Chlorine in PDB 3vmk: 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2:
1.1.1.85;

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2, PDB code: 3vmk 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)	25.77 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.972, 59.208, 119.779, 90.00, 95.12, 90.00
R / Rfree (%)	19.3 / 23.2

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2 (pdb code 3vmk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2, PDB code: 3vmk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:10.2 occ:1.00 O A:HOH747 3.0 22.0 1.0 N A:ILE142 3.2 9.5 1.0 N A:LEU246 3.3 6.9 1.0 CA A:GLY141 3.6 11.6 1.0 CG2 A:ILE142 3.7 9.6 1.0 CB A:ASN245 3.7 8.3 1.0 CB A:LEU246 3.8 11.2 1.0 O A:HOH517 3.8 28.1 1.0 N A:ASN245 3.8 7.4 1.0 C A:GLY141 3.9 12.0 1.0 CE A:MET163 4.0 12.2 1.0 OG A:SER244 4.0 17.4 1.0 CE1 A:TYR165 4.1 11.6 1.0 CA A:ASN245 4.1 7.6 1.0 CB A:ILE142 4.1 10.3 1.0 CA A:LEU246 4.1 8.7 1.0 CG A:MET163 4.2 8.4 1.0 OH A:TYR165 4.2 9.8 1.0 C A:ASN245 4.2 8.0 1.0 CB A:SER244 4.2 12.0 1.0 CA A:ILE142 4.2 9.6 1.0 SD A:MET163 4.5 10.9 1.0 CZ A:TYR165 4.6 9.2 1.0 C A:SER244 4.6 8.1 1.0 O A:GLY140 4.7 11.4 1.0 N A:GLY141 4.7 9.3 1.0 CD1 A:TYR143 4.9 10.4 1.0 N A:TYR143 5.0 9.5 1.0

Chlorine binding site 2 out of 2 in the 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 3-Isopropylmalate Dehydrogenase From Shewanella Benthica DB21 Mt-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:11.8 occ:1.00 O B:HOH803 2.9 17.5 1.0 N B:ILE142 3.2 11.4 1.0 N B:LEU246 3.3 9.8 1.0 CA B:GLY141 3.6 12.2 1.0 N B:ASN245 3.7 10.9 1.0 CB B:ASN245 3.7 11.2 1.0 CB B:LEU246 3.8 12.6 1.0 CE B:MET163 3.8 19.4 1.0 CG2 B:ILE142 3.8 12.5 1.0 O B:HOH538 3.9 34.8 1.0 C B:GLY141 3.9 12.4 1.0 CG B:MET163 4.0 9.8 1.0 CA B:ASN245 4.0 10.1 1.0 CE1 B:TYR165 4.1 11.9 1.0 C B:ASN245 4.1 10.1 1.0 CB B:ILE142 4.1 10.0 1.0 CA B:LEU246 4.2 8.7 1.0 OH B:TYR165 4.2 10.7 1.0 CA B:ILE142 4.3 10.6 1.0 CB B:SER244 4.3 16.3 1.0 OG B:SER244 4.4 21.0 1.0 SD B:MET163 4.4 11.8 1.0 C B:SER244 4.6 11.5 1.0 CZ B:TYR165 4.6 11.5 1.0 O B:GLY140 4.7 12.9 1.0 N B:GLY141 4.8 10.8 1.0 N B:TYR143 5.0 12.1 1.0 CD1 B:TYR143 5.0 11.9 1.0

T.Nagae, C.Kato, N.Watanabe. Structural Analysis of 3-Isopropylmalate Dehydrogenase From the Obligate Piezophile Shewanella Benthica DB21MT-2 and the Nonpiezophile Shewanella Oneidensis Mr-1 Acta Crystallogr.,Sect.F V. 68 265 2012.
ISSN: ESSN 1744-3091
PubMed: 22442218
DOI: 10.1107/S1744309112001443