Lead in PDB 5tao: Haloferax Volcanii Malate Synthase Lead(II) Complex

All present enzymatic activity of Haloferax Volcanii Malate Synthase Lead(II) Complex:
2.3.3.9;

The structure of Haloferax Volcanii Malate Synthase Lead(II) Complex, PDB code: 5tao was solved by B.R.Howard, M.J.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.81 / 2.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	155.353, 155.353, 139.412, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 21.7

The structure of Haloferax Volcanii Malate Synthase Lead(II) Complex also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Chlorine	(Cl)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Lead atom in the Haloferax Volcanii Malate Synthase Lead(II) Complex (pdb code 5tao). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 4 binding sites of Lead where determined in the Haloferax Volcanii Malate Synthase Lead(II) Complex, PDB code: 5tao:
Jump to Lead binding site number: 1; 2; 3; 4;

Lead binding site 1 out of 4 in the Haloferax Volcanii Malate Synthase Lead(II) Complex


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Haloferax Volcanii Malate Synthase Lead(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb505 b:44.2 occ:1.00 OD1 A:ASP196 2.6 31.0 1.0 O2 A:GLV503 2.6 44.0 1.0 OE1 A:GLU161 2.7 33.9 1.0 O3 A:GLV503 2.7 67.2 1.0 OE2 A:GLU161 2.7 59.5 1.0 O A:HOH779 2.8 28.8 0.5 C2 A:GLV503 2.9 57.5 1.0 CD A:GLU161 3.0 40.4 1.0 OD2 A:ASP196 3.0 38.9 1.0 CG A:ASP196 3.1 34.4 1.0 O A:HOH648 3.5 42.9 1.0 C1 A:GLV503 4.0 77.7 1.0 CG A:GLU161 4.5 42.7 1.0 O A:ASP196 4.6 30.3 1.0 NH2 A:ARG89 4.6 34.6 1.0 CB A:ASP196 4.6 32.6 1.0 O1 A:GLV503 4.6 88.4 1.0 NE A:ARG89 4.7 33.5 1.0 CB A:SER159 4.8 31.5 1.0 O A:HOH789 4.9 39.6 0.5 N A:GLY160 4.9 27.4 1.0 PB A:PB507 4.9 89.8 1.0 O A:HOH740 4.9 76.8 1.0 O A:HOH788 5.0 54.7 1.0

Lead binding site 2 out of 4 in the Haloferax Volcanii Malate Synthase Lead(II) Complex


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Haloferax Volcanii Malate Synthase Lead(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb506 b:50.4 occ:1.00 O3 A:GLV504 2.0 22.9 1.0 OD2 A:ASP192 2.2 42.4 1.0 OE1 A:GLU123 2.6 34.6 1.0 OD2 A:ASP52 2.8 32.8 1.0 O3 A:GLV502 2.9 62.3 1.0 C2 A:GLV504 2.9 52.2 1.0 OE2 A:GLU51 3.0 38.1 1.0 OE1 A:GLU158 3.0 38.4 1.0 OE2 A:GLU158 3.0 32.2 1.0 CD A:GLU158 3.3 36.1 1.0 O2 A:GLV504 3.3 55.4 1.0 CG A:ASP192 3.4 39.2 1.0 OE1 A:GLU51 3.4 36.7 1.0 CD A:GLU123 3.5 40.4 1.0 CG A:ASP52 3.5 44.1 1.0 OD1 A:ASP52 3.6 44.3 1.0 CG A:GLU123 3.6 34.4 1.0 CD A:GLU51 3.6 36.2 1.0 C2 A:GLV502 4.0 64.0 1.0 CB A:ASP192 4.1 34.9 1.0 C1 A:GLV504 4.2 66.8 1.0 OD1 A:ASP192 4.3 45.9 1.0 CB A:PRO122 4.4 32.8 1.0 NH1 A:ARG84 4.5 42.4 1.0 O A:HOH665 4.5 44.6 1.0 O1 A:GLV502 4.6 47.0 1.0 O1 A:GLV504 4.6 80.0 1.0 OE2 A:GLU123 4.6 32.7 1.0 CG A:GLU158 4.7 40.9 1.0 C1 A:GLV502 4.8 60.9 1.0 O2 A:GLV502 4.9 60.2 1.0 CB A:ASP52 5.0 38.7 1.0

Lead binding site 3 out of 4 in the Haloferax Volcanii Malate Synthase Lead(II) Complex


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of Haloferax Volcanii Malate Synthase Lead(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb507 b:89.8 occ:1.00 OD1 A:ASP90 2.7 44.3 1.0 OD2 A:ASP90 3.1 56.6 1.0 O2 A:GLV503 3.1 44.0 1.0 O A:HOH838 3.1 48.6 1.0 O A:HOH648 3.2 42.9 1.0 CG A:ASP90 3.2 44.0 1.0 C2 A:GLV503 3.3 57.5 1.0 O3 A:GLV503 3.3 67.2 1.0 O A:HOH833 3.3 71.6 1.0 OE2 A:GLU161 3.4 59.5 1.0 C1 A:GLV503 4.2 77.7 1.0 NE A:ARG89 4.3 33.5 1.0 CG A:ARG89 4.3 30.5 1.0 CD A:ARG89 4.3 30.7 1.0 O A:HOH740 4.4 76.8 1.0 CL A:CL515 4.4 40.0 1.0 CD A:GLU161 4.6 40.4 1.0 O A:HOH745 4.6 38.0 0.5 CB A:ASP90 4.7 37.8 1.0 PB A:PB505 4.9 44.2 1.0 O A:HOH800 4.9 41.0 0.5 O A:HOH847 5.0 69.7 1.0 O1 A:GLV503 5.0 88.4 1.0

Lead binding site 4 out of 4 in the Haloferax Volcanii Malate Synthase Lead(II) Complex


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 4 of Haloferax Volcanii Malate Synthase Lead(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb508 b:0.9 occ:1.00 O A:HOH752 2.6 81.0 1.0 OD2 A:ASP348 3.0 66.6 1.0 OD1 A:ASP348 3.0 67.5 1.0 OD2 A:ASP344 3.0 94.4 1.0 OD1 A:ASP344 3.0 64.3 1.0 CG A:ASP344 3.3 74.9 1.0 CG A:ASP348 3.3 68.9 1.0 O A:HOH784 3.5 71.9 1.0 NH2 A:ARG427 3.6 74.8 1.0 O A:HOH716 3.6 56.9 1.0 O A:HOH668 3.8 65.4 1.0 CZ A:ARG427 4.5 72.5 1.0 CB A:ASP344 4.7 69.5 1.0 CB A:ASP348 4.8 67.3 1.0 O A:ASP344 4.8 52.7 1.0 NH1 A:ARG427 4.9 78.3 1.0

M.J.Adams, B.R.Howard. X-Ray Analysis of Lead(II) Binding to Haloferax Volcanii Malate Synthase The Journal of the Utah V. 93 77 2016ACADEMY.
ISSN: ISSN 0083-4823