Magnesium in PDB 6b5k: Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp

All present enzymatic activity of Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp:
2.7.7.24;

The structure of Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp, PDB code: 6b5k was solved by H.A.Brown, H.A.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.60
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	96.403, 96.403, 151.924, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.7

The binding sites of Magnesium atom in the Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp (pdb code 6b5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp, PDB code: 6b5k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp


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 Mg/Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:13.4 occ:1.00 O2A A:TTP301 2.0 13.2 1.0 O A:HOH425 2.1 13.9 1.0 OD2 A:ASP108 2.1 12.1 1.0 O A:HOH528 2.1 15.6 1.0 OD1 A:ASP222 2.1 15.4 1.0 O A:HOH483 2.1 13.0 1.0 CG A:ASP108 3.0 11.5 1.0 CG A:ASP222 3.1 19.6 1.0 OD1 A:ASP108 3.3 13.4 1.0 PA A:TTP301 3.4 13.8 1.0 OD2 A:ASP222 3.5 19.7 1.0 NZ A:LYS23 3.8 11.8 1.0 C5' A:TTP301 4.1 12.8 1.0 O A:HOH565 4.1 17.4 1.0 O A:HOH608 4.2 33.6 1.0 NH1 A:ARG13 4.2 22.0 1.0 O A:HOH578 4.2 25.3 1.0 O5' A:TTP301 4.2 14.6 1.0 O1A A:TTP301 4.3 12.0 1.0 O3A A:TTP301 4.4 14.0 1.0 CB A:ASP108 4.4 10.9 1.0 CB A:ASP222 4.5 16.0 1.0 C3' A:TTP301 4.7 11.9 1.0 ND2 A:ASN109 4.7 14.3 1.0 O A:HOH571 4.8 23.0 1.0 O A:HOH562 4.8 31.8 1.0 C4' A:TTP301 4.8 11.8 1.0 CE A:LYS23 4.9 12.2 1.0

Magnesium binding site 2 out of 4 in the Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp


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 Mg/Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:15.3 occ:1.00 O1A A:TTP301 2.0 12.0 1.0 O2G A:TTP301 2.1 14.6 1.0 O2B A:TTP301 2.1 13.6 1.0 O A:HOH536 2.1 16.1 1.0 O A:HOH474 2.2 14.7 1.0 O A:HOH463 2.2 17.0 1.0 PB A:TTP301 3.2 13.9 1.0 PA A:TTP301 3.3 13.8 1.0 PG A:TTP301 3.3 13.9 1.0 O3B A:TTP301 3.5 12.5 1.0 O3A A:TTP301 3.6 14.0 1.0 O A:HOH484 3.9 36.5 1.0 O1G A:TTP301 3.9 13.9 1.0 O5' A:TTP301 4.0 14.6 1.0 NH1 A:ARG13 4.0 22.0 1.0 O A:HOH434 4.1 18.9 1.0 NH2 A:ARG191 4.2 28.7 1.0 O A:HOH572 4.2 22.2 1.0 O A:HOH571 4.4 23.0 1.0 OE2 A:GLU193 4.4 19.4 1.0 O2A A:TTP301 4.4 13.2 1.0 O A:HOH513 4.5 16.0 1.0 C5M A:TTP301 4.5 13.7 1.0 O3G A:TTP301 4.5 13.7 1.0 OE1 A:GLU193 4.5 17.8 1.0 O1B A:TTP301 4.5 14.1 1.0 O A:HOH519 4.9 35.2 1.0 CD A:GLU193 4.9 22.8 1.0

Magnesium binding site 3 out of 4 in the Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp


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 Mg/Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:28.3 occ:1.00 O B:HOH435 1.9 34.0 1.0 O2G B:TTP303 1.9 26.9 1.0 O2A B:TTP303 2.0 26.5 1.0 O B:HOH462 2.1 32.0 1.0 O1B B:TTP303 2.1 27.0 1.0 O B:HOH481 2.2 28.0 1.0 PB B:TTP303 3.2 26.3 1.0 PA B:TTP303 3.2 27.1 1.0 PG B:TTP303 3.3 27.0 1.0 O3B B:TTP303 3.6 26.0 1.0 O3A B:TTP303 3.6 25.9 1.0 O3G B:TTP303 4.0 26.0 1.0 O B:HOH436 4.0 30.9 1.0 NH1 B:ARG13 4.0 31.0 1.0 O5' B:TTP303 4.1 25.1 1.0 O B:HOH501 4.2 45.5 1.0 OE2 B:GLU193 4.4 32.8 1.0 O B:HOH476 4.5 28.6 1.0 O1A B:TTP303 4.5 25.2 1.0 O1G B:TTP303 4.5 26.8 1.0 C5M B:TTP303 4.6 32.2 1.0 O2B B:TTP303 4.6 27.6 1.0 OE1 B:GLU193 4.7 36.4 1.0 O B:HOH505 4.8 43.5 1.0

Magnesium binding site 4 out of 4 in the Mycobacterium Tuberculosis Rmla in Complex with Mg/Dttp


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 Mg/Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:24.5 occ:1.00 O B:HOH426 2.0 26.0 1.0 O B:HOH409 2.0 27.7 1.0 O1A B:TTP303 2.0 25.2 1.0 OD1 B:ASP222 2.1 25.1 1.0 OD2 B:ASP108 2.1 22.7 1.0 O B:HOH478 2.1 26.3 1.0 CG B:ASP108 3.0 19.2 1.0 CG B:ASP222 3.0 27.1 1.0 OD1 B:ASP108 3.3 22.4 1.0 OD2 B:ASP222 3.3 28.3 1.0 PA B:TTP303 3.5 27.1 1.0 O B:HOH494 3.9 28.6 1.0 NZ B:LYS23 3.9 23.2 1.0 C5' B:TTP303 4.1 24.5 1.0 O B:HOH502 4.2 35.8 1.0 O5' B:TTP303 4.2 25.1 1.0 NH1 B:ARG13 4.2 31.0 1.0 O2A B:TTP303 4.3 26.5 1.0 O3A B:TTP303 4.3 25.9 1.0 CB B:ASP108 4.4 23.9 1.0 CB B:ASP222 4.4 25.1 1.0 ND2 B:ASN109 4.7 29.4 1.0 C3' B:TTP303 4.8 24.1 1.0 O B:HOH505 4.8 43.5 1.0 C4' B:TTP303 4.8 28.9 1.0

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