Magnesium in PDB 7bzg: Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna

The structure of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna, PDB code: 7bzg was solved by R.Zhu, P.R.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.41 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.086, 109.309, 160.423, 90, 99.76, 90
R / Rfree (%)	17.9 / 22.3

The binding sites of Magnesium atom in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna (pdb code 7bzg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna, PDB code: 7bzg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:46.2 occ:1.00 O B:HOH309 2.3 63.1 1.0 O B:HOH314 2.3 59.7 1.0 O B:HOH307 2.5 57.2 1.0 OE1 B:GLU42 4.3 70.2 1.0 OE2 B:GLU81 4.4 63.3 1.0 O B:THR37 4.5 54.6 1.0 OE2 B:GLU42 4.6 77.9 1.0 CD B:GLU42 4.9 64.7 1.0

Magnesium binding site 2 out of 7 in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:68.2 occ:1.00 O D:HOH202 2.4 72.0 1.0 O C:HOH211 2.4 67.0 1.0 O C:HOH202 2.5 76.7 1.0 O4' C:DT6 4.4 78.6 1.0 N3 C:DA5 4.5 50.0 1.0 C5' D:DC18 4.7 42.5 1.0 O4' D:DC18 4.8 54.2 1.0 N3 D:DA17 4.8 52.4 1.0 C4' D:DC18 4.8 47.0 1.0 C4' C:DT6 4.9 57.4 1.0 C1' D:DA17 4.9 57.1 1.0

Magnesium binding site 3 out of 7 in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:55.4 occ:1.00 O F:HOH312 2.2 76.3 1.0 O F:HOH306 2.2 70.4 1.0 O F:THR37 4.5 49.9 1.0 OE2 F:GLU81 4.5 67.3 1.0 OE1 F:GLU42 4.5 76.8 1.0 OE2 F:GLU42 4.8 68.2 1.0

Magnesium binding site 4 out of 7 in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:58.8 occ:1.00 O G:HOH208 2.3 72.6 1.0 O K:HOH206 2.6 69.0 1.0 O G:HOH215 2.6 55.7 1.0 O G:HOH204 2.8 78.3 1.0 O6 G:DG11 3.9 69.2 1.0 N7 G:DG11 4.1 70.0 1.0 C5 G:DC10 4.4 60.4 1.0 C6 G:DC10 4.4 54.6 1.0 C6 G:DG11 4.7 64.7 1.0 C5 G:DG11 4.8 54.9 1.0 OP2 G:DC10 5.0 55.8 1.0

Magnesium binding site 5 out of 7 in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg102 b:75.3 occ:1.00 O H:HOH204 2.0 80.4 1.0 O G:HOH211 2.1 71.9 1.0 O G:HOH212 2.3 79.3 1.0 N3 H:DA5 4.1 60.7 1.0 O4' H:DT6 4.1 61.5 1.0 N3 G:DA17 4.4 66.3 1.0 C2 H:DA5 4.6 60.2 1.0 C4' H:DT6 4.7 52.8 1.0 O4' G:DC18 4.8 73.1 1.0 C4' G:DC18 5.0 67.6 1.0 C5' G:DC18 5.0 77.0 1.0 C2 G:DA17 5.0 58.3 1.0 O4' G:DA17 5.0 72.2 1.0

Magnesium binding site 6 out of 7 in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg101 b:94.2 occ:1.00 O H:HOH211 2.1 104.4 1.0 O H:HOH212 2.4 84.0 1.0 OP1 K:DC8 3.3 87.6 1.0 N7 H:DG11 4.0 84.1 1.0 C8 H:DG11 4.0 72.7 1.0 P K:DC8 4.4 95.3 1.0 O H:HOH207 4.5 69.0 1.0 OP2 K:DC8 4.7 55.7 1.0 N6 H:DA12 4.8 53.1 1.0 OP2 H:DG11 4.9 79.5 1.0 O5' K:DC8 5.0 80.4 1.0

Magnesium binding site 7 out of 7 in the Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Bacillus Subtilis Hxlr, Wild Type in Complex with Formaldehyde and Dna within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg102 b:67.5 occ:1.00 O K:HOH202 1.9 81.8 1.0 O L:HOH104 2.2 74.5 1.0 O G:HOH221 2.3 68.2 1.0 O K:HOH210 2.7 55.3 1.0 N3 K:DA5 3.7 49.1 1.0 O4' K:DT6 4.0 62.3 1.0 O L:HOH105 4.2 72.5 1.0 C2 K:DA5 4.3 39.0 1.0 N3 L:DA17 4.4 54.5 1.0 O G:HOH205 4.5 58.8 1.0 C4' K:DT6 4.5 42.0 1.0 C1' K:DA5 4.6 43.4 1.0 C5' K:DT6 4.6 62.1 1.0 C4 K:DA5 4.8 46.2 1.0 O4' K:DA5 4.8 51.8 1.0 O4' L:DC18 4.9 61.5 1.0 C2 L:DA17 4.9 43.2 1.0

R.Zhu, G.Zhang, M.Jing, Y.Han, J.Li, J.Zhao, Y.Li, P.R.Chen. Genetically Encoded Formaldehyde Sensors Inspired By A Protein Intra-Helical Crosslinking Reaction. Nat Commun V. 12 581 2021.
ISSN: ESSN 2041-1723
PubMed: 33495458
DOI: 10.1038/S41467-020-20754-4