Magnesium in PDB 6kqo: 328 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd

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

Binding sites:

The binding sites of Magnesium atom in the 328 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd (pdb code 6kqo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the 328 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd, PDB code: 6kqo:
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 328 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 328 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:93.7 occ:1.00 O05 A:9TY404 1.9 0.7 1.0 OE2 A:GLU195 2.0 93.2 1.0 OD2 A:ASP191 2.0 99.4 1.0 C04 A:9TY404 2.2 0.1 1.0 O06 A:9TY404 2.6 98.4 1.0 CD A:GLU195 3.0 90.0 1.0 CG A:ASP191 3.0 97.1 1.0 C03 A:9TY404 3.3 0.3 1.0 OE1 A:GLU195 3.5 88.0 1.0 OD1 A:ASP191 3.6 0.3 1.0 HG B:SER254 3.6 0.0 1.0 C02 A:9TY404 3.8 0.1 1.0 HB2 B:SER257 3.9 92.5 1.0 H4 A:9TY404 4.0 0.4 1.0 O01 A:9TY404 4.0 0.5 1.0 O A:ASP191 4.1 82.1 1.0 C08 A:9TY404 4.1 98.7 1.0 HB3 A:ASP191 4.2 0.6 1.0 OG B:SER254 4.2 89.2 1.0 CB A:ASP191 4.2 87.1 1.0 CG A:GLU195 4.3 80.9 1.0 HD23 A:LEU192 4.4 90.7 1.0 HG3 A:GLU195 4.4 97.0 1.0 HG2 A:GLU195 4.6 97.0 1.0 O09 A:9TY404 4.6 0.3 1.0 C07 A:9TY404 4.7 0.3 1.0 H3 A:9TY404 4.7 0.4 1.0 HB B:THR256 4.7 88.9 1.0 C A:ASP191 4.8 82.1 1.0 CB B:SER257 4.8 77.0 1.0 H1 A:9TY404 4.8 0.4 1.0 HO2N A:NAI403 4.9 0.5 0.5 HB2 A:ASP191 4.9 0.6 1.0 H B:SER257 5.0 92.0 1.0

Magnesium binding site 2 out of 24 in the 328 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 328 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:Mg402 b:0.3 occ:1.00 O01 A:9TY404 1.9 0.5 1.0 O09 A:9TY404 2.0 0.3 1.0 OD1 A:ASP191 2.2 0.3 1.0 C02 A:9TY404 2.2 0.1 1.0 OE2 B:GLU227 3.3 96.0 1.0 CG A:ASP191 3.4 97.1 1.0 OE1 B:GLU227 3.4 0.9 1.0 HA A:ASP191 3.6 98.5 1.0 CD B:GLU227 3.7 99.3 1.0 C03 A:9TY404 3.7 0.3 1.0 OE2 B:GLU233 3.9 0.3 1.0 OE1 B:GLU233 4.0 0.6 1.0 HD3 A:ARG130 4.1 0.0 1.0 HH11 A:ARG130 4.2 0.6 1.0 OD2 A:ASP191 4.2 99.4 1.0 NH1 A:ARG130 4.2 0.3 1.0 CB A:ASP191 4.3 87.1 1.0 CD B:GLU233 4.3 0.5 1.0 HH12 A:ARG130 4.4 0.6 1.0 O05 A:9TY404 4.4 0.7 1.0 CA A:ASP191 4.4 82.1 1.0 HB2 A:ASP191 4.4 0.6 1.0 H3 A:9TY404 4.5 0.4 1.0 CZ A:ARG130 4.5 0.0 1.0 C04 A:9TY404 4.6 0.1 1.0 H2 A:9TY404 4.6 0.4 1.0 HA A:ARG130 4.7 0.2 1.0 C08 A:9TY404 4.7 98.7 1.0 C07 A:9TY404 4.8 0.3 1.0 NE A:ARG130 4.8 0.0 1.0 O A:ASP191 4.8 82.1 1.0 CD A:ARG130 4.9 0.7 1.0 OE2 A:GLU195 4.9 93.2 1.0 O A:ARG130 5.0 0.3 1.0

