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Calcium in PDB 3vl4: 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 410 Mpa

Enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 410 Mpa

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 410 Mpa:
1.1.1.85;

Protein crystallography data

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 410 Mpa, PDB code: 3vl4 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) 48.63 / 1.88
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.610, 57.633, 75.504, 90.00, 118.98, 90.00
R / Rfree (%) 15.6 / 21.3

Other elements in 3vl4:

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 410 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 410 Mpa (pdb code 3vl4). 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 410 Mpa, PDB code: 3vl4:

Calcium binding site 1 out of 1 in 3vl4

Go back to Calcium Binding Sites List in 3vl4
Calcium binding site 1 out of 1 in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 410 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 410 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:10.8
occ:1.00
OD1 A:ASP249 2.2 14.0 1.0
O A:HOH552 2.3 20.8 1.0
OD2 A:ASP253 2.3 14.7 1.0
O3 A:IPM401 2.3 12.0 1.0
O A:HOH503 2.4 11.0 1.0
O1 A:IPM401 2.6 10.6 1.0
C1 A:IPM401 3.2 16.4 1.0
C2 A:IPM401 3.4 12.1 1.0
CG A:ASP253 3.4 13.6 1.0
CG A:ASP249 3.4 12.5 1.0
O A:ASP249 3.9 7.3 1.0
OD1 A:ASP253 3.9 15.8 1.0
OD2 A:ASP249 4.1 11.8 1.0
O A:HOH707 4.3 39.2 1.0
O2 A:IPM401 4.3 16.1 1.0
C4 A:IPM401 4.4 13.1 1.0
C A:ASP249 4.5 8.5 1.0
O A:HOH766 4.5 35.6 1.0
O5 A:IPM401 4.5 10.7 1.0
C3 A:IPM401 4.5 13.3 1.0
CB A:ASP249 4.5 9.0 1.0
CA A:ASP249 4.5 8.1 1.0
O A:HOH771 4.5 37.2 1.0
CB A:ASP253 4.6 7.9 1.0
NH2 A:ARG107 4.7 19.0 1.0
NH1 A:ARG136 4.8 8.5 1.0
O4 A:IPM401 4.9 10.6 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: Sat Dec 12 04:34:22 2020

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