Magnesium in PDB 4lr3: Crystal Structure of E. Coli Yfbu at 2.5 A Resolution

The structure of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution, PDB code: 4lr3 was solved by J.Wang, R.A.Wing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.80 / 2.50
Space group	P 2 3 1
Cell size a, b, c (Å), α, β, γ (°)	230.078, 230.078, 230.078, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution (pdb code 4lr3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 32 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution, PDB code: 4lr3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


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 E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:48.3 occ:1.00 O A:HOH506 2.2 56.3 1.0 O A:HOH508 2.2 53.4 1.0 O A:HOH507 2.2 53.5 1.0 O A:HOH510 2.2 46.6 1.0 O D:HOH303 2.2 42.9 1.0 O A:HOH509 2.2 50.2 1.0 OE1 A:GLU52 3.7 60.4 1.0 NH1 A:ARG51 4.1 0.5 1.0 NH2 D:ARG66 4.3 45.4 1.0 CG A:GLU52 4.5 48.7 1.0 CD A:GLU52 4.5 57.4 1.0 O A:HOH540 4.6 40.2 1.0

Magnesium binding site 2 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


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 E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:45.2 occ:1.00 O A:HOH511 2.2 51.2 1.0 O A:HOH513 2.2 46.5 1.0 O A:HOH512 2.2 48.1 1.0 O B:HOH302 2.2 45.9 1.0 O B:HOH301 2.2 46.2 1.0 O B:HOH303 2.2 52.6 1.0 OE2 A:GLU120 3.3 53.8 1.0 OE1 B:GLN49 3.8 39.8 1.0 OE2 B:GLU52 3.9 54.9 1.0 CD A:GLU120 4.0 57.6 1.0 CG A:GLU120 4.5 56.1 1.0 NH2 B:ARG37 4.6 56.5 1.0 CD B:GLN49 4.7 39.6 1.0 CE A:MET116 4.7 39.3 1.0 CG B:GLN49 4.7 36.6 1.0 OE1 A:GLU120 4.8 58.7 1.0 CB A:GLU120 4.8 50.1 1.0 CD B:GLU52 4.9 53.2 1.0

Magnesium binding site 3 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:54.0 occ:1.00 O B:HOH308 2.2 86.9 1.0 O B:HOH307 2.2 58.5 1.0 O B:HOH306 2.2 62.4 1.0 O A:HOH514 2.2 58.3 1.0 O B:HOH304 2.2 48.2 1.0 O B:HOH305 2.2 50.6 1.0 O B:HOH369 3.7 31.7 1.0 OE1 B:GLU52 3.8 54.3 1.0 NH2 A:ARG66 4.1 37.2 1.0 NE B:ARG51 4.4 71.1 1.0 CG B:GLU52 4.5 44.8 1.0 CD B:GLU52 4.7 53.2 1.0 NH1 A:ARG66 4.8 38.6 1.0 CD B:ARG51 4.9 63.0 1.0 CZ A:ARG66 5.0 38.2 1.0

Magnesium binding site 4 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:40.0 occ:1.00 O B:HOH311 2.2 46.4 1.0 O C:HOH304 2.2 44.4 1.0 O H:HOH304 2.2 42.2 1.0 O C:HOH303 2.2 45.3 1.0 O B:HOH312 2.2 40.8 1.0 O C:HOH302 2.2 42.8 1.0 OE2 B:GLU120 3.4 57.2 1.0 OE2 C:GLU52 3.8 48.3 1.0 ND1 H:HIS151 3.8 39.7 1.0 CG H:GLN156 3.9 51.2 1.0 OE1 H:GLN156 4.1 61.8 1.0 OE1 C:GLN49 4.2 33.3 1.0 CD H:GLN156 4.2 58.2 1.0 CE1 H:HIS151 4.2 42.9 1.0 CD B:GLU120 4.2 54.2 1.0 O B:HOH362 4.4 30.4 1.0 CG B:GLU120 4.4 51.3 1.0 CD C:GLU52 4.6 48.5 1.0 NH2 C:ARG37 4.6 49.4 1.0 CE B:MET116 4.7 42.1 1.0 OE1 C:GLU52 4.7 54.5 1.0 CG C:GLN49 4.8 29.8 1.0 O C:HOH310 4.9 30.8 1.0 CD C:GLN49 5.0 31.6 1.0

Magnesium binding site 5 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:47.0 occ:1.00 O B:HOH315 2.2 48.8 1.0 O B:HOH316 2.2 51.2 1.0 O E:HOH306 2.2 42.9 1.0 O E:HOH304 2.2 53.6 1.0 O E:HOH305 2.2 44.8 1.0 O B:HOH317 2.2 47.9 1.0 OD2 B:ASP70 4.0 40.3 1.0 NH2 E:ARG55 4.0 99.2 1.0 OG1 B:THR67 4.0 32.9 1.0 CZ E:ARG55 4.2 0.5 1.0 OE1 E:GLU52 4.4 54.1 1.0 NH1 E:ARG55 4.5 0.8 1.0 CG E:GLU52 4.5 49.7 1.0 CA B:THR67 4.5 28.2 1.0 NH2 H:ARG66 4.6 38.5 1.0 CG B:ASP70 4.7 43.1 1.0 CB B:ASP70 4.7 43.4 1.0 NE E:ARG55 4.7 92.1 1.0 CB B:THR67 4.8 32.3 1.0 NE2 B:HIS151 4.8 44.6 1.0 NE E:ARG51 4.9 78.1 1.0 CD E:GLU52 5.0 55.6 1.0 N B:THR67 5.0 25.1 1.0