Magnesium binding site 3 out of 24 in the 328 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 328 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:Mg405 b:0.4 occ:1.00 O09 B:9TY403 1.9 0.9 1.0 O01 B:9TY403 2.0 0.7 1.0 OD1 B:ASP191 2.2 0.1 1.0 C02 B:9TY403 2.2 1.0 1.0 CG B:ASP191 3.4 98.0 1.0 OE2 A:GLU227 3.4 95.7 1.0 OE1 A:GLU227 3.5 0.9 1.0 HA B:ASP191 3.6 99.5 1.0 C03 B:9TY403 3.7 0.5 1.0 OE2 A:GLU233 3.8 0.8 1.0 CD A:GLU227 3.8 99.5 1.0 OE1 A:GLU233 3.9 0.1 1.0 HD3 B:ARG130 4.1 0.1 1.0 HH11 B:ARG130 4.2 0.8 1.0 OD2 B:ASP191 4.2 99.6 1.0 NH1 B:ARG130 4.2 0.3 1.0 CD A:GLU233 4.3 0.0 1.0 CB B:ASP191 4.3 87.7 1.0 HH12 B:ARG130 4.4 0.8 1.0 O06 B:9TY403 4.4 0.5 1.0 CA B:ASP191 4.4 82.9 1.0 HB2 B:ASP191 4.4 0.3 1.0 H3 B:9TY403 4.5 0.1 1.0 CZ B:ARG130 4.5 0.4 1.0 C04 B:9TY403 4.6 0.5 1.0 H2 B:9TY403 4.6 0.1 1.0 HA B:ARG130 4.7 0.8 1.0 C08 B:9TY403 4.7 98.4 1.0 C07 B:9TY403 4.8 0.1 1.0 NE B:ARG130 4.8 0.8 1.0 O B:ASP191 4.8 82.9 1.0 CD B:ARG130 4.9 0.6 1.0 OE2 B:GLU195 4.9 93.3 1.0 H5N B:NAI402 4.9 0.8 0.5 O B:ARG130 5.0 0.9 1.0

Magnesium binding site 4 out of 24 in the 328 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 328 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:93.8 occ:1.00 O06 B:9TY403 1.9 0.5 1.0 OE2 B:GLU195 2.0 93.3 1.0 OD2 B:ASP191 2.0 99.6 1.0 C04 B:9TY403 2.2 0.5 1.0 O05 B:9TY403 2.6 98.4 1.0 CD B:GLU195 3.0 90.6 1.0 CG B:ASP191 3.0 98.0 1.0 C03 B:9TY403 3.3 0.5 1.0 OE1 B:GLU195 3.5 88.8 1.0 HG A:SER254 3.5 0.4 1.0 OD1 B:ASP191 3.6 0.1 1.0 C02 B:9TY403 3.8 1.0 1.0 HB2 A:SER257 3.9 92.0 1.0 H4 B:9TY403 4.0 0.1 1.0 O09 B:9TY403 4.0 0.9 1.0 O B:ASP191 4.1 82.9 1.0 C08 B:9TY403 4.1 98.4 1.0 OG A:SER254 4.2 91.2 1.0 HB3 B:ASP191 4.2 0.3 1.0 CB B:ASP191 4.2 87.7 1.0 CG B:GLU195 4.3 81.2 1.0 HD23 B:LEU192 4.4 91.1 1.0 HG3 B:GLU195 4.4 97.4 1.0 HG2 B:GLU195 4.6 97.4 1.0 O01 B:9TY403 4.6 0.7 1.0 HO2N B:NAI402 4.6 0.5 0.5 C07 B:9TY403 4.7 0.1 1.0 H3 B:9TY403 4.7 0.1 1.0 C B:ASP191 4.8 82.9 1.0 HB A:THR256 4.8 89.3 1.0 CB A:SER257 4.8 76.7 1.0 H1 B:9TY403 4.8 0.1 1.0 H2D B:NAI402 4.9 0.2 0.5 HB2 B:ASP191 4.9 0.3 1.0 H42N B:NAI402 4.9 0.5 0.5 H A:SER257 5.0 92.0 1.0

