Magnesium in PDB 5yrp: Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa

The structure of Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa, PDB code: 5yrp was solved by H.J.Chen, N.Li, Y.Luo, Y.L.Jiang, C.Z.Zhou, Y.Chen, Q.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.78 / 2.99
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.053, 129.053, 165.535, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 31

The binding sites of Magnesium atom in the Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa (pdb code 5yrp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa, PDB code: 5yrp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:35.8 occ:1.00 OE2 A:GLU476 2.3 71.9 1.0 OD1 A:ASP506 2.3 68.1 1.0 OE2 A:GLU384 2.4 53.9 1.0 O A:HOH804 2.6 34.8 1.0 OD1 A:ASN444 2.7 60.0 1.0 OD2 A:ASP506 2.7 68.6 1.0 CG A:ASP506 2.8 66.7 1.0 CD A:GLU476 3.4 71.1 1.0 CD A:GLU384 3.5 54.0 1.0 CG A:ASN444 3.6 60.2 1.0 ND2 A:ASN444 3.7 61.0 1.0 OE1 A:GLU476 3.9 72.6 1.0 OE1 A:GLU384 3.9 56.2 1.0 OE1 A:GLU563 4.1 59.3 1.0 CB A:ASP506 4.3 65.8 1.0 CG A:GLU476 4.6 69.5 1.0 NZ A:LYS527 4.7 67.4 1.0 CB A:GLU476 4.7 67.1 1.0 CG A:GLU384 4.7 53.4 1.0 CB A:ASN444 5.0 60.1 1.0 CD A:LYS527 5.0 63.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Eal Domain of Mycobacterium Smegmatis Dcpa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:49.6 occ:1.00 OE2 B:GLU384 2.1 56.6 1.0 OD2 B:ASP506 2.5 61.0 1.0 O B:HOH809 2.6 29.8 1.0 CD B:GLU384 2.8 56.5 1.0 OE1 B:GLU384 2.8 57.3 1.0 OE2 B:GLU476 2.8 59.5 1.0 OD1 B:ASP506 2.8 59.5 1.0 CG B:ASP506 3.0 59.2 1.0 OE1 B:GLU563 3.2 61.2 1.0 ND2 B:ASN444 3.4 65.3 1.0 CD B:GLU476 3.9 61.5 1.0 CD B:GLU563 4.1 61.9 1.0 NZ B:LYS527 4.2 57.0 1.0 OE1 B:GLU476 4.2 64.6 1.0 CG B:GLU384 4.2 55.4 1.0 OE2 B:GLU563 4.3 63.2 1.0 CG B:ASN444 4.4 65.5 1.0 CB B:ASP506 4.5 57.3 1.0 OD1 B:ASN444 4.6 64.4 1.0 CE B:LYS527 4.7 56.5 1.0 CD B:LYS527 4.7 56.3 1.0 NE2 B:GLN583 4.7 59.0 1.0

H.J.Chen, N.Li, Y.Luo, Y.L.Jiang, C.Z.Zhou, Y.Chen, Q.Li. The Gdp-Switched Gaf Domain of Dcpa Modulates the Concerted Synthesis/Hydrolysis of C-Di-Gmp Inmycobacterium Smegmatis. Biochem. J. V. 475 1295 2018.
ISSN: ESSN 1470-8728
PubMed: 29555845
DOI: 10.1042/BCJ20180079