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Calcium in PDB 3vkz: 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure

Enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure

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

Protein crystallography data

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure, PDB code: 3vkz 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) 22.15 / 1.84
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.797, 59.003, 76.754, 90.00, 119.07, 90.00
R / Rfree (%) 14.2 / 18.5

Other elements in 3vkz:

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure 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 Atmospheric Pressure (pdb code 3vkz). 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 Atmospheric Pressure, PDB code: 3vkz:

Calcium binding site 1 out of 1 in 3vkz

Go back to Calcium Binding Sites List in 3vkz
Calcium binding site 1 out of 1 in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure


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 Atmospheric Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:15.8
occ:1.00
OD1 A:ASP249 2.2 16.4 1.0
O3 A:IPM401 2.3 17.4 1.0
O A:HOH539 2.4 27.4 1.0
OD2 A:ASP253 2.4 19.8 1.0
O1 A:IPM401 2.5 15.0 1.0
O A:HOH501 2.5 15.9 1.0
C1 A:IPM401 3.2 21.1 1.0
C2 A:IPM401 3.4 16.8 1.0
CG A:ASP253 3.4 18.2 1.0
CG A:ASP249 3.4 18.1 1.0
OD1 A:ASP253 3.9 16.3 1.0
O A:ASP249 4.0 13.7 1.0
OD2 A:ASP249 4.1 19.4 1.0
O2 A:IPM401 4.3 19.4 1.0
C4 A:IPM401 4.4 16.6 1.0
O A:HOH636 4.5 43.5 1.0
O5 A:IPM401 4.5 17.5 1.0
CB A:ASP249 4.5 14.0 1.0
C3 A:IPM401 4.5 15.6 1.0
C A:ASP249 4.5 12.6 1.0
CA A:ASP249 4.5 12.1 1.0
CB A:ASP253 4.7 14.0 1.0
NH2 A:ARG107 4.8 22.4 1.0
NH1 A:ARG136 4.9 17.0 1.0
O4 A:IPM401 4.9 18.6 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 04:34:18 2020

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