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Magnesium in PDB 6kqk: 323 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd

Magnesium Binding Sites:

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Binding sites:

The binding sites of Magnesium atom in the 323 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd (pdb code 6kqk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the 323 K Cryoem Structure of Sso-Kari in Complex with MG2+, Nadh and Cpd, PDB code: 6kqk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in 6kqk

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Magnesium binding site 1 out of 24 in the 323 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 323 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:82.5
occ:1.00
O05 A:9TY403 1.9 90.7 1.0
OE2 A:GLU195 1.9 68.2 1.0
OD2 A:ASP191 2.0 75.5 1.0
C04 A:9TY403 2.4 90.7 1.0
O06 A:9TY403 2.8 90.7 1.0
CD A:GLU195 2.9 68.2 1.0
CG A:ASP191 3.1 75.5 1.0
OE1 A:GLU195 3.3 68.2 1.0
C03 A:9TY403 3.5 90.7 1.0
HG B:SER254 3.5 79.8 1.0
HB2 B:SER257 3.7 72.0 1.0
OD1 A:ASP191 3.7 75.5 1.0
C02 A:9TY403 3.9 90.7 1.0
O01 A:9TY403 4.2 90.7 1.0
HD23 A:LEU192 4.2 67.3 1.0
OG B:SER254 4.2 79.8 1.0
HB3 A:ASP191 4.2 75.5 1.0
CG A:GLU195 4.3 68.2 1.0
CB A:ASP191 4.3 75.5 1.0
H4 A:9TY403 4.4 90.7 1.0
HG3 A:GLU195 4.4 68.2 1.0
O A:ASP191 4.4 75.5 1.0
C08 A:9TY403 4.4 90.7 1.0
O09 A:9TY403 4.5 90.7 1.0
HG2 A:GLU195 4.6 68.2 1.0
HB B:THR256 4.6 69.7 1.0
CB B:SER257 4.6 72.0 1.0
H B:SER257 4.8 72.0 1.0
C A:ASP191 4.9 75.5 1.0
C07 A:9TY403 4.9 90.7 1.0
HA B:SER257 4.9 72.0 1.0
HB2 A:ASP191 5.0 75.5 1.0
H3 A:9TY403 5.0 90.7 1.0

Magnesium binding site 2 out of 24 in 6kqk

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Magnesium binding site 2 out of 24 in the 323 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 323 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:90.8
occ:1.00
O09 B:9TY404 1.9 90.2 1.0
O01 B:9TY404 2.0 90.2 1.0
OD1 B:ASP191 2.1 75.1 1.0
C02 B:9TY404 2.3 90.2 1.0
OE2 A:GLU227 2.7 83.4 1.0
CG B:ASP191 3.3 75.1 1.0
HA B:ASP191 3.4 75.1 1.0
CD A:GLU227 3.4 83.4 1.0
OE1 A:GLU227 3.4 83.4 1.0
OE1 A:GLU233 3.7 94.2 1.0
OE2 A:GLU233 3.7 94.2 1.0
C03 B:9TY404 3.8 90.2 1.0
OD2 B:ASP191 4.1 75.1 1.0
CD A:GLU233 4.1 94.2 1.0
CB B:ASP191 4.2 75.1 1.0
CA B:ASP191 4.2 75.1 1.0
HH11 B:ARG130 4.2 98.7 1.0
HD3 B:ARG130 4.3 98.7 1.0
NH1 B:ARG130 4.3 98.7 1.0
HB2 B:ASP191 4.4 75.1 1.0
HH12 B:ARG130 4.4 98.7 1.0
H3 B:9TY404 4.5 90.2 1.0
O06 B:9TY404 4.5 90.2 1.0
H2 B:9TY404 4.6 90.2 1.0
O B:ASP191 4.6 75.1 1.0
HB2 B:SER194 4.7 67.3 1.0
C04 B:9TY404 4.7 90.2 1.0
HG B:SER194 4.7 67.3 1.0
CZ B:ARG130 4.7 98.7 1.0
C08 B:9TY404 4.7 90.2 1.0
C07 B:9TY404 4.8 90.2 1.0
OE2 B:GLU195 4.9 67.7 1.0
CG A:GLU227 4.9 83.4 1.0
C B:ASP191 5.0 75.1 1.0
HG3 B:GLU195 5.0 67.7 1.0

