY404 4.9 0.6 1.0 HG2 B:GLU195 4.9 0.5 1.0 C B:ASP191 5.0 0.8 1.0

Magnesium binding site 3 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:0.8 occ:1.00 OE2 B:GLU227 2.1 0.7 1.0 CD B:GLU227 2.8 0.7 1.0 OE1 B:GLU227 2.8 0.7 1.0 O09 A:9TY403 2.8 0.1 1.0 OE1 B:GLU233 3.1 0.2 1.0 OD1 A:ASP191 3.3 0.1 1.0 O01 A:9TY403 3.4 0.1 1.0 HH11 A:ARG130 3.5 0.8 1.0 HG A:SER194 3.5 0.1 1.0 C02 A:9TY403 3.5 0.1 1.0 OE2 B:GLU233 3.7 0.2 1.0 HH12 A:ARG130 3.7 0.8 1.0 HA A:ASP191 3.7 0.1 1.0 CD B:GLU233 3.8 0.2 1.0 NH1 A:ARG130 3.8 0.8 1.0 HB2 A:SER194 3.9 0.1 1.0 OG A:SER194 4.1 0.1 1.0 CG B:GLU227 4.2 0.7 1.0 HB3 A:SER194 4.3 0.1 1.0 CB A:SER194 4.3 0.1 1.0 CG A:ASP191 4.3 0.1 1.0 HD3 A:ARG130 4.5 0.8 1.0 HG3 B:GLU227 4.5 0.7 1.0 O B:GLU227 4.5 0.7 1.0 HG2 B:GLU227 4.6 0.7 1.0 CA A:ASP191 4.6 0.1 1.0 HA B:GLU227 4.7 0.7 1.0 O A:ASP191 4.9 0.1 1.0 CZ A:ARG130 4.9 0.8 1.0

Magnesium binding site 4 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:0.8 occ:1.00 O05 B:9TY404 1.8 0.6 1.0 OE2 B:GLU195 1.9 0.5 1.0 O09 B:9TY404 1.9 0.6 1.0 OD2 B:ASP191 2.0 0.8 1.0 C02 B:9TY404 2.2 0.6 1.0 C04 B:9TY404 2.2 0.6 1.0 C03 B:9TY404 2.3 0.6 1.0 CG B:ASP191 2.8 0.8 1.0 CD B:GLU195 3.1 0.5 1.0 C08 B:9TY404 3.1 0.6 1.0 OD1 B:ASP191 3.1 0.8 1.0 O01 B:9TY404 3.3 0.6 1.0 O06 B:9TY404 3.4 0.6 1.0 H3 B:9TY404 3.4 0.6 1.0 H4 B:9TY404 3.4 0.6 1.0 O B:ASP191 3.7 0.8 1.0 C07 B:9TY404 3.8 0.6 1.0 MG A:MG404 3.9 0.8 1.0 OE1 B:GLU195 3.9 0.5 1.0 HG3 B:GLU195 4.0 0.5 1.0 HB2 A:SER257 4.0 0.6 1.0 CG B:GLU195 4.0 0.5 1.0 CB B:ASP191 4.1 0.8 1.0 HG2 B:GLU195 4.2 0.5 1.0 HB3 B:ASP191 4.2 0.8 1.0 H2 B:9TY404 4.3 0.6 1.0 H1 B:9TY404 4.3 0.6 1.0 C B:ASP191 4.4 0.8 1.0 HA B:ASP191 4.6 0.8 1.0 CA B:ASP191 4.6 0.8 1.0 HD23 B:LEU192 4.7 0.5 1.0 OG A:SER254 4.8 0.4 1.0 HB2 B:ASP191 4.8 0.8 1.0 CB A:SER257 5.0 0.6 1.0 HG A:SER254 5.0 0.4 1.0

Magnesium binding site 5 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:0.8 occ:1.00 MG C:MG404 1.2 0.9 1.0 OE2 C:GLU227 2.1 0.6 1.0 CD C:GLU227 2.8 0.6 1.0 OE1 C:GLU227 2.8 0.6 1.0 O09 D:9TY404 2.8 0.0 1.0 OE1 C:GLU233 3.1 0.8 1.0 O01 D:9TY404 3.3 0.0 1.0 OD1 D:ASP191 3.4 0.8 1.0 C02 D:9TY404 3.5 0.0 1.0 HH11 D:ARG130 3.5 0.3 1.0 HG D:SER194 3.5 0.4 1.0 OE2 C:GLU233 3.7 0.8 1.0 CD C:GLU233 3.8 0.8 1.0 HH12 D:ARG130 3.8 0.3 1.0 HA D:ASP191 3.8 0.8 1.0 HB2 D:SER194 3.9 0.4 1.0 NH1 D:ARG130 3.9 0.3 1.0 OG D:SER194 4.2 0.4 1.0 CG C:GLU227 4.2 0.6 1.0 HB3 D:SER194 4.3 0.4 1.0 CB D:SER194 4.3 0.4 1.0 CG D:ASP191 4.4 0.8 1.0 HD3 D:ARG130 4.5 0.3 1.0 HG3 C:GLU227 4.5 0.6 1.0 O C:GLU227 4.5 0.6 1.0 HG2 C:GLU227 4.6 0.6 1.0 HA C:GLU227 4.7 0.6 1.0 CA D:ASP191 4.7 0.8 1.0 MG D:MG402 4.9 0.6 1.0 O D:ASP191 5.0 0.8 1.0 CZ D:ARG130 5.0 0.3 1.0