Magnesium binding site 6 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:48.2 occ:1.00 O D:HOH306 2.2 55.1 1.0 O D:HOH304 2.2 53.8 1.0 O C:HOH307 2.2 53.2 1.0 O C:HOH305 2.2 55.6 1.0 O D:HOH305 2.2 43.8 1.0 O C:HOH306 2.2 46.3 1.0 OE1 D:GLU52 4.0 51.5 1.0 NH2 C:ARG66 4.1 44.5 1.0 O C:HOH338 4.4 34.7 1.0 O D:HOH301 4.5 33.6 1.0 CG D:GLU52 4.7 43.7 1.0 NH1 C:ARG66 4.7 37.6 1.0 CD D:GLU52 4.8 50.4 1.0 CZ C:ARG66 4.9 37.9 1.0

Magnesium binding site 7 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:36.6 occ:1.00 O C:HOH308 2.2 41.2 1.0 O D:HOH310 2.2 38.9 1.0 O D:HOH308 2.2 40.6 1.0 O C:HOH309 2.2 50.0 1.0 O D:HOH309 2.2 37.1 1.0 O D:HOH307 2.2 36.7 1.0 OE1 C:GLU120 3.2 48.9 1.0 OE2 D:GLU52 3.9 52.6 1.0 CD C:GLU120 4.1 45.1 1.0 OE1 D:GLN49 4.3 40.1 1.0 NH2 D:ARG37 4.6 44.9 1.0 CG C:GLU120 4.7 44.3 1.0 CD D:GLU52 4.8 50.4 1.0 CE C:MET116 4.8 36.7 1.0 O D:HOH346 4.8 36.0 1.0 CG D:GLN49 4.8 36.8 1.0 OE1 D:GLU52 4.9 51.5 1.0

Magnesium binding site 8 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:43.5 occ:1.00 O D:HOH302 2.2 48.0 1.0 O A:HOH504 2.2 42.9 1.0 O A:HOH503 2.2 44.2 1.0 O A:HOH505 2.2 63.0 1.0 O A:HOH501 2.2 43.5 1.0 O A:HOH502 2.2 44.5 1.0 OE1 D:GLU120 3.4 55.4 1.0 OE2 A:GLU52 3.9 58.8 1.0 NH2 A:ARG37 4.3 57.1 1.0 CD D:GLU120 4.3 49.7 1.0 OE1 A:GLN49 4.4 48.9 1.0 CG D:GLU120 4.7 53.6 1.0 CG A:GLN49 4.8 38.6 1.0 CD A:GLU52 4.8 57.4 1.0 CE D:MET116 4.8 37.7 1.0 O A:HOH540 4.9 40.2 1.0

Magnesium binding site 9 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:37.6 occ:1.00 O E:HOH308 2.2 40.1 1.0 O E:HOH307 2.2 43.6 1.0 O F:HOH301 2.2 35.6 1.0 O E:HOH309 2.2 40.3 1.0 O F:HOH302 2.2 36.1 1.0 O F:HOH303 2.2 38.4 1.0 OE1 E:GLU120 3.6 52.3 1.0 OE2 F:GLU52 3.7 50.5 1.0 OE1 F:GLN49 4.4 39.5 1.0 CD E:GLU120 4.4 52.8 1.0 CD F:GLU52 4.5 49.1 1.0 OE1 F:GLU52 4.6 52.7 1.0 NH2 F:ARG37 4.7 50.7 1.0 CG E:GLU120 4.7 56.2 1.0 CG F:GLN49 4.8 34.0 1.0 CE E:MET116 4.9 29.0 1.0

Magnesium binding site 10 out of 32 in the Crystal Structure of E. Coli Yfbu at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of E. Coli Yfbu at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:42.4 occ:1.00 O E:HOH311 2.2 50.3 1.0 O F:HOH305 2.2 47.8 1.0 O E:HOH310 2.2 46.0 1.0 O F:HOH306 2.2 44.4 1.0 O F:HOH304 2.2 38.8 1.0 O F:HOH307 2.2 49.0 1.0 NH2 E:ARG66 4.0 34.7 1.0 OE1 F:GLU52 4.3 52.7 1.0 CG F:GLU52 4.6 45.2 1.0 NH1 E:ARG66 4.7 31.6 1.0 NE F:ARG51 4.8 76.6 1.0 CZ E:ARG66 4.8 33.6 1.0 CD F:ARG51 4.9 65.8 1.0 CD F:GLU52 5.0 49.1 1.0

J.Wang, R.A.Wing. Diamonds in the Rough: A Strong Case For the Inclusion of Weak-Intensity X-Ray Diffraction Data. Acta Crystallogr.,Sect.D V. 70 1491 2014.
ISSN: ISSN 0907-4449
PubMed: 24816117
DOI: 10.1107/S1399004714005318