Magnesium binding site 3 out of 24 in 6kqk

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Magnesium binding site 3 out of 24 in the 323 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 323 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:90.2
occ:1.00
O01 A:9TY403 1.9 90.7 1.0
O09 A:9TY403 2.0 90.7 1.0
OD1 A:ASP191 2.1 75.5 1.0
C02 A:9TY403 2.3 90.7 1.0
OE2 B:GLU227 2.6 83.6 1.0
CG A:ASP191 3.3 75.5 1.0
CD B:GLU227 3.4 83.6 1.0
OE1 B:GLU227 3.4 83.6 1.0
HA A:ASP191 3.4 75.5 1.0
OE1 B:GLU233 3.6 94.3 1.0
OE2 B:GLU233 3.7 94.3 1.0
C03 A:9TY403 3.8 90.7 1.0
OD2 A:ASP191 4.1 75.5 1.0
CD B:GLU233 4.1 94.3 1.0
CB A:ASP191 4.2 75.5 1.0
CA A:ASP191 4.2 75.5 1.0
HH11 A:ARG130 4.2 98.2 1.0
HD3 A:ARG130 4.3 98.2 1.0
NH1 A:ARG130 4.3 98.2 1.0
HB2 A:ASP191 4.4 75.5 1.0
HH12 A:ARG130 4.4 98.2 1.0
H3 A:9TY403 4.5 90.7 1.0
O05 A:9TY403 4.5 90.7 1.0
H2 A:9TY403 4.6 90.7 1.0
O A:ASP191 4.6 75.5 1.0
HB2 A:SER194 4.7 67.7 1.0
C04 A:9TY403 4.7 90.7 1.0
HG A:SER194 4.7 67.7 1.0
CZ A:ARG130 4.7 98.2 1.0
C08 A:9TY403 4.7 90.7 1.0
C07 A:9TY403 4.8 90.7 1.0
CG B:GLU227 4.8 83.6 1.0
OE2 A:GLU195 4.9 68.2 1.0
C A:ASP191 5.0 75.5 1.0
HG3 A:GLU195 5.0 68.2 1.0

Magnesium binding site 4 out of 24 in 6kqk

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Magnesium binding site 4 out of 24 in the 323 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 323 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:81.7
occ:1.00
O06 B:9TY404 1.9 90.2 1.0
OE2 B:GLU195 1.9 67.7 1.0
OD2 B:ASP191 2.0 75.1 1.0
C04 B:9TY404 2.4 90.2 1.0
O05 B:9TY404 2.8 90.2 1.0
CD B:GLU195 2.9 67.7 1.0
CG B:ASP191 3.1 75.1 1.0
OE1 B:GLU195 3.3 67.7 1.0
HG A:SER254 3.5 79.6 1.0
C03 B:9TY404 3.5 90.2 1.0
HB2 A:SER257 3.6 71.5 1.0
OD1 B:ASP191 3.7 75.1 1.0
C02 B:9TY404 3.9 90.2 1.0
OG A:SER254 4.1 79.6 1.0
O09 B:9TY404 4.2 90.2 1.0
HD23 B:LEU192 4.2 66.9 1.0
HB3 B:ASP191 4.2 75.1 1.0
CG B:GLU195 4.3 67.7 1.0
CB B:ASP191 4.3 75.1 1.0
H4 B:9TY404 4.4 90.2 1.0
HG3 B:GLU195 4.4 67.7 1.0
O B:ASP191 4.4 75.1 1.0
C08 B:9TY404 4.4 90.2 1.0
O01 B:9TY404 4.5 90.2 1.0
HG2 B:GLU195 4.6 67.7 1.0
HB A:THR256 4.6 69.1 1.0
CB A:SER257 4.6 71.5 1.0
H A:SER257 4.8 71.5 1.0
C B:ASP191 4.9 75.1 1.0
C07 B:9TY404 4.9 90.2 1.0
HA A:SER257 4.9 71.5 1.0
HB3 A:SER257 5.0 71.5 1.0
HB2 B:ASP191 5.0 75.1 1.0
H3 B:9TY404 5.0 90.2 1.0

