Manganese in PDB 5esd: Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+

All present enzymatic activity of Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+:
2.2.1.9;

The structure of Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+, PDB code: 5esd was solved by J.M.Johnston, E.N.M.Jirgis, G.Bashiri, E.M.M.Bulloch, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.625, 138.657, 165.386, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.5

The binding sites of Manganese atom in the Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+ (pdb code 5esd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+, PDB code: 5esd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:34.6 occ:1.00 O21 A:TDP602 1.9 34.1 1.0 O A:HOH728 2.0 30.5 1.0 O12 A:TDP602 2.1 31.0 1.0 OD1 A:ASP469 2.1 33.1 1.0 OD1 A:ASP440 2.3 30.3 1.0 O A:GLY471 2.4 34.6 1.0 P2 A:TDP602 3.1 35.9 1.0 CG A:ASP469 3.1 33.5 1.0 P1 A:TDP602 3.3 33.4 1.0 CG A:ASP440 3.3 30.4 1.0 O11 A:TDP602 3.4 33.0 1.0 OD2 A:ASP469 3.5 33.3 1.0 C A:GLY471 3.6 35.5 1.0 O22 A:TDP602 3.7 33.7 1.0 OD2 A:ASP440 3.8 31.1 1.0 N A:GLY473 3.9 40.2 1.0 O5G A:TDP602 3.9 36.0 1.0 N A:ASP440 3.9 28.8 1.0 N A:ASP469 4.2 31.6 1.0 N A:GLY471 4.2 34.3 1.0 O A:SER467 4.3 28.6 1.0 O23 A:TDP602 4.4 36.9 1.0 N A:GLY472 4.4 37.5 1.0 CA A:GLY472 4.4 38.7 1.0 CB A:ASP469 4.4 33.7 1.0 CB A:ASP440 4.5 29.5 1.0 CA A:GLY471 4.5 35.0 1.0 O13 A:TDP602 4.6 31.1 1.0 N A:LEU441 4.6 29.7 1.0 CA A:ASP469 4.6 33.0 1.0 O A:HOH732 4.6 33.3 1.0 C A:GLY472 4.6 42.0 1.0 CA A:GLY473 4.6 41.9 1.0 C A:ASP469 4.6 33.2 1.0 CA A:GLY439 4.6 28.6 1.0 N A:ASN470 4.7 33.0 1.0 CA A:ASP440 4.7 29.2 1.0 C A:GLY439 4.8 27.8 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:34.4 occ:1.00 O B:HOH709 1.7 30.5 1.0 O13 B:TDP601 1.9 31.2 1.0 OD1 B:ASP440 2.1 32.0 1.0 O B:GLY471 2.1 33.6 1.0 OD1 B:ASP469 2.2 32.8 1.0 O22 B:TDP601 2.2 33.9 1.0 CG B:ASP440 3.1 31.5 1.0 P1 B:TDP601 3.2 32.5 1.0 CG B:ASP469 3.2 33.8 1.0 P2 B:TDP601 3.3 33.1 1.0 C B:GLY471 3.4 35.1 1.0 O11 B:TDP601 3.5 31.7 1.0 OD2 B:ASP469 3.6 33.1 1.0 OD2 B:ASP440 3.7 32.2 1.0 O21 B:TDP601 3.8 32.3 1.0 O5G B:TDP601 3.8 33.7 1.0 N B:ASP440 3.9 29.9 1.0 N B:GLY471 4.0 34.5 1.0 N B:ASP469 4.1 33.1 1.0 N B:GLY473 4.1 42.4 1.0 N B:GLY472 4.3 36.8 1.0 CA B:GLY471 4.3 34.6 1.0 CB B:ASP440 4.3 31.8 1.0 CA B:GLY472 4.3 38.4 1.0 O B:SER467 4.4 32.1 1.0 O B:HOH715 4.5 31.2 1.0 O12 B:TDP601 4.5 31.1 1.0 CB B:ASP469 4.5 33.5 1.0 N B:LEU441 4.5 30.6 1.0 C B:GLY472 4.6 41.4 1.0 CA B:ASP440 4.6 31.0 1.0 CA B:ASP469 4.6 33.4 1.0 O23 B:TDP601 4.6 33.8 1.0 C B:ASP469 4.6 33.5 1.0 N B:ASN470 4.7 33.5 1.0 CA B:GLY439 4.8 30.2 1.0 C B:GLY439 4.8 30.