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Magnesium in PDB 4yb4: Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh

Enzymatic activity of Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh

All present enzymatic activity of Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh:
1.1.1.87;

Protein crystallography data

The structure of Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh, PDB code: 4yb4 was solved by K.Takahashi, T.Tomita, T.Kuzuyama, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.663, 159.663, 148.517, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh (pdb code 4yb4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh, PDB code: 4yb4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4yb4

Go back to Magnesium Binding Sites List in 4yb4
Magnesium binding site 1 out of 4 in the Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:25.3
occ:1.00
 OD1 A:ASP228 1.9 25.3 1.0
OD2 B:ASP204 2.0 26.6 1.0
O B:HOH582 2.1 22.7 1.0
O A:HOH563 2.1 21.8 1.0
OAF A:48Y402 2.1 26.1 1.0
OAD A:48Y402 2.3 26.0 1.0
CAK A:48Y402 3.0 26.4 1.0
CG A:ASP228 3.1 25.1 1.0
CG B:ASP204 3.1 27.3 1.0
CAM A:48Y402 3.1 27.8 1.0
OD2 A:ASP228 3.6 24.8 1.0
CB B:ASP204 3.7 27.1 1.0
OD1 A:ASP232 3.7 28.8 1.0
NH1 A:ARG98 3.8 28.3 1.0
O A:ASP228 4.0 22.7 1.0
O A:HOH537 4.1 22.9 1.0
OAB A:48Y402 4.1 26.9 1.0
OD1 B:ASP204 4.2 28.5 1.0
CG A:ASP232 4.3 28.8 1.0
CB A:ASP228 4.3 23.6 1.0
NZ B:LYS171 4.3 26.4 1.0
CAL A:48Y402 4.4 27.4 1.0
CAN A:48Y402 4.4 28.6 1.0
O A:HOH512 4.4 26.4 1.0
OD2 A:ASP232 4.5 28.3 1.0
CA A:ASP228 4.5 23.7 1.0
C A:ASP228 4.6 24.5 1.0
OAC A:48Y402 4.6 25.1 1.0
NH1 A:ARG118 4.6 29.4 1.0
O A:VAL259 4.7 24.1 1.0
OAG A:48Y402 4.7 24.9 1.0
O A:HOH566 4.9 27.4 1.0
C5N A:NAI403 4.9 29.9 1.0

Magnesium binding site 2 out of 4 in 4yb4

Go back to Magnesium Binding Sites List in 4yb4
Magnesium binding site 2 out of 4 in the Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:25.0
occ:1.00
 OD1 B:ASP228 2.1 27.4 1.0
OD2 A:ASP204 2.1 23.2 1.0
O B:HOH585 2.1 19.8 1.0
OAF B:48Y401 2.1 24.2 1.0
O B:HOH584 2.1 32.8 1.0
OAD B:48Y401 2.2 22.6 1.0
CAK B:48Y401 3.0 24.8 1.0
CAM B:48Y401 3.1 23.4 1.0
CG B:ASP228 3.2 25.1 1.0
CG A:ASP204 3.2 22.8 1.0
OD2 B:ASP228 3.7 27.0 1.0
NH1 B:ARG98 3.7 28.8 1.0
OD1 B:ASP232 3.8 26.8 1.0
CB A:ASP204 3.8 22.3 1.0
O B:ASP228 4.0 23.0 1.0
O B:HOH531 4.1 26.8 1.0
O B:HOH598 4.2 24.4 1.0
OAB B:48Y401 4.2 26.4 1.0
NZ A:LYS171 4.2 23.6 1.0
OD1 A:ASP204 4.3 21.2 1.0
CG B:ASP232 4.3 26.4 1.0
CAN B:48Y401 4.4 23.6 1.0
CAL B:48Y401 4.4 24.1 1.0
CB B:ASP228 4.4 24.4 1.0
O B:VAL259 4.5 18.0 1.0
OD2 B:ASP232 4.5 26.1 1.0
C5N B:NAI402 4.6 51.7 1.0
CA B:ASP228 4.6 24.2 1.0
NH1 B:ARG118 4.6 31.9 1.0
OAG B:48Y401 4.6 25.1 1.0
C B:ASP228 4.7 23.8 1.0
OAC B:48Y401 4.7 25.2 1.0
O B:HOH530 4.8 15.9 1.0
CG1 B:VAL259 4.9 21.3 1.0
CZ B:ARG98 4.9 27.1 1.0

Magnesium binding site 3 out of 4 in 4yb4

Go back to Magnesium Binding Sites List in 4yb4
Magnesium binding site 3 out of 4 in the Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:25.5
occ:1.00
 OD1 C:ASP228 2.0 28.6 1.0
O C:HOH593 2.0 25.5 1.0
OD2 D:ASP204 2.1 27.5 1.0
OAB C:48Y402 2.1 26.2 1.0
OAD C:48Y402 2.2 25.6 1.0
O C:HOH559 2.3 19.9 1.0
CAK C:48Y402 3.0 27.4 1.0
CAM C:48Y402 3.1 28.0 1.0
CG C:ASP228 3.2 26.8 1.0
CG D:ASP204 3.2 26.6 1.0
NH1 C:ARG98 3.7 28.7 1.0
CB D:ASP204 3.8 25.9 1.0
OD2 C:ASP228 3.8 27.2 1.0
OD1 C:ASP232 3.9 23.1 1.0
O C:ASP228 4.1 21.3 1.0
OAF C:48Y402 4.2 28.7 1.0
OD1 D:ASP204 4.2 26.1 1.0
O C:HOH597 4.3 24.1 1.0
NZ D:LYS171 4.3 24.4 1.0
CB C:ASP228 4.3 25.1 1.0
CAL C:48Y402 4.3 28.0 1.0
CAN C:48Y402 4.3 29.2 1.0
CG C:ASP232 4.4 24.1 1.0
O C:HOH580 4.4 24.2 1.0
CA C:ASP228 4.4 23.4 1.0
OAG C:48Y402 4.5 29.9 1.0
OD2 C:ASP232 4.5 24.5 1.0
C C:ASP228 4.5 22.6 1.0
OAC C:48Y402 4.5 26.8 1.0
O C:VAL259 4.7 19.9 1.0
C5N C:NAI403 4.8 25.7 1.0
NH1 C:ARG118 4.9 26.0 1.0
O D:HOH586 4.9 16.8 1.0
CZ C:ARG98 5.0 27.1 1.0

Magnesium binding site 4 out of 4 in 4yb4

Go back to Magnesium Binding Sites List in 4yb4
Magnesium binding site 4 out of 4 in the Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium Ion (II) and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:27.4
occ:1.00
 OD1 D:ASP228 2.0 31.8 1.0
OD2 C:ASP204 2.0 24.4 1.0
OAB D:48Y401 2.0 22.5 1.0
O D:HOH574 2.0 18.9 1.0
O D:HOH573 2.1 24.2 1.0
OAD D:48Y401 2.4 23.0 1.0
CAK D:48Y401 2.9 22.9 1.0
CG C:ASP204 3.1 23.3 1.0
CG D:ASP228 3.1 27.9 1.0
CAM D:48Y401 3.2 22.8 1.0
CB C:ASP204 3.6 22.2 1.0
NH1 D:ARG98 3.7 31.6 1.0
OD1 D:ASP232 3.8 28.8 1.0
OD2 D:ASP228 3.8 29.3 1.0
O D:ASP228 3.9 23.6 1.0
NZ C:LYS171 4.1 24.1 1.0
OAF D:48Y401 4.1 23.4 1.0
OD1 C:ASP204 4.1 22.4 1.0
O D:HOH537 4.2 26.9 1.0
CG D:ASP232 4.2 28.4 1.0
CB D:ASP228 4.2 26.6 1.0
OD2 D:ASP232 4.3 27.7 1.0
CA D:ASP228 4.4 25.3 1.0
CAL D:48Y401 4.4 22.7 1.0
O D:HOH520 4.4 20.6 1.0
CAN D:48Y401 4.4 22.9 1.0
C D:ASP228 4.4 24.1 1.0
OAG D:48Y401 4.6 23.8 1.0
O D:VAL259 4.6 20.4 1.0
NH1 D:ARG118 4.6 32.2 1.0
OAC D:48Y401 4.7 23.2 1.0
C5N D:NAI402 4.8 51.5 1.0
O C:HOH595 4.8 19.6 1.0
CG1 D:VAL259 5.0 21.4 1.0
CZ D:ARG98 5.0 29.5 1.0

Reference:

K.Takahashi, T.Tomita, T.Kuzuyama, M.Nishiyama. Structure of Homoisocitrate Dehydrogenase From Thermus Thermophilus in Complex with Homoisocitrate, Magnesium(II) and Nadh To Be Published.
Page generated: Tue Aug 12 04:08:09 2025

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