Magnesium binding site 5 out of 24 in 6kqk

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Magnesium binding site 5 out of 24 in the 323 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 323 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:80.5
occ:1.00
O06 C:9TY403 1.9 89.8 1.0
OE2 C:GLU195 1.9 68.0 1.0
OD2 C:ASP191 2.0 75.5 1.0
C04 C:9TY403 2.4 89.8 1.0
O05 C:9TY403 2.8 89.8 1.0
CD C:GLU195 2.9 68.0 1.0
CG C:ASP191 3.1 75.5 1.0
OE1 C:GLU195 3.3 68.0 1.0
HG D:SER254 3.4 79.3 1.0
C03 C:9TY403 3.5 89.8 1.0
HB2 D:SER257 3.7 71.4 1.0
OD1 C:ASP191 3.7 75.5 1.0
C02 C:9TY403 3.9 89.8 1.0
OG D:SER254 4.1 79.3 1.0
O01 C:9TY403 4.2 89.8 1.0
HD23 C:LEU192 4.2 67.1 1.0
HB3 C:ASP191 4.2 75.5 1.0
CG C:GLU195 4.3 68.0 1.0
CB C:ASP191 4.3 75.5 1.0
H4 C:9TY403 4.4 89.8 1.0
HG3 C:GLU195 4.4 68.0 1.0
O C:ASP191 4.4 75.5 1.0
C08 C:9TY403 4.4 89.8 1.0
O09 C:9TY403 4.5 89.8 1.0
HB D:THR256 4.6 68.9 1.0
HG2 C:GLU195 4.6 68.0 1.0
CB D:SER257 4.6 71.4 1.0
H D:SER257 4.8 71.4 1.0
C C:ASP191 4.9 75.5 1.0
C07 C:9TY403 4.9 89.8 1.0
HA D:SER257 4.9 71.4 1.0
HB3 D:SER257 5.0 71.4 1.0
HB2 C:ASP191 5.0 75.5 1.0
H3 C:9TY403 5.0 89.8 1.0

Magnesium binding site 6 out of 24 in 6kqk

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Magnesium binding site 6 out of 24 in the 323 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 323 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:90.7
occ:1.00
O01 D:9TY404 1.9 90.5 1.0
O09 D:9TY404 2.0 90.5 1.0
OD1 D:ASP191 2.1 75.4 1.0
C02 D:9TY404 2.3 90.5 1.0
OE2 C:GLU227 2.6 84.0 1.0
CG D:ASP191 3.3 75.4 1.0
CD C:GLU227 3.3 84.0 1.0
OE1 C:GLU227 3.3 84.0 1.0
HA D:ASP191 3.4 75.4 1.0
OE1 C:GLU233 3.7 94.2 1.0
OE2 C:GLU233 3.8 94.2 1.0
C03 D:9TY404 3.8 90.5 1.0
OD2 D:ASP191 4.1 75.4 1.0
CD C:GLU233 4.2 94.2 1.0
CB D:ASP191 4.2 75.4 1.0
CA D:ASP191 4.2 75.4 1.0
HH11 D:ARG130 4.2 97.5 1.0
HD3 D:ARG130 4.3 97.5 1.0
NH1 D:ARG130 4.3 97.5 1.0
HB2 D:ASP191 4.4 75.4 1.0
HH12 D:ARG130 4.4 97.5 1.0
H3 D:9TY404 4.5 90.5 1.0
O06 D:9TY404 4.5 90.5 1.0
H2 D:9TY404 4.6 90.5 1.0
O D:ASP191 4.6 75.4 1.0
HB2 D:SER194 4.7 67.8 1.0
C04 D:9TY404 4.7 90.5 1.0
CZ D:ARG130 4.7 97.5 1.0
C08 D:9TY404 4.7 90.5 1.0
HG D:SER194 4.7 67.8 1.0
C07 D:9TY404 4.8 90.5 1.0
CG C:GLU227 4.8 84.0 1.0
OE2 D:GLU195 4.9 68.0 1.0
C D:ASP191 5.0 75.4 1.0
HG3 D:GLU195 5.0 68.0 1.0

Magnesium binding site 7 out of 24 in 6kqk

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Magnesium binding site 7 out of 24 in the 323 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 323 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:89.6
occ:1.00
O01 C:9TY403 1.9 89.8 1.0
O09 C:9TY403 2.0 89.8 1.0
OD1 C:ASP191 2.1 75.5 1.0
C02 C:9TY403 2.3 89.8 1.0
OE2 D:GLU227 2.7 83.0 1.0
CG C:ASP191 3.3 75.5 1.0
HA C:ASP191 3.4 75.5 1.0
OE1 D:GLU227 3.4 83.0 1.0
CD D:GLU227 3.5 83.0 1.0
OE1 D:GLU233 3.7 93.7 1.0
OE2 D:GLU233 3.7 93.7 1.0
C03 C:9TY403 3.8 89.8 1.0
OD2 C:ASP191 4.1 75.5 1.0
CD D:GLU233 4.1 93.7 1.0
CB C:ASP191 4.2 75.5 1.0
CA C:ASP191 4.2 75.5 1.0
HH11 C:ARG130 4.2 98.7 1.0
HD3 C:ARG130 4.3 98.7 1.0
NH1 C:ARG130 4.3 98.7 1.0
HB2 C:ASP191 4.4 75.5 1.0
HH12 C:ARG130 4.4 98.7 1.0
H3 C:9TY403 4.5 89.8 1.0
O06 C:9TY403 4.5 89.8 1.0
H2 C:9TY403 4.6 89.8 1.0
O C:ASP191 4.6 75.5 1.0
HG C:SER194 4.7 67.6 1.0
HB2 C:SER194 4.7 67.6 1.0
C04 C:9TY403 4.7 89.8 1.0
CZ C:ARG130 4.7 98.7 1.0
C08 C:9TY403 4.7 89.8 1.0
C07 C:9TY403 4.8 89.8 1.0
OE2 C:GLU195 4.9 68.0 1.0
CG D:GLU227 4.9 83.0 1.0
C C:ASP191 5.0 75.5 1.0
HG3 C:GLU195 5.0 68.0 1.0

Magnesium binding site 8 out of 24 in 6kqk

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Magnesium binding site 8 out of 24 in the 323 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 323 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:83.1
occ:1.00
O06 D:9TY404 1.9 90.5 1.0
OE2 D:GLU195 1.9 68.0 1.0
OD2 D:ASP191 2.0 75.4 1.0
C04 D:9TY404 2.4 90.5 1.0
O05 D:9TY404 2.8 90.5 1.0
CD D:GLU195 2.9 68.0 1.0
CG D:ASP191 3.1 75.4 1.0
OE1 D:GLU195 3.3 68.0 1.0
C03 D:9TY404 3.5 90.5 1.0
HG C:SER254 3.6 80.0 1.0
OD1 D:ASP191 3.7 75.4 1.0
HB2 C:SER257 3.8 71.7 1.0
C02 D:9TY404 3.9 90.5 1.0
HD23 D:LEU192 4.2 67.2 1.0
O01 D:9TY404 4.2 90.5 1.0
HB3 D:ASP191 4.2 75.4 1.0
OG C:SER254 4.2 80.0 1.0
CG D:GLU195 4.3 68.0 1.0
CB D:ASP191 4.3 75.4 1.0
H4 D:9TY404 4.3 90.5 1.0
HG3 D:GLU195 4.4 68.0 1.0
O D:ASP191 4.4 75.4 1.0
C08 D:9TY404 4.4 90.5 1.0
O09 D:9TY404 4.5 90.5 1.0
HG2 D:GLU195 4.6 68.0 1.0
HB C:THR256 4.6 69.1 1.0
CB C:SER257 4.7 71.7 1.0
C D:ASP191 4.9 75.4 1.0
C07 D:9TY404 4.9 90.5 1.0
H C:SER257 4.9 71.7 1.0
HA C:SER257 5.0 71.7 1.0
HB2 D:ASP191 5.0 75.4 1.0
H3 D:9TY404 5.0 90.5 1.0

