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Magnesium in PDB 1oy0: The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping

Enzymatic activity of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping

All present enzymatic activity of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping:
2.1.2.11;

Protein crystallography data

The structure of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping, PDB code: 1oy0 was solved by B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, T.O.Yeates, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.53 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.800, 106.800, 224.400, 90.00, 90.00, 120.00
R / Rfree (%) 23.9 / 27.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping (pdb code 1oy0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping, PDB code: 1oy0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1oy0

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Magnesium binding site 1 out of 5 in the The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:48.9
occ:1.00
 OD2 A:ASP62 1.9 50.4 1.0
O A:HOH928 2.8 27.6 1.0
CG A:ASP62 2.9 50.4 1.0
O A:HOH914 3.0 40.8 1.0
OE1 A:GLU133 3.0 79.0 1.0
OD1 A:ASP62 3.5 50.4 1.0
CB A:ASP62 4.0 50.4 1.0
CD A:GLU133 4.2 79.0 1.0
OG1 A:THR74 4.2 26.0 1.0
OD2 A:ASP101 4.4 40.2 1.0
CB A:THR74 4.5 26.0 1.0
OE2 A:GLU133 4.8 79.0 1.0
OD1 A:ASP101 4.9 40.2 1.0
CB A:GLU133 5.0 79.0 1.0
CG2 A:THR74 5.0 26.0 1.0

Magnesium binding site 2 out of 5 in 1oy0

Go back to Magnesium Binding Sites List in 1oy0
Magnesium binding site 2 out of 5 in the The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:55.9
occ:1.00
 OE1 B:GLU133 2.5 0.6 1.0
O B:HOH920 2.7 35.9 1.0
OD2 B:ASP62 2.8 50.5 1.0
O B:HOH911 2.9 44.9 1.0
CD B:GLU133 3.5 0.6 1.0
CG B:ASP62 3.6 50.5 1.0
OD1 B:ASP62 3.6 50.5 1.0
OE2 B:GLU133 4.1 0.6 1.0
CB B:GLU133 4.3 0.6 1.0
OG1 B:THR74 4.5 20.9 1.0
CG B:GLU133 4.5 0.6 1.0
OH B:TYR107 4.8 41.1 1.0
CB B:ASP62 4.9 50.5 1.0
CB B:THR74 5.0 20.9 1.0

Magnesium binding site 3 out of 5 in 1oy0

Go back to Magnesium Binding Sites List in 1oy0
Magnesium binding site 3 out of 5 in the The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:52.2
occ:1.00
 OD2 C:ASP62 2.2 34.8 1.0
OE1 C:GLU133 2.7 62.7 1.0
O C:HOH922 2.9 29.9 1.0
CG C:ASP62 3.0 34.8 1.0
O C:HOH914 3.0 48.4 1.0
OD1 C:ASP62 3.3 34.8 1.0
CD C:GLU133 3.9 62.7 1.0
CB C:ASP62 4.3 34.8 1.0
OG1 C:THR74 4.4 33.3 1.0
OD2 C:ASP101 4.6 46.4 1.0
OE2 C:GLU133 4.6 62.7 1.0
CB C:THR74 4.7 33.3 1.0
CB C:GLU133 4.7 62.7 1.0
CG C:GLU133 4.9 62.7 1.0

Magnesium binding site 4 out of 5 in 1oy0

Go back to Magnesium Binding Sites List in 1oy0
Magnesium binding site 4 out of 5 in the The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:49.4
occ:1.00
 O D:HOH917 2.3 61.1 1.0
OD2 D:ASP62 2.4 32.8 1.0
OE1 D:GLU133 2.5 74.9 1.0
O D:HOH923 2.9 31.4 1.0
CG D:ASP62 3.1 32.8 1.0
OD1 D:ASP62 3.5 32.8 1.0
CD D:GLU133 3.6 74.9 1.0
O D:HOH924 4.1 25.5 1.0
OD2 D:ASP101 4.1 41.0 1.0
CB D:ASP62 4.3 32.8 1.0
CB D:GLU133 4.3 74.9 1.0
OE2 D:GLU133 4.4 74.9 1.0
CG D:GLU133 4.6 74.9 1.0
OG1 D:THR74 4.7 20.5 1.0
O D:LEU102 4.8 26.8 1.0
CG D:ASP101 4.9 41.0 1.0
OD1 D:ASP101 4.9 41.0 1.0

Magnesium binding site 5 out of 5 in 1oy0

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Magnesium binding site 5 out of 5 in the The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase From Mycobacterium Tuberculosis Shows A Decameric Assembly and Terminal Helix-Swapping within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg905

b:42.8
occ:1.00
 OD2 E:ASP62 2.3 58.7 1.0
OE1 E:GLU133 2.7 65.6 1.0
O E:HOH924 2.8 37.7 1.0
O E:HOH917 3.1 52.9 1.0
CG E:ASP62 3.2 58.7 1.0
OD1 E:ASP62 3.5 58.7 1.0
CD E:GLU133 3.8 65.6 1.0
OG1 E:THR74 4.2 15.8 1.0
OE2 E:GLU133 4.3 65.6 1.0
CB E:ASP62 4.4 58.7 1.0
OD2 E:ASP101 4.6 50.0 1.0
CB E:THR74 4.7 15.8 1.0
CB E:GLU133 4.7 65.6 1.0
CG E:GLU133 4.8 65.6 1.0

Reference:

B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, T.O.Yeates. The Crystal Structure of the First Enzyme in the Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase, From M. Tuberculosis Structure V. 11 753 2003.
ISSN: ISSN 0969-2126
PubMed: 12842039
DOI: 10.1016/S0969-2126(03)00106-0
Page generated: Tue Aug 13 10:45:06 2024

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