Magnesium in PDB 6kph: 343 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 343 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd (pdb code 6kph). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the 343 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd, PDB code: 6kph:
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 343 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 343 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:92.5 occ:1.00 O05 A:9TY404 1.8 99.5 1.0 OE2 A:GLU195 1.9 84.2 1.0 OD2 A:ASP191 2.0 87.3 1.0 C04 A:9TY404 2.6 99.5 1.0 O06 A:9TY404 2.9 99.5 1.0 CD A:GLU195 3.0 84.2 1.0 CG A:ASP191 3.2 87.3 1.0 HG B:SER254 3.3 92.1 1.0 OE1 A:GLU195 3.3 84.2 1.0 OD1 A:ASP191 3.8 87.3 1.0 C03 A:9TY404 3.8 99.5 1.0 HB2 B:SER257 3.9 85.2 1.0 OG B:SER254 4.0 92.1 1.0 HD23 A:LEU192 4.1 82.6 1.0 HB3 A:ASP191 4.1 87.3 1.0 CB A:ASP191 4.2 87.3 1.0 CG A:GLU195 4.3 84.2 1.0 C02 A:9TY404 4.3 99.5 1.0 HB B:THR256 4.3 84.1 1.0 O01 A:9TY404 4.4 99.5 1.0 HG3 A:GLU195 4.4 84.2 1.0 HG2 A:GLU195 4.5 84.2 1.0 H4 A:9TY404 4.7 99.5 1.0 HD21 A:LEU192 4.8 82.6 1.0 C08 A:9TY404 4.8 99.5 1.0 H B:SER257 4.8 85.2 1.0 CD2 A:LEU192 4.8 82.6 1.0 HB2 A:ASP191 4.9 87.3 1.0 HO2N A:NAI403 4.9 0.5 1.0 CB B:SER257 4.9 85.2 1.0 H2D A:NAI403 5.0 0.5 1.0

Magnesium binding site 2 out of 24 in the 343 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 343 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:95.4 occ:1.00 O01 A:9TY404 1.9 99.5 1.0 O09 A:9TY404 2.0 99.5 1.0 OD1 A:ASP191 2.0 87.3 1.0 C02 A:9TY404 2.2 99.5 1.0 CG A:ASP191 3.2 87.3 1.0 OE2 B:GLU227 3.3 94.1 1.0 C03 A:9TY404 3.7 99.5 1.0 OE2 B:GLU233 3.7 1.0 1.0 HD3 A:ARG130 3.7 0.1 1.0 HA A:ASP191 3.8 87.3 1.0 OE1 B:GLU227 3.9 94.1 1.0 OD2 A:ASP191 3.9 87.3 1.0 HH11 A:ARG130 3.9 0.1 1.0 CD B:GLU227 4.0 94.1 1.0 OE1 B:GLU233 4.0 1.0 1.0 O05 A:9TY404 4.1 99.5 1.0 HA A:ARG130 4.2 0.1 1.0 NH1 A:ARG130 4.3 0.1 1.0 CD B:GLU233 4.3 1.0 1.0 CB A:ASP191 4.3 87.3 1.0 C04 A:9TY404 4.4 99.5 1.0 HB2 A:ASP191 4.4 87.3 1.0 CA A:ASP191 4.5 87.3 1.0 HH12 A:ARG130 4.5 0.1 1.0 CD A:ARG130 4.6 0.1 1.0 H2 A:9TY404 4.6 99.5 1.0 H3 A:9TY404 4.7 99.5 1.0 C07 A:9TY404 4.7 99.5 1.0 C08 A:9TY404 4.8 99.5 1.0 OE2 A:GLU195 4.8 84.2 1.0 CZ A:ARG130 4.8 0.1 1.0 HD2 A:ARG130 4.8 0.1 1.0 HB2 A:SER194 4.9 83.5 1.0 O A:PRO129 5.0 0.9 1.0 NE A:ARG130 5.0 0.1 1.0

Magnesium binding site 3 out of 24 in the 343 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 343 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:92.6 occ:1.00 O06 B:9TY404 1.8 98.8 1.0 OE2 B:GLU195 1.9 83.2 1.0 OD2 B:ASP191 2.0 86.6 1.0 C04 B:9TY404 2.6 98.8 1.0 O05 B:9TY404 2.9 98.8 1.0 CD B:GLU195 3.0 83.2 1.0 CG B:ASP191 3.2 86.6 1.0 OE1 B:GLU195 3.3 83.2 1.0 HG A:SER254 3.4 92.2 1.0 OD1 B:ASP191 3.8 86.6 1.0 C03 B:9TY404 3.8 98.8 1.0 HB2 A:SER257 3.9 84.8 1.0 OG A:SER254 4.1 92.2 1.0 HD23 B:LEU192 4.1 82.1 1.0 HB3 B:ASP191 4.1 86.6 1.0 HB A:THR256 4.2 83.9 1.0 CB B:ASP191 4.2 86.6 1.0 CG B:GLU195 4.3 83.2 1.0 C02 B:9TY404 4.3 98.8 1.0 O09 B:9TY404 4.4 98.8 1.0 HG3 B:GLU195 4.4 83.2 1.0 HG2 B:GLU195 4.5 83.2 1.0 H4 B:9TY404 4.7 98.8 1.0 HD21 B:LEU192 4.7 82.1 1.0 H A:SER257 4.8 84.8 1.0 C08 B:9TY404 4.8 98.8 1.0 HG21 A:THR256 4.8 83.9 1.0 CD2 B:LEU192 4.8 82.1 1.0 CB A:SER257 4.9 84.8 1.0 HB2 B:ASP191 4.9 86.6 1.0 HG22 A:THR256 4.9 83.9 1.0 HO2N B:NAI403 4.9 0.1 1.0 H2D B:NAI403 5.0 0.1 1.0

Magnesium binding site 4 out of 24 in the 343 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 343 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:96.0 occ:1.00 O09 B:9TY404 1.9 98.8 1.0 O01 B:9TY404 2.0 98.8 1.0 OD1 B:ASP191 2.0 86.6 1.0 C02 B:9TY404 2.2 98.8 1.0 OE2 A:GLU227 3.1 94.6 1.0 CG B:ASP191 3.2 86.6 1.0 C03 B:9TY404 3.7 98.8 1.0 HD3 B:ARG130 3.7 0.6 1.0 HA B:ASP191 3.8 86.6 1.0 OE1 A:GLU227 3.8 94.6 1.0 CD A:GLU227 3.9 94.6 1.0 OE2 A:GLU233 3.9 0.2 1.0 OD2 B:ASP191 3.9 86.6 1.0 HH11 B:ARG130 3.9 0.6 1.0 O06 B:9TY404 4.1 98.8 1.0 OE1 A:GLU233 4.1 0.2 1.0 HA B:ARG130 4.2 0.6 1.0 NH1 B:ARG130 4.3 0.6 1.0 CB B:ASP191 4.3 86.6 1.0 C04 B:9TY404 4.4 98.8 1.0 HB2 B:ASP191 4.4 86.6 1.0 CD A:GLU233 4.5 0.2 1.0 CA B:ASP191 4.5 86.6 1.0 HH12 B:ARG130 4.5 0.6 1.0 CD B:ARG130 4.6 0.6 1.0 H2 B:9TY404 4.6 98.8 1.0 H3 B:9TY404 4.7 98.8 1.0 C07 B:9TY404 4.7 98.8 1.0 C08 B:9TY404 4.8 98.8 1.0 OE2 B:GLU195 4.8 83.2 1.0 CZ B:ARG130 4.8 0.6 1.0 HD2 B:ARG130 4.8 0.6 1.0 HB2 B:SER194 4.9 82.5 1.0 O B:PRO129 5.0 0.3 1.0 NE B:ARG130 5.0 0.6 1.0

Magnesium binding site 5 out of 24 in the 343 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 343 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:93.1 occ:1.00 O06 C:9TY404 1.8 98.3 1.0 OE2 C:GLU195 1.9 83.5 1.0 OD2 C:ASP191 2.0 86.3 1.0 C04 C:9TY404 2.6 98.3 1.0 O05 C:9TY404 2.9 98.3 1.0 CD C:GLU195 3.0 83.5 1.0 CG C:ASP191 3.2 86.3 1.0 OE1 C:GLU195 3.3 83.5 1.0 HG D:SER254 3.5 91.8 1.0 OD1 C:ASP191 3.8 86.3 1.0 C03 C:9TY404 3.8 98.3 1.0 HB2 D:SER257 4.0 84.4 1.0 HD23 C:LEU192 4.1 82.4 1.0 HB3 C:ASP191 4.1 86.3 1.0 OG D:SER254 4.1 91.8 1.0 HB D:THR256 4.2 83.5 1.0 CB C:ASP191 4.3 86.3 1.0 CG C:GLU195 4.3 83.5 1.0 C02 C:9TY404 4.3 98.3 1.0 O01 C:9TY404 4.4 98.3 1.0 HG3 C:GLU195 4.4 83.5 1.0 HG2 C:GLU195 4.5 83.5 1.0 H4 C:9TY404 4.7 98.3 1.0 HD21 C:LEU192 4.7 82.4 1.0 HG21 D:THR256 4.8 83.5 1.0 C08 C:9TY404 4.8 98.3 1.0 H D:SER257 4.8 84.4 1.0 CD2 C:LEU192 4.8 82.4 1.0 HO2N C:NAI403 4.9 0.7 1.0 HB2 C:ASP191 4.9 86.3 1.0 HG22 D:THR256 4.9 83.5 1.0 CB D:SER257 4.9 84.4 1.0 H2D C:NAI403 5.0 0.7 1.0

Magnesium binding site 6 out of 24 in the 343 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 343 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:95.0 occ:1.00 O01 C:9TY404 1.9 98.3 1.0 O09 C:9TY404 2.0 98.3 1.0 OD1 C:ASP191 2.0 86.3 1.0 C02 C:9TY404 2.2 98.3 1.0 OE2 D:GLU227 3.1 94.2 1.0 CG C:ASP191 3.2 86.3 1.0 C03 C:9TY404 3.7 98.3 1.0 HD3 C:ARG130 3.7 0.9 1.0 OE1 D:GLU227 3.8 94.2 1.0 HA C:ASP191 3.8 86.3 1.0 CD D:GLU227 3.8 94.2 1.0 OD2 C:ASP191 3.9 86.3 1.0 HH11 C:ARG130 3.9 0.9 1.0 OE2 D:GLU233 3.9 0.9 1.0 O06 C:9TY404 4.1 98.3 1.0 OE1 D:GLU233 4.2 0.9 1.0 HA C:ARG130 4.2 0.9 1.0 NH1 C:ARG130 4.3 0.9 1.0 CB C:ASP191 4.3 86.3 1.0 C04 C:9TY404 4.4 98.3 1.0 HB2 C:ASP191 4.4 86.3 1.0 CD D:GLU233 4.5 0.9 1.0 CA C:ASP191 4.5 86.3 1.0 HH12 C:ARG130 4.5 0.9 1.0 CD C:ARG130 4.6 0.9 1.0 H2 C:9TY404 4.6 98.3 1.0 H3 C:9TY404 4.7 98.3 1.0 C07 C:9TY404 4.7 98.3 1.0 C08 C:9TY404 4.8 98.3 1.0 OE2 C:GLU195 4.8 83.5 1.0 CZ C:ARG130 4.8 0.9 1.0 HD2 C:ARG130 4.8 0.9 1.0 HB2 C:SER194 4.9 82.7 1.0 O C:PRO129 5.0 0.6 1.0 NE C:ARG130 5.0 0.9 1.0

