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Calcium in PDB 3vl7: 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa

Enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa:
1.1.1.85;

Protein crystallography data

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa, PDB code: 3vl7 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) 48.57 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.135, 57.561, 75.067, 90.00, 118.67, 90.00
R / Rfree (%) 16.6 / 24.4

Other elements in 3vl7:

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa (pdb code 3vl7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa, PDB code: 3vl7:

Calcium binding site 1 out of 1 in 3vl7

Go back to Calcium Binding Sites List in 3vl7
Calcium binding site 1 out of 1 in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.8
occ:1.00
OD1 A:ASP249 2.1 13.4 1.0
O3 A:IPM401 2.2 10.8 1.0
OD2 A:ASP253 2.5 12.9 1.0
O A:HOH518 2.5 7.5 1.0
O A:HOH600 2.5 22.3 1.0
O1 A:IPM401 2.6 13.7 1.0
C1 A:IPM401 3.1 19.2 1.0
C2 A:IPM401 3.3 17.4 1.0
CG A:ASP249 3.3 13.3 1.0
CG A:ASP253 3.5 10.7 1.0
OD1 A:ASP253 3.8 11.3 1.0
O A:ASP249 3.9 6.9 1.0
OD2 A:ASP249 4.0 17.4 1.0
O2 A:IPM401 4.3 21.9 1.0
CB A:ASP249 4.4 9.3 1.0
C A:ASP249 4.5 7.6 1.0
CA A:ASP249 4.5 8.0 1.0
C4 A:IPM401 4.5 17.1 1.0
O5 A:IPM401 4.5 16.5 1.0
O A:HOH664 4.6 24.1 1.0
C3 A:IPM401 4.6 16.8 1.0
CB A:ASP253 4.7 8.4 1.0
NH1 A:ARG107 4.7 18.9 1.0
NH1 A:ARG136 4.8 4.1 1.0

Reference:

T.Nagae, T.Kawamura, L.M.G.Chavas, K.Niwa, M.Hasegawa, C.Kato, N.Watanabe. High-Pressure-Induced Water Penetration Into 3-Isopropylmalate Dehydrogenase Acta Crystallogr.,Sect.D V. 68 300 2012.
ISSN: ISSN 0907-4449
PubMed: 22349232
DOI: 10.1107/S0907444912001862
Page generated: Tue Jul 8 17:38:46 2025

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