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Magnesium in PDB 3vml: Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O

Enzymatic activity of Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O

All present enzymatic activity of Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O:
1.1.1.85;

Protein crystallography data

The structure of Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O, PDB code: 3vml was solved by T.Nagae, N.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.25 / 1.56
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.008, 107.523, 83.109, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 3vml:

The structure of Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O (pdb code 3vml). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O, PDB code: 3vml:

Magnesium binding site 1 out of 1 in 3vml

Go back to Magnesium Binding Sites List in 3vml
Magnesium binding site 1 out of 1 in the Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella Oneidensis Mr-1 (O) and Shewanella Benthica DB21 Mt-2 (M) From N-Terminal: 20% O Middle 70% M Residual 10% O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:10.2
occ:1.00
 O A:HOH952 2.1 9.5 1.0
OD1 A:ASP249 2.1 10.1 1.0
O A:HOH963 2.1 11.0 1.0
O3 A:IPM401 2.1 9.1 1.0
O1 A:IPM401 2.2 10.6 1.0
C1 A:IPM401 2.9 11.0 1.0
C2 A:IPM401 3.1 10.7 1.0
CG A:ASP249 3.2 10.0 1.0
OD2 A:ASP249 3.7 9.6 1.0
O A:ASP249 4.1 8.8 1.0
O2 A:IPM401 4.1 11.8 1.0
OD1 A:ASP253 4.1 11.8 1.0
C4 A:IPM401 4.2 13.5 1.0
O A:HOH530 4.2 14.1 1.0
O5 A:IPM401 4.2 11.8 1.0
O A:HOH557 4.2 17.1 1.0
C3 A:IPM401 4.3 8.1 1.0
CB A:ASP249 4.3 8.3 1.0
O A:HOH797 4.4 31.6 1.0
CG A:ASP253 4.4 12.8 1.0
NH2 A:ARG107 4.4 12.3 1.0
OD2 A:ASP253 4.5 12.3 1.0
CA A:ASP249 4.5 8.8 1.0
O4 A:IPM401 4.5 10.8 1.0
C A:ASP249 4.6 8.9 1.0
O A:HOH645 4.6 24.1 1.0
NH1 A:ARG136 4.6 9.1 1.0

Reference:

Y.Hamajima, T.Nagae, N.Watanabe, C.Kato. Structure Analysis of Chimeric 3-Isopropylmalate Dehydrogenase Between the Obligate Piezophile Shewanella Benthica DB21MT-2 and the Nonpiezophile Shewanella Oneidensis Mr-1 To Be Published.
Page generated: Mon Aug 11 04:39:19 2025

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