Magnesium binding site 5 out of 24 in the 328 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 328 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:95.6 occ:1.00 O05 C:9TY404 1.9 0.2 1.0 OE2 C:GLU195 2.0 94.1 1.0 OD2 C:ASP191 2.0 99.7 1.0 C04 C:9TY404 2.2 0.2 1.0 O06 C:9TY404 2.6 99.3 1.0 CD C:GLU195 3.0 90.5 1.0 CG C:ASP191 3.0 97.8 1.0 C03 C:9TY404 3.3 0.5 1.0 OE1 C:GLU195 3.5 87.7 1.0 HG D:SER254 3.5 0.9 1.0 OD1 C:ASP191 3.6 0.7 1.0 C02 C:9TY404 3.8 0.1 1.0 HB2 D:SER257 4.0 93.1 1.0 H4 C:9TY404 4.0 0.1 1.0 O01 C:9TY404 4.0 0.5 1.0 O C:ASP191 4.1 82.7 1.0 C08 C:9TY404 4.1 99.2 1.0 HB3 C:ASP191 4.2 0.7 1.0 OG D:SER254 4.2 90.8 1.0 CB C:ASP191 4.3 87.2 1.0 CG C:GLU195 4.3 81.1 1.0 HD23 C:LEU192 4.4 90.4 1.0 HG3 C:GLU195 4.4 97.3 1.0 HG2 C:GLU195 4.6 97.3 1.0 O09 C:9TY404 4.6 0.9 1.0 HO2N C:NAI403 4.6 0.9 0.5 C07 C:9TY404 4.7 0.5 1.0 H3 C:9TY404 4.7 0.1 1.0 C C:ASP191 4.8 82.7 1.0 HB D:THR256 4.8 88.9 1.0 H1 C:9TY404 4.8 0.8 1.0 CB D:SER257 4.9 77.6 1.0 HB2 C:ASP191 4.9 0.7 1.0

Magnesium binding site 6 out of 24 in the 328 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 328 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:Mg402 b:0.4 occ:1.00 O01 C:9TY404 1.9 0.5 1.0 O09 C:9TY404 2.0 0.9 1.0 OD1 C:ASP191 2.2 0.7 1.0 C02 C:9TY404 2.2 0.1 1.0 CG C:ASP191 3.4 97.8 1.0 OE1 D:GLU227 3.4 0.3 1.0 OE2 D:GLU227 3.4 95.6 1.0 HA C:ASP191 3.6 99.3 1.0 C03 C:9TY404 3.7 0.5 1.0 CD D:GLU227 3.8 99.1 1.0 OE2 D:GLU233 3.9 0.6 1.0 OE1 D:GLU233 4.0 0.1 1.0 HD3 C:ARG130 4.1 0.2 1.0 HH11 C:ARG130 4.2 0.8 1.0 OD2 C:ASP191 4.2 99.7 1.0 NH1 C:ARG130 4.2 0.3 1.0 CB C:ASP191 4.3 87.2 1.0 HH12 C:ARG130 4.4 0.8 1.0 O05 C:9TY404 4.4 0.2 1.0 CA C:ASP191 4.4 82.7 1.0 CD D:GLU233 4.4 0.1 1.0 HB2 C:ASP191 4.4 0.7 1.0 H3 C:9TY404 4.5 0.1 1.0 CZ C:ARG130 4.5 0.9 1.0 C04 C:9TY404 4.6 0.2 1.0 H2 C:9TY404 4.6 0.8 1.0 HA C:ARG130 4.7 1.0 1.0 C08 C:9TY404 4.7 99.2 1.0 C07 C:9TY404 4.8 0.5 1.0 NE C:ARG130 4.8 0.4 1.0 O C:ASP191 4.8 82.7 1.0 CD C:ARG130 4.9 0.7 1.0 OE2 C:GLU195 4.9 94.1 1.0 O C:ARG130 5.0 0.5 1.0

