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Magnesium in PDB 6b5e: Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose

Enzymatic activity of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose

All present enzymatic activity of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose:
2.7.7.24;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose, PDB code: 6b5e was solved by H.A.Brown, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.323, 111.264, 290.363, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.8

Other elements in 6b5e:

The structure of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose (pdb code 6b5e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose, PDB code: 6b5e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6b5e

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Magnesium binding site 1 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:12.1
occ:1.00
 O2P A:DAU301 1.9 16.4 1.0
O A:HOH417 2.0 11.9 1.0
OD1 A:ASP222 2.0 13.3 1.0
O A:HOH492 2.1 15.2 1.0
OD2 A:ASP108 2.1 9.0 1.0
O4P A:DAU301 2.2 14.3 1.0
CG A:ASP108 3.0 10.3 1.0
CG A:ASP222 3.1 11.8 1.0
P2 A:DAU301 3.2 18.4 1.0
P A:DAU301 3.2 16.3 1.0
OD1 A:ASP108 3.4 9.7 1.0
OPP A:DAU301 3.4 15.0 1.0
OD2 A:ASP222 3.4 15.5 1.0
O A:HOH467 3.7 34.8 1.0
NZ A:LYS23 3.8 10.7 1.0
O A:HOH522 3.8 29.7 1.0
O6 A:DAU301 3.9 15.4 1.0
C5' A:DAU301 4.0 14.5 1.0
O5' A:DAU301 4.2 14.9 1.0
O5 A:DAU301 4.2 13.1 1.0
O3P A:DAU301 4.3 17.3 1.0
O1 A:DAU301 4.3 15.1 1.0
O1P A:DAU301 4.4 15.3 1.0
CB A:ASP108 4.4 9.4 1.0
CB A:ASP222 4.5 15.1 1.0
C1 A:DAU301 4.7 14.6 1.0
C3' A:DAU301 4.7 13.3 1.0
ND2 A:ASN109 4.8 16.6 1.0
C5 A:DAU301 4.8 14.5 1.0
C4' A:DAU301 4.9 13.2 1.0
C6 A:DAU301 5.0 17.7 1.0
CE A:LYS23 5.0 11.1 1.0

Magnesium binding site 2 out of 9 in 6b5e

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Magnesium binding site 2 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:10.9
occ:1.00
 O1P B:DAU301 1.9 12.9 1.0
O B:HOH451 2.0 9.1 1.0
O B:HOH416 2.1 11.4 1.0
OD2 B:ASP108 2.1 9.0 1.0
OD1 B:ASP222 2.1 12.8 1.0
O3P B:DAU301 2.2 12.9 1.0
CG B:ASP108 3.0 10.1 1.0
CG B:ASP222 3.1 11.8 1.0
P B:DAU301 3.2 14.4 1.0
P2 B:DAU301 3.2 14.5 1.0
OD1 B:ASP108 3.3 8.9 1.0
OD2 B:ASP222 3.4 13.8 1.0
OPP B:DAU301 3.5 14.1 1.0
NZ B:LYS23 3.8 10.2 1.0
O B:HOH463 3.8 21.7 1.0
O6 B:DAU301 3.9 11.2 1.0
O B:HOH554 4.0 26.4 1.0
C5' B:DAU301 4.0 12.2 1.0
O5' B:DAU301 4.2 12.8 1.0
O4P B:DAU301 4.2 15.0 1.0
O5 B:DAU301 4.3 11.7 1.0
CB B:ASP108 4.4 9.0 1.0
O2P B:DAU301 4.4 12.5 1.0
O1 B:DAU301 4.4 13.8 1.0
CB B:ASP222 4.6 10.7 1.0
C3' B:DAU301 4.6 11.1 1.0
ND2 B:ASN109 4.7 11.7 1.0
C1 B:DAU301 4.8 12.2 1.0
C4' B:DAU301 4.8 11.6 1.0
C5 B:DAU301 5.0 10.6 1.0
CE B:LYS23 5.0 10.1 1.0