Magnesium binding site 9 out of 24 in 6kqk

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Magnesium binding site 9 out of 24 in the 323 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 323 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:82.7
occ:1.00
O06 E:9TY403 1.9 90.3 1.0
OE2 E:GLU195 1.9 68.1 1.0
OD2 E:ASP191 2.0 75.9 1.0
C04 E:9TY403 2.4 90.3 1.0
O05 E:9TY403 2.8 90.3 1.0
CD E:GLU195 2.9 68.1 1.0
CG E:ASP191 3.1 75.9 1.0
OE1 E:GLU195 3.3 68.1 1.0
HG F:SER254 3.5 78.9 1.0
C03 E:9TY403 3.5 90.3 1.0
HB2 F:SER257 3.7 71.9 1.0
OD1 E:ASP191 3.7 75.9 1.0
C02 E:9TY403 3.9 90.3 1.0
OG F:SER254 4.1 78.9 1.0
O09 E:9TY403 4.2 90.3 1.0
HD23 E:LEU192 4.2 67.4 1.0
HB3 E:ASP191 4.2 75.9 1.0
CG E:GLU195 4.3 68.1 1.0
CB E:ASP191 4.3 75.9 1.0
H4 E:9TY403 4.3 90.3 1.0
HG3 E:GLU195 4.4 68.1 1.0
O E:ASP191 4.4 75.9 1.0
C08 E:9TY403 4.4 90.3 1.0
O01 E:9TY403 4.5 90.3 1.0
HB F:THR256 4.5 69.2 1.0
HG2 E:GLU195 4.6 68.1 1.0
CB F:SER257 4.7 71.9 1.0
H F:SER257 4.8 71.9 1.0
C E:ASP191 4.9 75.9 1.0
C07 E:9TY403 4.9 90.3 1.0
HA F:SER257 4.9 71.9 1.0
HB2 E:ASP191 5.0 75.9 1.0
H3 E:9TY403 5.0 90.3 1.0

Magnesium binding site 10 out of 24 in 6kqk

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Magnesium binding site 10 out of 24 in the 323 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 323 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:91.0
occ:1.00
O01 F:9TY404 1.9 89.7 1.0
O09 F:9TY404 2.0 89.7 1.0
OD1 F:ASP191 2.1 75.0 1.0
C02 F:9TY404 2.3 89.7 1.0
OE2 E:GLU227 2.7 83.1 1.0
CG F:ASP191 3.3 75.0 1.0
HA F:ASP191 3.4 75.0 1.0
OE1 E:GLU227 3.5 83.1 1.0
CD E:GLU227 3.5 83.1 1.0
OE2 E:GLU233 3.8 93.6 1.0
OE1 E:GLU233 3.8 93.6 1.0
C03 F:9TY404 3.8 89.7 1.0
OD2 F:ASP191 4.1 75.0 1.0
CD E:GLU233 4.2 93.6 1.0
CB F:ASP191 4.2 75.0 1.0
CA F:ASP191 4.2 75.0 1.0
HH11 F:ARG130 4.2 98.7 1.0
HD3 F:ARG130 4.3 98.7 1.0
NH1 F:ARG130 4.3 98.7 1.0
HB2 F:ASP191 4.4 75.0 1.0
HH12 F:ARG130 4.4 98.7 1.0
H3 F:9TY404 4.5 89.7 1.0
O05 F:9TY404 4.5 89.7 1.0
H2 F:9TY404 4.6 89.7 1.0
O F:ASP191 4.6 75.0 1.0
HB2 F:SER194 4.7 67.1 1.0
C04 F:9TY404 4.7 89.7 1.0
CZ F:ARG130 4.7 98.7 1.0
C08 F:9TY404 4.7 89.7 1.0
HG F:SER194 4.7 67.1 1.0
C07 F:9TY404 4.8 89.7 1.0
OE2 F:GLU195 4.9 67.5 1.0
CG E:GLU227 4.9 83.1 1.0
C F:ASP191 5.0 75.0 1.0
HG3 F:GLU195 5.0 67.5 1.0

Reference:

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
Page generated: Tue Oct 1 09:51:40 2024

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