Magnesium binding site 7 out of 24 in the 328 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 328 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:Mg405 b:0.2 occ:1.00 O01 D:9TY403 1.9 0.0 1.0 O09 D:9TY403 2.0 0.2 1.0 OD1 D:ASP191 2.2 0.9 1.0 C02 D:9TY403 2.2 0.5 1.0 OE1 C:GLU227 3.3 0.4 1.0 OE2 C:GLU227 3.3 95.9 1.0 CG D:ASP191 3.4 97.4 1.0 HA D:ASP191 3.6 98.8 1.0 CD C:GLU227 3.7 0.2 1.0 C03 D:9TY403 3.7 0.3 1.0 OE2 C:GLU233 4.0 0.3 1.0 OE1 C:GLU233 4.0 0.5 1.0 HD3 D:ARG130 4.1 0.2 1.0 HH11 D:ARG130 4.2 0.1 1.0 OD2 D:ASP191 4.2 99.5 1.0 NH1 D:ARG130 4.2 0.7 1.0 CB D:ASP191 4.3 87.2 1.0 HH12 D:ARG130 4.4 0.1 1.0 O05 D:9TY403 4.4 0.4 1.0 CA D:ASP191 4.4 82.4 1.0 HB2 D:ASP191 4.4 0.6 1.0 CD C:GLU233 4.5 0.7 1.0 H3 D:9TY403 4.5 0.1 1.0 CZ D:ARG130 4.5 0.8 1.0 C04 D:9TY403 4.6 0.8 1.0 H2 D:9TY403 4.6 0.5 1.0 HA D:ARG130 4.7 0.4 1.0 C08 D:9TY403 4.7 99.2 1.0 C07 D:9TY403 4.8 0.2 1.0 NE D:ARG130 4.8 0.3 1.0 O D:ASP191 4.8 83.0 1.0 CD D:ARG130 4.9 0.8 1.0 OE2 D:GLU195 4.9 93.8 1.0 O D:ARG130 5.0 0.9 1.0

Magnesium binding site 8 out of 24 in the 328 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 328 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:95.3 occ:1.00 O05 D:9TY403 1.9 0.4 1.0 OE2 D:GLU195 2.0 93.8 1.0 OD2 D:ASP191 2.0 99.5 1.0 C04 D:9TY403 2.2 0.8 1.0 O06 D:9TY403 2.6 99.2 1.0 CD D:GLU195 3.0 90.8 1.0 CG D:ASP191 3.0 97.4 1.0 C03 D:9TY403 3.3 0.3 1.0 OE1 D:GLU195 3.5 89.5 1.0 OD1 D:ASP191 3.6 0.9 1.0 HG C:SER254 3.8 0.8 1.0 C02 D:9TY403 3.8 0.5 1.0 H4 D:9TY403 4.0 0.1 1.0 O01 D:9TY403 4.0 0.0 1.0 HB2 C:SER257 4.1 91.5 1.0 O D:ASP191 4.1 83.0 1.0 C08 D:9TY403 4.1 99.2 1.0 HB3 D:ASP191 4.2 0.6 1.0 CB D:ASP191 4.2 87.2 1.0 CG D:GLU195 4.3 81.1 1.0 HD23 D:LEU192 4.4 90.9 1.0 OG C:SER254 4.4 87.3 1.0 HG3 D:GLU195 4.4 97.3 1.0 HG2 D:GLU195 4.6 97.3 1.0 O09 D:9TY403 4.6 0.2 1.0 C07 D:9TY403 4.7 0.2 1.0 H3 D:9TY403 4.7 0.1 1.0 C D:ASP191 4.8 82.4 1.0 HO2N D:NAI402 4.8 0.7 0.5 H1 D:9TY403 4.8 0.5 1.0 HB C:THR256 4.9 88.0 1.0 HB2 D:ASP191 4.9 0.6 1.0