Magnesium binding site 3 out of 9 in 6b5e

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Magnesium binding site 3 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:34.1
occ:1.00
 O B:HOH607 2.0 30.8 1.0
O B:HOH478 2.3 16.2 1.0
NH2 B:ARG2 2.7 20.0 0.5
NH1 B:ARG2 3.5 31.4 0.5
CZ B:ARG2 3.5 26.7 0.5
NH2 B:ARG2 3.9 24.5 0.5
O B:HOH449 3.9 30.1 1.0
ND1 B:HIS96 4.3 14.9 1.0
O B:HOH472 4.4 30.2 1.0
OG B:SER76 4.4 23.5 1.0
O B:HIS96 4.7 15.8 1.0
CA B:HIS96 4.7 17.1 1.0
NE B:ARG2 4.8 25.8 0.5
CZ B:ARG2 4.9 25.6 0.5
O B:HOH521 4.9 16.3 1.0

Magnesium binding site 4 out of 9 in 6b5e

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Magnesium binding site 4 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:20.2
occ:1.00
 O C:HOH417 2.0 19.9 1.0
O3P C:DAU301 2.0 24.6 1.0
O1P C:DAU301 2.1 21.8 1.0
OD1 C:ASP222 2.1 21.0 1.0
O C:HOH424 2.1 18.8 1.0
OD2 C:ASP108 2.2 18.6 1.0
CG C:ASP222 3.0 26.4 1.0
CG C:ASP108 3.2 20.2 1.0
P2 C:DAU301 3.2 28.0 1.0
P C:DAU301 3.3 26.2 1.0
OD2 C:ASP222 3.3 26.6 1.0
OD1 C:ASP108 3.4 19.5 1.0
OPP C:DAU301 3.5 25.7 1.0
NZ C:LYS23 3.9 22.9 1.0
O6 C:DAU301 3.9 21.5 1.0
C5' C:DAU301 4.1 23.3 1.0
O5' C:DAU301 4.2 25.0 1.0
O5 C:DAU301 4.2 21.0 1.0
O4P C:DAU301 4.2 27.3 1.0
CB C:ASP222 4.4 21.4 1.0
O1 C:DAU301 4.4 24.1 1.0
O2P C:DAU301 4.5 26.4 1.0
CB C:ASP108 4.5 17.2 1.0
C1 C:DAU301 4.7 22.6 1.0
ND2 C:ASN109 4.7 22.2 1.0
C3' C:DAU301 4.7 21.9 1.0
C5 C:DAU301 4.9 22.2 1.0
O C:HOH412 4.9 34.1 1.0
C4' C:DAU301 4.9 22.2 1.0

Magnesium binding site 5 out of 9 in 6b5e

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Magnesium binding site 5 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:18.0
occ:1.00
 O D:HOH417 2.0 19.2 1.0
O1P D:DAU301 2.1 20.9 1.0
O4P D:DAU301 2.1 23.5 1.0
O D:HOH422 2.1 17.7 1.0
OD1 D:ASP222 2.1 25.2 1.0
OD2 D:ASP108 2.2 17.7 1.0
CG D:ASP222 3.1 23.9 1.0
CG D:ASP108 3.1 16.3 1.0
P2 D:DAU301 3.3 23.5 1.0
P D:DAU301 3.3 21.2 1.0
OD2 D:ASP222 3.3 23.4 1.0
OD1 D:ASP108 3.4 19.4 1.0
OPP D:DAU301 3.5 22.8 1.0
O D:HOH467 3.8 30.8 1.0
NZ D:LYS23 3.8 18.9 1.0
O6 D:DAU301 3.8 24.4 1.0
O D:HOH455 3.9 35.1 1.0
C5' D:DAU301 4.1 21.5 1.0
O5' D:DAU301 4.2 19.9 1.0
O3P D:DAU301 4.2 20.8 1.0
O5 D:DAU301 4.3 22.3 1.0
O2P D:DAU301 4.4 20.2 1.0
O1 D:DAU301 4.4 22.3 1.0
CB D:ASP108 4.5 17.0 1.0
CB D:ASP222 4.5 24.9 1.0
C3' D:DAU301 4.7 21.8 1.0
C1 D:DAU301 4.7 20.9 1.0
ND2 D:ASN109 4.7 19.9 1.0
C4' D:DAU301 4.9 23.9 1.0
C5 D:DAU301 4.9 26.2 1.0
C6 D:DAU301 5.0 27.0 1.0

