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Magnesium in PDB 4a6a: A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp

Enzymatic activity of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp

All present enzymatic activity of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp:
3.5.4.13;

Protein crystallography data

The structure of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp, PDB code: 4a6a was solved by M.N.Lovgreen, E.Ucar, M.Willemoes, P.Harris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.42 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.590, 179.510, 99.810, 90.00, 96.28, 90.00
R / Rfree (%) 25.3 / 29

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp (pdb code 4a6a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp, PDB code: 4a6a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 4a6a

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Magnesium binding site 1 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:29.0
occ:1.00
 O2B A:TTP201 2.3 39.5 1.0
O1A A:TTP201 2.5 37.1 1.0
O2G A:TTP201 2.6 40.2 1.0
OE1 E:GLN28 3.2 56.2 1.0
OE1 E:GLN148 3.5 46.6 1.0
PB A:TTP201 3.6 39.7 1.0
OD2 E:ASP33 3.7 53.0 1.0
OD1 E:ASP33 3.7 51.1 1.0
PA A:TTP201 3.7 35.4 1.0
CD E:GLN28 3.8 54.7 1.0
CG E:GLN28 3.8 51.2 1.0
PG A:TTP201 3.8 40.5 1.0
CG E:ASP33 4.1 49.7 1.0
O3A A:TTP201 4.2 38.3 1.0
O3B A:TTP201 4.2 40.7 1.0
O2A A:TTP201 4.3 34.0 1.0
O A:HOH2002 4.4 20.8 1.0
NZ E:LYS101 4.4 43.1 1.0
CD E:GLN148 4.4 45.2 1.0
O1G A:TTP201 4.5 40.3 1.0
CB E:GLN28 4.6 49.2 1.0
NE2 E:GLN148 4.8 45.5 1.0
O1B A:TTP201 4.8 38.8 1.0
OD1 A:ASP119 4.9 49.4 1.0
NE2 E:GLN28 4.9 55.0 1.0
O3G A:TTP201 5.0 41.3 1.0
CD E:LYS101 5.0 41.1 1.0

Magnesium binding site 2 out of 14 in 4a6a

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Magnesium binding site 2 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:19.4
occ:1.00
 O1A B:TTP201 2.1 27.4 1.0
O2B B:TTP201 2.1 30.7 1.0
O2G B:TTP201 2.3 31.0 1.0
OE1 D:GLN28 3.4 44.9 1.0
PA B:TTP201 3.5 25.4 1.0
PB B:TTP201 3.5 30.6 1.0
PG B:TTP201 3.7 31.3 1.0
OE1 D:GLN148 3.7 35.4 1.0
OD2 D:ASP33 3.8 42.4 1.0
O3A B:TTP201 4.0 29.2 1.0
CD D:GLN28 4.0 43.8 1.0
O3B B:TTP201 4.0 31.8 1.0
OD1 D:ASP33 4.0 40.6 1.0
CG D:GLN28 4.1 40.4 1.0
O2A B:TTP201 4.1 24.7 1.0
CG D:ASP33 4.4 39.1 1.0
NZ D:LYS101 4.4 32.4 1.0
O1G B:TTP201 4.4 31.3 1.0
CD D:GLN148 4.5 34.4 1.0
O1B B:TTP201 4.7 30.2 1.0
NE2 D:GLN148 4.7 34.8 1.0
O5' B:TTP201 4.7 25.4 1.0
O3G B:TTP201 4.8 32.0 1.0
OD1 B:ASP119 4.8 39.4 1.0
CB D:GLN28 4.9 38.4 1.0
CD D:LYS101 5.0 30.8 1.0

Magnesium binding site 3 out of 14 in 4a6a

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Magnesium binding site 3 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:44.1
occ:1.00
 OE1 D:GLU99 3.2 46.6 1.0
OE2 D:GLU99 3.2 46.4 1.0
OE2 B:GLU99 3.3 46.7 1.0
CD D:GLU99 3.6 44.6 1.0
O B:THR114 3.7 46.7 1.0
CE1 B:HIS112 3.8 46.0 1.0
O B:VAL115 4.3 41.5 1.0
CD B:GLU99 4.3 44.9 1.0
OE1 B:GLU99 4.5 46.9 1.0
C B:THR114 4.5 45.7 1.0
O B:HOH2001 4.5 34.2 1.0
ND1 B:HIS112 4.7 46.1 1.0
CE1 D:HIS112 4.7 57.4 1.0
NE2 B:HIS112 4.8 47.0 1.0
OE2 F:GLU99 4.9 47.5 1.0
C B:VAL115 4.9 40.9 1.0
NE2 D:HIS112 5.0 58.1 1.0