Magnesium binding site 6 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:0.9 occ:1.00 MG C:MG401 1.2 0.8 1.0 O01 D:9TY404 2.1 0.0 1.0 O09 D:9TY404 2.2 0.0 1.0 C02 D:9TY404 2.5 0.0 1.0 OD1 D:ASP191 2.7 0.8 1.0 OE2 C:GLU227 2.9 0.6 1.0 HA D:ASP191 3.4 0.8 1.0 CG D:ASP191 3.6 0.8 1.0 CD C:GLU227 3.7 0.6 1.0 OE1 C:GLU227 3.7 0.6 1.0 HB2 D:SER194 3.7 0.4 1.0 MG D:MG402 3.7 0.6 1.0 OE2 C:GLU233 3.8 0.8 1.0 HH12 D:ARG130 3.8 0.3 1.0 OE1 C:GLU233 3.8 0.8 1.0 C03 D:9TY404 4.0 0.0 1.0 HG D:SER194 4.0 0.4 1.0 HH11 D:ARG130 4.0 0.3 1.0 O D:ASP191 4.1 0.8 1.0 NH1 D:ARG130 4.2 0.3 1.0 OD2 D:ASP191 4.2 0.8 1.0 CA D:ASP191 4.2 0.8 1.0 CD C:GLU233 4.2 0.8 1.0 HG3 D:GLU195 4.3 0.2 1.0 CB D:SER194 4.4 0.4 1.0 OG D:SER194 4.4 0.4 1.0 CB D:ASP191 4.5 0.8 1.0 OE2 D:GLU195 4.5 0.2 1.0 HB3 D:SER194 4.5 0.4 1.0 H3 D:9TY404 4.6 0.0 1.0 H2 D:9TY404 4.7 0.0 1.0 C D:ASP191 4.7 0.8 1.0 HB2 D:ASP191 4.8 0.8 1.0 HG2 D:GLU195 4.9 0.2 1.0 C08 D:9TY404 4.9 0.0 1.0 C07 D:9TY404 4.9 0.0 1.0 C04 D:9TY404 4.9 0.0 1.0 CG D:GLU195 5.0 0.2 1.0

Magnesium binding site 7 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:0.0 occ:1.00 OE2 D:GLU227 2.1 0.6 1.0 CD D:GLU227 2.8 0.6 1.0 OE1 D:GLU227 2.8 0.6 1.0 OE1 D:GLU233 3.1 0.5 1.0 O09 C:9TY403 3.1 0.9 1.0 HG C:SER194 3.4 0.3 1.0 OD1 C:ASP191 3.4 0.7 1.0 HH11 C:ARG130 3.5 0.7 1.0 O01 C:9TY403 3.5 0.9 1.0 OE2 D:GLU233 3.7 0.5 1.0 HH12 C:ARG130 3.7 0.7 1.0 HA C:ASP191 3.7 0.7 1.0 C02 C:9TY403 3.7 0.9 1.0 CD D:GLU233 3.8 0.5 1.0 HB2 C:SER194 3.8 0.3 1.0 NH1 C:ARG130 3.9 0.7 1.0 OG C:SER194 4.1 0.3 1.0 HB3 C:SER194 4.2 0.3 1.0 CG D:GLU227 4.2 0.6 1.0 CB C:SER194 4.3 0.3 1.0 HD3 C:ARG130 4.4 0.7 1.0 CG C:ASP191 4.4 0.7 1.0 HG3 D:GLU227 4.5 0.6 1.0 O D:GLU227 4.5 0.6 1.0 HG2 D:GLU227 4.6 0.6 1.0 CA C:ASP191 4.7 0.7 1.0 HA D:GLU227 4.7 0.6 1.0 CZ C:ARG130 5.0 0.7 1.0 O C:ASP191 5.0 0.7 1.0