Magnesium binding site 6 out of 9 in 6b5e

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Magnesium binding site 6 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:17.5
occ:1.00
 O2P E:DAU301 2.0 15.8 1.0
O E:HOH417 2.0 13.8 1.0
O4P E:DAU301 2.1 14.9 1.0
OD2 E:ASP108 2.1 13.6 1.0
OD1 E:ASP222 2.2 18.3 1.0
O E:HOH434 2.2 18.4 1.0
CG E:ASP222 3.1 16.6 1.0
CG E:ASP108 3.1 15.6 1.0
P E:DAU301 3.2 16.9 1.0
P2 E:DAU301 3.2 17.0 1.0
OD2 E:ASP222 3.3 17.6 1.0
OD1 E:ASP108 3.3 14.8 1.0
OPP E:DAU301 3.4 14.8 1.0
NZ E:LYS23 3.8 15.5 1.0
O6 E:DAU301 3.8 16.7 1.0
O E:HOH564 4.1 42.6 1.0
C5' E:DAU301 4.1 13.8 1.0
O5' E:DAU301 4.1 16.3 1.0
O5 E:DAU301 4.2 16.5 1.0
O E:HOH491 4.2 28.4 1.0
O3P E:DAU301 4.4 19.2 1.0
O1 E:DAU301 4.4 17.3 1.0
O1P E:DAU301 4.5 18.4 1.0
CB E:ASP108 4.5 14.5 1.0
CB E:ASP222 4.5 16.5 1.0
C1 E:DAU301 4.6 15.9 1.0
C3' E:DAU301 4.6 14.3 1.0
C5 E:DAU301 4.8 16.8 1.0
O E:HOH493 4.8 34.0 1.0
C4' E:DAU301 4.9 14.6 1.0
ND2 E:ASN109 4.9 14.4 1.0
C6 E:DAU301 5.0 16.7 1.0

Magnesium binding site 7 out of 9 in 6b5e

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Magnesium binding site 7 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:18.7
occ:1.00
 O4P F:DAU301 1.9 23.7 1.0
O F:HOH434 2.0 16.0 1.0
O2P F:DAU301 2.1 20.9 1.0
O F:HOH428 2.1 14.9 1.0
OD1 F:ASP222 2.2 20.7 1.0
OD2 F:ASP108 2.2 20.0 1.0
CG F:ASP222 3.1 23.0 1.0
CG F:ASP108 3.1 16.7 1.0
P2 F:DAU301 3.3 23.6 1.0
P F:DAU301 3.3 24.1 1.0
OD1 F:ASP108 3.3 16.7 1.0
OD2 F:ASP222 3.4 22.1 1.0
OPP F:DAU301 3.5 22.4 1.0
O F:HOH504 3.8 30.6 1.0
O F:HOH540 3.8 33.8 1.0
NZ F:LYS23 3.9 17.7 1.0
O6 F:DAU301 4.0 19.3 1.0
C5' F:DAU301 4.2 19.7 1.0
O5' F:DAU301 4.2 21.4 1.0
O5 F:DAU301 4.2 20.0 1.0
O3P F:DAU301 4.3 24.9 1.0
O1P F:DAU301 4.4 23.2 1.0
CB F:ASP108 4.4 17.0 1.0
O1 F:DAU301 4.5 21.4 1.0
CB F:ASP222 4.5 18.6 1.0
ND2 F:ASN109 4.7 17.4 1.0
C3' F:DAU301 4.7 18.6 1.0
C1 F:DAU301 4.7 21.2 1.0
C4' F:DAU301 4.9 20.6 1.0
C5 F:DAU301 5.0 19.1 1.0
CA F:GLY224 5.0 19.6 1.0