Magnesium binding site 4 out of 14 in 4a6a

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Magnesium binding site 4 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:28.6
occ:1.00
 O2B C:TTP201 1.9 39.0 1.0
O1A C:TTP201 2.1 37.0 1.0
O2G C:TTP201 2.3 40.7 1.0
O A:HOH2001 2.5 17.9 1.0
PB C:TTP201 3.2 38.9 1.0
PA C:TTP201 3.4 33.6 1.0
PG C:TTP201 3.5 41.1 1.0
OE1 A:GLN148 3.6 42.8 1.0
OE1 A:GLN28 3.7 51.0 1.0
O3A C:TTP201 3.8 37.3 1.0
O3B C:TTP201 3.8 40.5 1.0
OD1 A:ASP33 3.9 47.2 1.0
OD2 A:ASP33 4.1 48.6 1.0
O2A C:TTP201 4.1 32.3 1.0
CG A:GLN28 4.2 47.0 1.0
CD A:GLN28 4.3 50.0 1.0
O1G C:TTP201 4.3 41.4 1.0
CD A:GLN148 4.4 41.5 1.0
CG A:ASP33 4.5 45.7 1.0
O1B C:TTP201 4.5 38.2 1.0
NZ A:LYS101 4.5 38.3 1.0
NE2 A:GLN148 4.6 41.9 1.0
O5' C:TTP201 4.6 33.9 1.0
O3G C:TTP201 4.6 41.7 1.0
OD1 C:ASP119 4.8 48.7 1.0
C5' C:TTP201 5.0 34.9 1.0

Magnesium binding site 5 out of 14 in 4a6a

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Magnesium binding site 5 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:21.4
occ:1.00
 O2B D:TTP201 2.0 32.3 1.0
O2G D:TTP201 2.3 32.8 1.0
O1A D:TTP201 2.3 29.2 1.0
O D:HOH2001 2.4 18.2 1.0
PB D:TTP201 3.4 32.2 1.0
OE1 F:GLN28 3.4 46.8 1.0
PG D:TTP201 3.6 33.1 1.0
PA D:TTP201 3.6 26.8 1.0
OE1 F:GLN148 3.8 37.7 1.0
OD1 F:ASP33 3.8 43.0 1.0
OD2 F:ASP33 3.8 44.7 1.0
O3A D:TTP201 3.9 30.9 1.0
O3B D:TTP201 3.9 33.4 1.0
CD F:GLN28 4.0 45.5 1.0
CG F:GLN28 4.1 42.4 1.0
NZ F:LYS101 4.1 34.6 1.0
O2A D:TTP201 4.2 25.9 1.0
O1G D:TTP201 4.2 34.0 1.0
CG F:ASP33 4.2 41.8 1.0
O1B D:TTP201 4.5 31.4 1.0
CD F:GLN148 4.6 36.1 1.0
O3G D:TTP201 4.7 34.2 1.0
NE2 F:GLN148 4.9 36.4 1.0
O5' D:TTP201 4.9 27.3 1.0
CD F:LYS101 4.9 33.1 1.0
CB F:GLN28 5.0 40.4 1.0
OD1 D:ASP119 5.0 41.3 1.0

Magnesium binding site 6 out of 14 in 4a6a

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Magnesium binding site 6 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:31.2
occ:1.00
 O2B E:TTP201 2.2 42.1 1.0
O1A E:TTP201 2.2 39.1 1.0
O2G E:TTP201 2.3 43.2 1.0
OE1 C:GLN28 3.3 51.7 1.0
PB E:TTP201 3.5 42.0 1.0
PA E:TTP201 3.5 36.7 1.0
PG E:TTP201 3.6 43.2 1.0
OE1 C:GLN148 3.7 41.8 1.0
OD2 C:ASP33 3.8 48.6 1.0
OD1 C:ASP33 3.9 46.9 1.0
CD C:GLN28 3.9 50.7 1.0
CG C:GLN28 3.9 47.4 1.0
O3A E:TTP201 4.0 40.3 1.0
O3B E:TTP201 4.0 43.5 1.0
O2A E:TTP201 4.1 36.1 1.0
CG C:ASP33 4.3 45.4 1.0
O1G E:TTP201 4.3 43.4 1.0
NZ C:LYS101 4.4 38.4 1.0
CD C:GLN148 4.5 40.5 1.0
O3G E:TTP201 4.7 44.2 1.0
OD1 E:ASP119 4.7 50.9 1.0
O1B E:TTP201 4.7 41.4 1.0
CB C:GLN28 4.8 45.5 1.0
NE2 C:GLN148 4.8 40.6 1.0
O5' E:TTP201 4.8 36.8 1.0

Magnesium binding site 7 out of 14 in 4a6a

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Magnesium binding site 7 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:19.9
occ:1.00
 O2B F:TTP201 2.3 30.7 1.0
O2G F:TTP201 2.4 31.6 1.0
O1A F:TTP201 2.6 28.7 1.0
OE1 B:GLN28 3.1 44.7 1.0
OD2 B:ASP33 3.6 41.8 1.0
PB F:TTP201 3.6 31.1 1.0
CD B:GLN28 3.6 43.2 1.0
PG F:TTP201 3.7 32.1 1.0
CG B:GLN28 3.8 39.9 1.0
OD1 B:ASP33 3.8 40.5 1.0
PA F:TTP201 3.9 26.1 1.0
OE1 B:GLN148 4.0 35.8 1.0
O3B F:TTP201 4.1 32.5 1.0
CG B:ASP33 4.2 38.9 1.0
O3A F:TTP201 4.3 30.1 1.0
O1G F:TTP201 4.3 31.6 1.0
NZ B:LYS101 4.3 33.1 1.0
O2A F:TTP201 4.6 25.5 1.0
CB B:GLN28 4.6 37.9 1.0
NE2 B:GLN28 4.8 43.1 1.0
CD B:GLN148 4.8 34.4 1.0
O1B F:TTP201 4.9 30.6 1.0
O3G F:TTP201 4.9 33.0 1.0
OD1 F:ASP119 4.9 41.0 1.0