Magnesium binding site 8 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:0.6 occ:1.00 OE2 D:GLU195 1.9 0.2 1.0 O06 D:9TY404 1.9 0.0 1.0 O01 D:9TY404 1.9 0.0 1.0 OD2 D:ASP191 1.9 0.8 1.0 C04 D:9TY404 2.2 0.0 1.0 C02 D:9TY404 2.2 0.0 1.0 C03 D:9TY404 2.3 0.0 1.0 CG D:ASP191 2.7 0.8 1.0 OD1 D:ASP191 3.1 0.8 1.0 CD D:GLU195 3.1 0.2 1.0 C08 D:9TY404 3.1 0.0 1.0 O05 D:9TY404 3.3 0.0 1.0 O09 D:9TY404 3.3 0.0 1.0 H4 D:9TY404 3.4 0.0 1.0 H3 D:9TY404 3.4 0.0 1.0 O D:ASP191 3.6 0.8 1.0 MG C:MG404 3.7 0.9 1.0 C07 D:9TY404 3.8 0.0 1.0 HG3 D:GLU195 3.9 0.2 1.0 OE1 D:GLU195 3.9 0.2 1.0 CG D:GLU195 4.0 0.2 1.0 CB D:ASP191 4.0 0.8 1.0 HG2 D:GLU195 4.1 0.2 1.0 HB3 D:ASP191 4.2 0.8 1.0 HB2 C:SER257 4.2 0.6 1.0 H1 D:9TY404 4.3 0.0 1.0 H2 D:9TY404 4.3 0.0 1.0 C D:ASP191 4.4 0.8 1.0 HA D:ASP191 4.5 0.8 1.0 CA D:ASP191 4.6 0.8 1.0 HD23 D:LEU192 4.7 0.5 1.0 HB2 D:ASP191 4.7 0.8 1.0 MG C:MG401 4.9 0.8 1.0 OG C:SER254 5.0 0.6 1.0

Magnesium binding site 9 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:0.0 occ:1.00 MG E:MG404 1.3 0.7 1.0 OE2 E:GLU227 2.1 0.7 1.0 CD E:GLU227 2.8 0.7 1.0 OE1 E:GLU227 2.8 0.7 1.0 O09 F:9TY404 3.0 0.1 1.0 OE1 E:GLU233 3.1 0.1 1.0 OD1 F:ASP191 3.2 0.5 1.0 HH11 F:ARG130 3.3 0.6 1.0 HG F:SER194 3.4 0.8 1.0 HH12 F:ARG130 3.5 0.6 1.0 O01 F:9TY404 3.6 0.1 1.0 HA F:ASP191 3.6 0.5 1.0 NH1 F:ARG130 3.7 0.6 1.0 OE2 E:GLU233 3.7 0.1 1.0 C02 F:9TY404 3.7 0.1 1.0 CD E:GLU233 3.8 0.1 1.0 HB2 F:SER194 3.8 0.8 1.0 OG F:SER194 4.1 0.8 1.0 CG E:GLU227 4.2 0.7 1.0 CG F:ASP191 4.2 0.5 1.0 HD3 F:ARG130 4.3 0.6 1.0 CB F:SER194 4.3 0.8 1.0 HG3 E:GLU227 4.5 0.7 1.0 CA F:ASP191 4.5 0.5 1.0 O E:GLU227 4.5 0.7 1.0 HG2 E:GLU227 4.5 0.7 1.0 HA E:GLU227 4.7 0.7 1.0 HB3 F:SER194 4.7 0.8 1.0 CZ F:ARG130 4.8 0.6 1.0 CB F:ASP191 4.9 0.5 1.0 O F:ASP191 4.9 0.5 1.0

Magnesium binding site 10 out of 24 in the 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 298 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg404 b:0.7 occ:1.00 MG E:MG401 1.3 0.0 1.0 O09 F:9TY404 2.1 0.1 1.0 O01 F:9TY404 2.4 0.1 1.0 C02 F:9TY404 2.6 0.1 1.0 OD1 F:ASP191 2.9 0.5 1.0 OE2 E:GLU233 3.1 0.1 1.0 OE2 E:GLU227 3.2 0.7 1.0 OE1 E:GLU233 3.3 0.1 1.0 CD E:GLU233 3.6 0.1 1.0 HA F:ASP191 3.8 0.5 1.0 CG F:ASP191 3.9 0.5 1.0 HH12 F:ARG130 3.9 0.6 1.0 HB2 F:SER194 3.9 0.8 1.0 CD E:GLU227 4.0 0.7 1.0 OE1 E:GLU227 4.0 0.7 1.0 MG F:MG402 4.1 0.5 1.0 HG F:SER194 4.1 0.8 1.0 HH11 F:ARG130 4.1 0.6 1.0 C03 F:9TY404 4.1 0.1 1.0 NH1 F:ARG130 4.2 0.6 1.0 OD2 F:ASP191 4.4 0.5 1.0 O F:ASP191 4.5 0.5 1.0 HG3 F:GLU195 4.6 0.8 1.0 H2 F:9TY404 4.6 0.1 1.0 CA F:ASP191 4.6 0.5 1.0 CB F:SER194 4.6 0.8 1.0 H3 F:9TY404 4.7 0.1 1.0 OG F:SER194 4.7 0.8 1.0 OE2 F:GLU195 4.7 0.8 1.0 CB F:ASP191 4.8 0.5 1.0 C07 F:9TY404 4.9 0.1 1.0 C08 F:9TY404 5.0 0.1 1.0

C.Y.Chen, Y.C.Chang, B.L.Lin, C.H.Huang, M.D.Tsai. Temperature-Resolved Cryo-Em Uncovers Structural Bases of Temperature-Dependent Enzyme Functions. J.Am.Chem.Soc. V. 141 19983 2019.
ISSN: ESSN 1520-5126
PubMed: 31829582
DOI: 10.1021/JACS.9B10687