Magnesium binding site 7 out of 24 in the 343 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 343 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:92.8 occ:1.00 O06 D:9TY404 1.8 99.0 1.0 OE2 D:GLU195 1.9 83.8 1.0 OD2 D:ASP191 2.0 87.0 1.0 C04 D:9TY404 2.6 99.0 1.0 O05 D:9TY404 2.9 99.0 1.0 CD D:GLU195 3.0 83.8 1.0 CG D:ASP191 3.1 87.0 1.0 HG C:SER254 3.3 92.4 1.0 OE1 D:GLU195 3.3 83.8 1.0 OD1 D:ASP191 3.8 87.0 1.0 C03 D:9TY404 3.8 99.0 1.0 HB2 C:SER257 4.0 85.1 1.0 OG C:SER254 4.0 92.4 1.0 HD23 D:LEU192 4.1 82.3 1.0 HB3 D:ASP191 4.1 87.0 1.0 CB D:ASP191 4.2 87.0 1.0 CG D:GLU195 4.3 83.8 1.0 C02 D:9TY404 4.3 99.0 1.0 HB C:THR256 4.3 83.6 1.0 O01 D:9TY404 4.4 99.0 1.0 HG3 D:GLU195 4.4 83.8 1.0 HG2 D:GLU195 4.5 83.8 1.0 H4 D:9TY404 4.7 99.0 1.0 HD21 D:LEU192 4.8 82.3 1.0 C08 D:9TY404 4.8 99.0 1.0 H C:SER257 4.8 85.1 1.0 CD2 D:LEU192 4.8 82.3 1.0 HB2 D:ASP191 4.9 87.0 1.0 CB C:SER257 4.9 85.1 1.0 H2D D:NAI403 5.0 0.4 1.0 HO2N D:NAI403 5.0 0.4 1.0 HG21 C:THR256 5.0 83.6 1.0

Magnesium binding site 8 out of 24 in the 343 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 343 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:95.3 occ:1.00 O01 D:9TY404 1.9 99.0 1.0 O09 D:9TY404 2.0 99.0 1.0 OD1 D:ASP191 2.0 87.0 1.0 C02 D:9TY404 2.2 99.0 1.0 CG D:ASP191 3.2 87.0 1.0 OE2 C:GLU227 3.3 93.7 1.0 C03 D:9TY404 3.7 99.0 1.0 OE2 C:GLU233 3.7 0.6 1.0 HD3 D:ARG130 3.7 0.1 1.0 HA D:ASP191 3.8 87.0 1.0 OE1 C:GLU227 3.9 93.7 1.0 OD2 D:ASP191 3.9 87.0 1.0 HH11 D:ARG130 3.9 0.1 1.0 CD C:GLU227 4.0 93.7 1.0 OE1 C:GLU233 4.0 0.6 1.0 O06 D:9TY404 4.1 99.0 1.0 HA D:ARG130 4.2 0.1 1.0 NH1 D:ARG130 4.3 0.1 1.0 CB D:ASP191 4.3 87.0 1.0 CD C:GLU233 4.3 0.6 1.0 C04 D:9TY404 4.4 99.0 1.0 HB2 D:ASP191 4.4 87.0 1.0 CA D:ASP191 4.5 87.0 1.0 HH12 D:ARG130 4.5 0.1 1.0 CD D:ARG130 4.6 0.1 1.0 H2 D:9TY404 4.6 99.0 1.0 H3 D:9TY404 4.7 99.0 1.0 C07 D:9TY404 4.7 99.0 1.0 C08 D:9TY404 4.8 99.0 1.0 OE2 D:GLU195 4.8 83.8 1.0 CZ D:ARG130 4.8 0.1 1.0 HD2 D:ARG130 4.8 0.1 1.0 HB2 D:SER194 4.9 83.4 1.0 O D:PRO129 5.0 0.7 1.0 NE D:ARG130 5.0 0.1 1.0

