Magnesium in PDB 3znu: Crystal Structure of Clcf in Crystal Form 2

The structure of Crystal Structure of Clcf in Crystal Form 2, PDB code: 3znu was solved by C.Roth, J.A.D.Groening, S.R.Kaschabek, M.Schloemann, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.828 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.242, 103.574, 141.667, 90.00, 90.00, 90.00
R / Rfree (%)	15.73 / 19.09

The structure of Crystal Structure of Clcf in Crystal Form 2 also contains other interesting chemical elements:

Chlorine

(Cl)

14 atoms

The binding sites of Magnesium atom in the Crystal Structure of Clcf in Crystal Form 2 (pdb code 3znu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Clcf in Crystal Form 2, PDB code: 3znu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Clcf in Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Clcf in Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1097 b:39.7 occ:1.00 O D:HOH2028 2.0 39.4 1.0 O D:HOH2122 2.1 38.8 1.0 O D:HOH2046 2.1 39.8 1.0 O D:HOH2030 2.1 38.8 1.0 O D:HOH2123 2.1 39.5 1.0 O D:HOH2124 2.2 39.5 1.0 HB2 D:LEU11 3.6 29.3 1.0 HA D:ARG13 3.8 49.2 1.0 HG2 D:ARG13 4.1 59.2 1.0 OE2 D:GLU20 4.2 32.1 1.0 O D:PRO12 4.3 29.1 1.0 OE1 D:GLU20 4.4 40.8 1.0 HD13 D:LEU11 4.4 35.2 1.0 O D:HOH2037 4.4 38.7 1.0 O D:LEU11 4.4 26.7 1.0 O D:HOH2017 4.5 25.0 1.0 CB D:LEU11 4.6 24.4 1.0 O D:HOH2060 4.6 46.3 1.0 CD D:GLU20 4.7 33.7 1.0 HB3 D:LEU11 4.7 29.3 1.0 CA D:ARG13 4.8 41.0 1.0 C D:PRO12 4.9 22.9 1.0 C D:LEU11 5.0 27.5 1.0 CG D:ARG13 5.0 49.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Clcf in Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Clcf in Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1101 b:44.2 occ:1.00 O D:HOH2112 2.1 44.1 1.0 O D:HOH2126 2.1 43.9 1.0 O D:HOH2108 2.1 44.0 1.0 O D:HOH2130 2.1 44.6 1.0 O D:HOH2129 2.1 44.6 1.0 HO2 D:EDO1098 3.8 25.7 1.0 HB3 D:ASP80 3.8 21.6 1.0 O D:HOH2110 4.1 25.5 1.0 O D:VAL81 4.3 15.1 1.0 O2 D:EDO1098 4.3 21.4 1.0 OD1 D:ASP80 4.4 33.7 1.0 H D:VAL81 4.5 16.1 1.0 O J:HOH2094 4.5 28.6 1.0 O A:HOH2013 4.6 39.4 1.0 HB3 D:GLU82 4.6 33.8 1.0 O D:HOH2111 4.6 27.5 1.0 CB D:ASP80 4.7 18.0 1.0 HA D:ASP80 4.9 18.0 1.0 O J:HOH2098 4.9 51.7 1.0 CG D:ASP80 4.9 31.5 1.0 O D:HOH2125 4.9 45.0 1.0 N D:VAL81 5.0 13.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Clcf in Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Clcf in Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1095 b:42.8 occ:1.00 O H:HOH2030 2.0 43.1 1.0 O H:HOH2031 2.1 42.3 1.0 O H:HOH2043 2.1 42.9 1.0 O H:HOH2122 2.1 42.7 1.0 O H:HOH2123 2.1 42.9 1.0 HB2 H:LEU11 3.8 28.3 1.0 OE2 H:GLU20 3.9 29.8 1.0 HA H:ARG13 3.9 39.6 1.0 OE1 H:GLU20 3.9 29.8 1.0 O H:HOH2008 4.0 42.7 1.0 CD H:GLU20 4.3 35.8 1.0 O H:PRO12 4.4 25.3 1.0 O H:LEU11 4.6 28.4 1.0 HD13 H:LEU11 4.6 33.6 1.0 CB H:LEU11 4.6 23.6 1.0 HB3 H:LEU11 4.6 28.3 1.0 CA H:ARG13 4.8 33.0 1.0 O H:HOH2017 4.9 32.5 1.0 HB3 D:PRO75 4.9 30.9 1.0 O H:HOH2035 5.0 32.4 1.0 O H:HOH2012 5.0 51.3 1.0

C.Roth, A.D.Janosch, S.R.Kaschabek, M.Schloemann, N.Straeter. Crystal Structure and Catalytic Mechanism of Chloromuconolactone Dehalogenase Clcf From Rhodococcus Opacus 1CP. Mol.Microbiol. V. 88 254 2013.
ISSN: ISSN 0950-382X
PubMed: 23421784
DOI: 10.1111/MMI.12182