Magnesium binding site 8 out of 9 in 6b5e

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Magnesium binding site 8 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:14.7
occ:1.00
 O1P G:DAU301 2.0 15.7 1.0
OD1 G:ASP222 2.1 17.3 1.0
O4P G:DAU301 2.1 14.9 1.0
O G:HOH415 2.1 13.8 1.0
O G:HOH436 2.1 14.9 1.0
OD2 G:ASP108 2.2 13.0 1.0
CG G:ASP108 3.1 14.3 1.0
CG G:ASP222 3.1 15.9 1.0
P2 G:DAU301 3.3 18.6 1.0
P G:DAU301 3.3 17.5 1.0
OD1 G:ASP108 3.3 14.7 1.0
OD2 G:ASP222 3.4 17.4 1.0
OPP G:DAU301 3.5 17.6 1.0
O6 G:DAU301 3.9 13.8 1.0
NZ G:LYS23 3.9 14.1 1.0
O G:HOH548 4.0 33.0 1.0
C5' G:DAU301 4.1 15.6 1.0
O5' G:DAU301 4.2 17.6 1.0
O5 G:DAU301 4.2 16.0 1.0
O3P G:DAU301 4.3 18.5 1.0
O1 G:DAU301 4.4 16.3 1.0
CB G:ASP222 4.4 15.4 1.0
CB G:ASP108 4.4 13.5 1.0
O2P G:DAU301 4.5 18.0 1.0
C1 G:DAU301 4.6 16.8 1.0
C3' G:DAU301 4.7 14.7 1.0
ND2 G:ASN109 4.7 13.6 1.0
C5 G:DAU301 4.8 15.4 1.0
C4' G:DAU301 4.9 15.6 1.0
C6 G:DAU301 5.0 16.8 1.0

Magnesium binding site 9 out of 9 in 6b5e

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Magnesium binding site 9 out of 9 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:30.3
occ:1.00
 O4P H:DAU301 1.9 33.5 1.0
O2P H:DAU301 2.1 31.3 1.0
O H:HOH405 2.1 22.8 1.0
O H:HOH417 2.2 27.7 1.0
OD2 H:ASP108 2.2 23.1 1.0
OD1 H:ASP222 2.3 23.6 1.0
CG H:ASP108 3.1 24.7 1.0
P2 H:DAU301 3.2 31.9 1.0
CG H:ASP222 3.2 27.8 1.0
P H:DAU301 3.3 36.0 1.0
OD2 H:ASP222 3.3 24.9 1.0
OD1 H:ASP108 3.3 26.4 1.0
OPP H:DAU301 3.4 33.0 1.0
O6 H:DAU301 3.8 25.8 1.0
NZ H:LYS23 3.8 23.8 1.0
C5' H:DAU301 4.1 28.2 1.0
O3P H:DAU301 4.1 28.4 1.0
O5' H:DAU301 4.2 31.9 1.0
O5 H:DAU301 4.3 29.1 1.0
O1 H:DAU301 4.4 27.1 1.0
CB H:ASP108 4.4 25.8 1.0
O1P H:DAU301 4.4 34.4 1.0
CB H:ASP222 4.6 22.1 1.0
C3' H:DAU301 4.6 26.9 1.0
C1 H:DAU301 4.7 30.5 1.0
ND2 H:ASN109 4.7 27.8 1.0
C4' H:DAU301 4.8 28.5 1.0
C5 H:DAU301 4.8 26.9 1.0
C6 H:DAU301 4.9 25.9 1.0
CE H:LYS23 5.0 26.1 1.0

Reference:

H.A.Brown, J.B.Thoden, P.A.Tipton, H.M.Holden. The Structure of Glucose-1-Phosphate Thymidylyltransferase From Mycobacterium Tuberculosis Reveals the Location of An Essential Magnesium Ion in the Rmla-Type Enzymes. Protein Sci. V. 27 441 2018.
ISSN: ESSN 1469-896X
PubMed: 29076563
DOI: 10.1002/PRO.3333
Page generated: Wed Aug 13 02:28:40 2025

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