Calcium in PDB 3vl6: 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 580 Mpa

Enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 580 Mpa

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 580 Mpa:
1.1.1.85;

Protein crystallography data

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 580 Mpa, PDB code: 3vl6 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)*	48.45 / 2.07
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	103.144, 57.380, 75.213, 90.00, 118.76, 90.00
*R / R_free (%)*	17.4 / 23.5

Other elements in 3vl6:

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 580 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 580 Mpa (pdb code 3vl6). 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 580 Mpa, PDB code: 3vl6:

Calcium binding site 1 out of 1 in 3vl6

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Calcium Binding Sites List in 3vl6

Calcium binding site 1 out of 1 in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 580 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 580 Mpa within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca402 b:13.2 occ:1.00	O	A:HOH637	2.2	16.9	1.0
	O3	A:IPM401	2.3	7.7	1.0
	OD1	A:ASP249	2.3	16.2	1.0
	OD2	A:ASP253	2.4	15.8	1.0
	O1	A:IPM401	2.5	6.2	1.0
	O	A:HOH502	2.6	6.8	1.0
	C1	A:IPM401	3.1	14.6	1.0
	C2	A:IPM401	3.3	14.9	1.0
	CG	A:ASP253	3.5	11.9	1.0
	CG	A:ASP249	3.5	13.6	1.0
	O	A:ASP249	3.9	7.8	1.0
	OD1	A:ASP253	4.0	13.0	1.0
	OD2	A:ASP249	4.1	17.9	1.0
	O	A:HOH694	4.3	30.3	1.0
	O2	A:IPM401	4.3	16.4	1.0
	C4	A:IPM401	4.4	16.2	1.0
	O5	A:IPM401	4.4	13.1	1.0
	C3	A:IPM401	4.4	14.6	1.0
	CB	A:ASP249	4.6	12.0	1.0
	CB	A:ASP253	4.6	6.6	1.0
	C	A:ASP249	4.6	9.8	1.0
	O	A:HOH610	4.6	24.3	1.0
	CA	A:ASP249	4.7	9.6	1.0
	NH2	A:ARG107	4.8	13.8	1.0
	NH1	A:ARG136	4.8	7.0	1.0
	O4	A:IPM401	4.9	15.8	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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