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

Enzymatic activity of 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;

Protein crystallography data

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

Manganese Binding Sites:

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 5esd

Go back to Manganese Binding Sites List in 5esd
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 5esd

Go back to Manganese Binding Sites List in 5esd
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 5esd

Go back to Manganese Binding Sites List in 5esd
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 5esd

Go back to Manganese Binding Sites List in 5esd
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

Reference:

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
Page generated: Sun Oct 6 00:09:19 2024

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