Magnesium binding site 9 out of 24 in the 328 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 328 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:94.5 occ:1.00 O06 E:9TY404 1.9 0.4 1.0 OE2 E:GLU195 2.0 93.4 1.0 OD2 E:ASP191 2.0 100.0 1.0 C04 E:9TY404 2.2 0.9 1.0 O05 E:9TY404 2.6 98.2 1.0 CD E:GLU195 3.0 90.5 1.0 CG E:ASP191 3.0 97.4 1.0 C03 E:9TY404 3.3 0.5 1.0 OE1 E:GLU195 3.5 88.6 1.0 HG F:SER254 3.5 1.0 1.0 OD1 E:ASP191 3.6 0.1 1.0 C02 E:9TY404 3.8 0.9 1.0 HB2 F:SER257 3.9 91.9 1.0 O01 E:9TY404 4.0 0.0 1.0 H4 E:9TY404 4.0 1.0 1.0 O E:ASP191 4.1 82.5 1.0 C08 E:9TY404 4.1 98.3 1.0 HB3 E:ASP191 4.2 0.1 1.0 OG F:SER254 4.2 89.1 1.0 CB E:ASP191 4.2 86.8 1.0 CG E:GLU195 4.3 80.9 1.0 HD23 E:LEU192 4.4 91.4 1.0 HG3 E:GLU195 4.4 97.0 1.0 HG2 E:GLU195 4.6 97.0 1.0 O09 E:9TY404 4.6 0.1 1.0 C07 E:9TY404 4.7 0.2 1.0 H3 E:9TY404 4.7 1.0 1.0 HB F:THR256 4.7 89.0 1.0 C E:ASP191 4.8 82.5 1.0 HO2N E:NAI403 4.8 0.3 0.5 CB F:SER257 4.8 76.6 1.0 H1 E:9TY404 4.8 0.3 1.0 HB2 E:ASP191 4.9 0.1 1.0 H F:SER257 5.0 91.9 1.0 H2D E:NAI403 5.0 0.5 0.5

Magnesium binding site 10 out of 24 in the 328 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 328 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:Mg402 b:0.9 occ:1.00 O01 E:9TY404 1.9 0.0 1.0 O09 E:9TY404 2.0 0.1 1.0 OD1 E:ASP191 2.2 0.1 1.0 C02 E:9TY404 2.2 0.9 1.0 OE2 F:GLU227 3.3 96.6 1.0 OE1 F:GLU227 3.4 0.2 1.0 CG E:ASP191 3.4 97.4 1.0 HA E:ASP191 3.6 99.0 1.0 CD F:GLU227 3.7 0.5 1.0 C03 E:9TY404 3.7 0.5 1.0 OE2 F:GLU233 3.9 0.8 1.0 OE1 F:GLU233 4.0 0.9 1.0 HD3 E:ARG130 4.1 0.8 1.0 HH11 E:ARG130 4.2 0.9 1.0 OD2 E:ASP191 4.2 100.0 1.0 NH1 E:ARG130 4.2 0.6 1.0 CB E:ASP191 4.3 86.8 1.0 HH12 E:ARG130 4.4 0.9 1.0 O06 E:9TY404 4.4 0.4 1.0 CA E:ASP191 4.4 82.5 1.0 HB2 E:ASP191 4.4 0.1 1.0 CD F:GLU233 4.4 0.0 1.0 H3 E:9TY404 4.5 1.0 1.0 CZ E:ARG130 4.5 0.2 1.0 C04 E:9TY404 4.6 0.9 1.0 H2 E:9TY404 4.6 0.3 1.0 HA E:ARG130 4.7 0.2 1.0 C08 E:9TY404 4.7 98.3 1.0 C07 E:9TY404 4.8 0.2 1.0 NE E:ARG130 4.8 0.6 1.0 O E:ASP191 4.8 82.5 1.0 CD E:ARG130 4.9 0.3 1.0 OE2 E:GLU195 4.9 93.4 1.0 O E:ARG130 5.0 0.8 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