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn602 b:35.5 occ:1.00 O C:GLY471 1.8 37.6 1.0 O21 C:TDP601 1.9 36.8 1.0 OD1 C:ASP440 2.1 36.7 1.0 O C:HOH728 2.1 35.5 1.0 OD1 C:ASP469 2.2 38.2 1.0 O12 C:TDP601 2.3 35.4 1.0 C C:GLY471 3.0 38.8 1.0 CG C:ASP440 3.2 36.5 1.0 CG C:ASP469 3.2 39.6 1.0 P2 C:TDP601 3.2 34.8 1.0 P1 C:TDP601 3.5 33.6 1.0 O11 C:TDP601 3.6 34.0 1.0 OD2 C:ASP469 3.6 38.7 1.0 OD2 C:ASP440 3.8 36.0 1.0 N C:GLY473 3.8 39.5 1.0 O22 C:TDP601 3.9 34.4 1.0 N C:GLY471 3.9 38.8 1.0 N C:ASP440 3.9 34.1 1.0 N C:GLY472 3.9 39.3 1.0 CA C:GLY472 4.0 38.7 1.0 CA C:GLY471 4.1 39.4 1.0 N C:ASP469 4.1 38.6 1.0 O5G C:TDP601 4.2 35.6 1.0 CB C:ASP440 4.3 36.5 1.0 O C:SER467 4.4 36.2 1.0 O23 C:TDP601 4.4 36.6 1.0 C C:GLY472 4.4 39.1 1.0 CB C:ASP469 4.5 40.6 1.0 N C:LEU441 4.6 34.4 1.0 CA C:ASP469 4.6 39.7 1.0 C C:ASP469 4.6 39.4 1.0 CA C:ASP440 4.7 34.9 1.0 CA C:GLY439 4.7 33.8 1.0 N C:ASN470 4.8 39.1 1.0 O13 C:TDP601 4.8 34.1 1.0 C C:GLY439 4.8 33.8 1.0 CA C:GLY473 4.8 41.1 1.0 CG C:LEU441 4.9 36.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of M. Tuberculosis Mend Bound to Thdp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn602 b:29.5 occ:1.00 O22 D:TDP601 1.7 31.5 1.0 O D:GLY471 2.0 30.1 1.0 OD1 D:ASP469 2.2 30.9 1.0 O D:HOH704 2.2 28.1 1.0 OD1 D:ASP440 2.3 29.0 1.0 O13 D:TDP601 2.4 28.0 1.0 CG D:ASP440 3.2 28.8 1.0 P2 D:TDP601 3.2 29.4 1.0 C D:GLY471 3.2 31.9 1.0 CG D:ASP469 3.2 32.0 1.0 P1 D:TDP601 3.5 28.2 1.0 OD2 D:ASP440 3.5 29.1 1.0 O11 D:TDP601 3.7 27.1 1.0 OD2 D:ASP469 3.7 31.6 1.0 N D:ASP440 3.9 27.7 1.0 N D:GLY473 4.0 33.4 1.0 N D:GLY471 4.0 32.6 1.0 O21 D:TDP601 4.1 29.0 1.0 N D:GLY472 4.1 32.9 1.0 N D:ASP469 4.1 30.7 1.0 O23 D:TDP601 4.1 31.2 1.0 O5G D:TDP601 4.2 28.1 1.0 CA D:GLY472 4.2 33.5 1.0 CA D:GLY471 4.2 32.4 1.0 O D:SER467 4.3 27.5 1.0 CB D:ASP440 4.4 29.2 1.0 CB D:ASP469 4.5 32.0 1.0 N D:LEU441 4.5 28.1 1.0 C D:GLY472 4.6 37.2 1.0 CA D:ASP469 4.6 32.2 1.0 C D:ASP469 4.6 31.7 1.0 CA D:GLY439 4.6 26.3 1.0 CA D:ASP440 4.6 27.6 1.0 O D:HOH717 4.7 28.6 1.0 O D:HOH742 4.7 29.7 1.0 C D:GLY439 4.7 27.1 1.0 N D:ASN470 4.7 31.6 1.0 O12 D:TDP601 4.8 27.3 1.0 CD1 D:LEU441 4.9 30.3 1.0 CA D:GLY473 5.0 35.6 1.0

E.N.Jirgis, G.Bashiri, E.M.Bulloch, J.M.Johnston, E.N.Baker. Structural Views Along the Mycobacterium Tuberculosis Mend Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms. Structure V. 24 1167 2016.
ISSN: ISSN 0969-2126
PubMed: 27291649
DOI: 10.1016/J.STR.2016.04.018