Magnesium binding site 9 out of 24 in the 343 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 343 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:92.5 occ:1.00 O06 E:9TY404 1.8 98.7 1.0 OE2 E:GLU195 1.9 83.6 1.0 OD2 E:ASP191 2.0 86.7 1.0 C04 E:9TY404 2.6 98.7 1.0 O05 E:9TY404 2.9 98.7 1.0 CD E:GLU195 3.0 83.6 1.0 CG E:ASP191 3.2 86.7 1.0 HG F:SER254 3.3 92.0 1.0 OE1 E:GLU195 3.3 83.6 1.0 OD1 E:ASP191 3.8 86.7 1.0 C03 E:9TY404 3.8 98.7 1.0 OG F:SER254 3.9 92.0 1.0 HB2 F:SER257 4.0 84.8 1.0 HD23 E:LEU192 4.1 82.3 1.0 HB3 E:ASP191 4.1 86.7 1.0 HB F:THR256 4.2 83.6 1.0 CB E:ASP191 4.2 86.7 1.0 CG E:GLU195 4.3 83.6 1.0 C02 E:9TY404 4.3 98.7 1.0 O01 E:9TY404 4.4 98.7 1.0 HG3 E:GLU195 4.4 83.6 1.0 HG2 E:GLU195 4.5 83.6 1.0 H4 E:9TY404 4.7 98.7 1.0 HD21 E:LEU192 4.8 82.3 1.0 H F:SER257 4.8 84.8 1.0 C08 E:9TY404 4.8 98.7 1.0 CD2 E:LEU192 4.8 82.3 1.0 HB2 E:ASP191 4.9 86.7 1.0 HG21 F:THR256 4.9 83.6 1.0 CB F:SER257 4.9 84.8 1.0 HO2N E:NAI403 4.9 0.9 1.0 H2D E:NAI403 5.0 0.9 1.0

Magnesium binding site 10 out of 24 in the 343 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 343 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:96.8 occ:1.00 O01 E:9TY404 1.9 98.7 1.0 O09 E:9TY404 2.0 98.7 1.0 OD1 E:ASP191 2.0 86.7 1.0 C02 E:9TY404 2.2 98.7 1.0 CG E:ASP191 3.2 86.7 1.0 OE2 F:GLU227 3.3 93.3 1.0 C03 E:9TY404 3.7 98.7 1.0 HD3 E:ARG130 3.7 0.8 1.0 HA E:ASP191 3.8 86.7 1.0 OE2 F:GLU233 3.8 0.5 1.0 OD2 E:ASP191 3.9 86.7 1.0 OE1 F:GLU227 3.9 93.3 1.0 HH11 E:ARG130 3.9 0.8 1.0 CD F:GLU227 4.0 93.3 1.0 O06 E:9TY404 4.1 98.7 1.0 OE1 F:GLU233 4.1 0.5 1.0 HA E:ARG130 4.2 0.8 1.0 NH1 E:ARG130 4.3 0.8 1.0 CB E:ASP191 4.3 86.7 1.0 C04 E:9TY404 4.4 98.7 1.0 CD F:GLU233 4.4 0.5 1.0 HB2 E:ASP191 4.4 86.7 1.0 CA E:ASP191 4.5 86.7 1.0 HH12 E:ARG130 4.5 0.8 1.0 CD E:ARG130 4.6 0.8 1.0 H2 E:9TY404 4.6 98.7 1.0 H3 E:9TY404 4.7 98.7 1.0 C07 E:9TY404 4.7 98.7 1.0 C08 E:9TY404 4.8 98.7 1.0 OE2 E:GLU195 4.8 83.6 1.0 CZ E:ARG130 4.8 0.8 1.0 HD2 E:ARG130 4.8 0.8 1.0 HB2 E:SER194 4.9 82.7 1.0 O E:PRO129 5.0 0.3 1.0 NE 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