Magnesium binding site 8 out of 14 in 4a6a

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Magnesium binding site 8 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:26.7
occ:1.00
 O2B G:TTP201 2.3 37.1 1.0
O2G G:TTP201 2.6 38.1 1.0
O1A G:TTP201 2.6 35.1 1.0
OE1 K:GLN28 3.3 50.5 1.0
PB G:TTP201 3.6 37.6 1.0
OE1 K:GLN148 3.6 40.9 1.0
OD2 K:ASP33 3.7 47.9 1.0
PG G:TTP201 3.8 38.1 1.0
CG K:GLN28 3.8 45.7 1.0
PA G:TTP201 3.8 33.0 1.0
CD K:GLN28 3.8 49.1 1.0
OD1 K:ASP33 3.8 45.9 1.0
O3B G:TTP201 4.1 38.4 1.0
O3A G:TTP201 4.2 36.1 1.0
O G:HOH2003 4.2 35.7 1.0
CG K:ASP33 4.2 44.5 1.0
O2A G:TTP201 4.4 31.8 1.0
NZ K:LYS101 4.4 37.6 1.0
O1G G:TTP201 4.4 38.1 1.0
CD K:GLN148 4.5 39.6 1.0
CB K:GLN28 4.6 43.9 1.0
NE2 K:GLN148 4.8 39.9 1.0
O1B G:TTP201 4.8 36.6 1.0
OD1 G:ASP119 4.9 47.2 1.0
O3G G:TTP201 4.9 39.0 1.0
NE2 K:GLN28 5.0 49.1 1.0

Magnesium binding site 9 out of 14 in 4a6a

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Magnesium binding site 9 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:20.5
occ:1.00
 O2B H:TTP201 2.1 30.9 1.0
O1A H:TTP201 2.2 28.5 1.0
O2G H:TTP201 2.4 31.9 1.0
PB H:TTP201 3.4 30.9 1.0
OE1 J:GLN28 3.5 47.1 1.0
PA H:TTP201 3.5 26.4 1.0
OE1 J:GLN148 3.7 37.5 1.0
PG H:TTP201 3.7 32.1 1.0
OD2 J:ASP33 3.7 43.8 1.0
O3A H:TTP201 3.9 29.9 1.0
OD1 J:ASP33 4.0 42.4 1.0
CG J:GLN28 4.0 42.5 1.0
O3B H:TTP201 4.0 32.3 1.0
CD J:GLN28 4.0 45.8 1.0
O2A H:TTP201 4.2 25.1 1.0
NZ J:LYS101 4.3 33.8 1.0
CG J:ASP33 4.3 40.9 1.0
O1G H:TTP201 4.4 32.3 1.0
CD J:GLN148 4.4 36.3 1.0
O1B H:TTP201 4.6 30.4 1.0
NE2 J:GLN148 4.7 36.7 1.0
O5' H:TTP201 4.8 26.9 1.0
OD1 H:ASP119 4.8 40.9 1.0
O3G H:TTP201 4.8 33.0 1.0
CB J:GLN28 4.9 40.8 1.0
CD J:LYS101 5.0 31.9 1.0

Magnesium binding site 10 out of 14 in 4a6a

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Magnesium binding site 10 out of 14 in the A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of A115V Variant of Dctp Deaminase-Dutpase From Mycobacterium Tuberculosis in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg203

b:42.9
occ:1.00
 OE2 H:GLU99 2.9 47.0 1.0
OE2 J:GLU99 3.3 47.9 1.0
OE1 J:GLU99 3.8 47.9 1.0
CD H:GLU99 3.8 45.2 1.0
OE2 L:GLU99 3.9 47.9 1.0
CD J:GLU99 3.9 45.9 1.0
OE1 H:GLU99 3.9 47.1 1.0
CE1 H:HIS112 4.5 55.5 1.0
O H:VAL115 4.6 45.7 1.0
CD L:GLU99 4.7 46.2 1.0
OE1 L:GLU99 4.7 48.3 1.0

Reference:

M.N.Lovgreen, P.Harris, E.Ucar, M.Willemoes. Dttp Inhibition of the Bifunctional Dctp Deaminase- Dutpase From Mycobacterium Tuberculosis Is pH Dependent: Kinetic Analyses and Crystal Structure of A115V Variant To Be Published.
Page generated: Thu Aug 15 14:21:15 2024

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