Atomistry » Magnesium » PDB 6b4o-6bcb » 6b5e
Atomistry »
  Magnesium »
    PDB 6b4o-6bcb »
      6b5e »

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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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

Go back to Magnesium Binding Sites List in 6b5e
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: Mon Sep 30 19:32:56 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy