Atomistry » Magnesium » PDB 4lja-4lsh » 4lr3
Atomistry »
  Magnesium »
    PDB 4lja-4lsh »
      4lr3 »

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

Protein crystallography data

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

Magnesium Binding Sites:

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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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 4lr3

Go back to Magnesium Binding Sites List in 4lr3
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

Reference:

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
Page generated: Mon Aug 11 20:05:36 2025

Last articles

Mg in 4RJK
Mg in 4RKD
Mg in 4RKF
Mg in 4RJJ
Mg in 4RKE
Mg in 4RKC
Mg in 4RGE
Mg in 4RJL
Mg in 4RJI
Mg in 4RIY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy