Atomistry » Magnesium » PDB 8bux-8c0k » 8bz8
Atomistry »
  Magnesium »
    PDB 8bux-8c0k »
      8bz8 »

Magnesium in PDB 8bz8: Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose

Protein crystallography data

The structure of Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose, PDB code: 8bz8 was solved by T.B.Cereija, J.H.Morais-Cabral, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.76 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.397, 292.381, 93.075, 90, 100.5, 90
R / Rfree (%) 19.1 / 22.8

Other elements in 8bz8:

The structure of Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose (pdb code 8bz8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose, PDB code: 8bz8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 1 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:26.6
occ:1.00
 O B:ASP370 2.3 42.9 0.4
O A:ASP370 2.4 41.8 0.4
O A:ASP370 2.4 46.0 0.6
O B:HOH836 2.4 42.4 1.0
O B:ASP370 2.4 42.8 0.6
O A:HOH851 2.5 39.1 1.0
OH B:TYR347 2.5 46.8 1.0
OH A:TYR347 2.5 44.0 1.0
OD2 A:ASP370 2.9 38.7 0.6
OD2 B:ASP370 3.0 39.9 0.6
CG A:ASP370 3.4 43.5 0.6
CG B:ASP370 3.4 44.5 0.6
C B:ASP370 3.6 44.8 0.4
C A:ASP370 3.6 42.2 0.6
C A:ASP370 3.6 42.6 0.4
C B:ASP370 3.6 46.2 0.6
O B:HOH801 3.6 47.1 1.0
OD1 A:ASP370 3.8 42.1 0.6
OD1 B:ASP370 3.8 40.6 0.6
CZ A:TYR347 3.8 40.0 1.0
CZ B:TYR347 3.8 38.6 1.0
O A:HOH801 3.9 42.9 1.0
CB B:ASP370 4.2 45.5 0.4
CB B:ASP370 4.2 43.6 0.6
CB A:ASP370 4.3 46.6 0.6
CB A:ASP370 4.3 43.3 0.4
CA B:ASP370 4.4 48.5 0.4
CA B:ASP370 4.4 42.6 0.6
CA A:ASP370 4.4 44.2 0.6
CA A:ASP370 4.4 41.6 0.4
CE2 A:TYR347 4.5 40.3 1.0
N B:LYS371 4.5 42.2 1.0
N A:LYS371 4.5 42.8 1.0
CE2 B:TYR347 4.6 39.6 1.0
CA B:LYS371 4.6 39.3 1.0
CA A:LYS371 4.6 42.9 1.0
CE1 A:TYR347 4.8 37.3 1.0
CE1 B:TYR347 4.8 43.2 1.0
O B:LYS371 4.9 45.6 1.0
O A:LYS371 5.0 44.6 1.0

Magnesium binding site 2 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 2 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:67.3
occ:1.00
 O A:HOH814 2.1 50.6 1.0
OD2 A:ASP112 2.2 62.7 1.0
OD1 A:ASP112 2.2 58.6 1.0
O A:HOH845 2.2 52.0 1.0
O1P A:TRH703 2.3 68.0 1.0
O4P A:TRH703 2.4 75.4 1.0
CG A:ASP112 2.4 57.4 1.0
P A:TRH703 3.4 81.3 1.0
P2 A:TRH703 3.6 88.8 1.0
OPP A:TRH703 3.6 83.3 1.0
OD1 A:ASP113 3.9 45.8 1.0
CB A:ASP112 3.9 51.6 1.0
O2P A:TRH703 3.9 80.4 1.0
O A:ILE224 4.3 56.0 1.0
OD2 A:ASP113 4.3 45.5 1.0
CB A:ASP110 4.3 55.5 1.0
OD2 A:ASP110 4.4 62.4 1.0
NE1 A:TRP223 4.4 49.2 1.0
CG A:ASP113 4.4 47.6 1.0
ND2 A:ASN229 4.4 93.1 1.0
CD1 A:TRP223 4.6 48.6 1.0
O3P A:TRH703 4.6 77.9 1.0
O1 A:TRH703 4.7 96.9 1.0
O5' A:TRH703 4.7 81.2 1.0
CA A:ASP112 4.7 50.2 1.0
N A:ASP112 4.8 54.9 1.0
C A:ASP112 4.8 51.6 1.0
CG A:ASP110 4.8 58.3 1.0

Magnesium binding site 3 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 3 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:76.9
occ:1.00
 O4P B:TRH702 2.0 86.4 1.0
OD1 B:ASP112 2.0 75.1 1.0
OD2 B:ASP112 2.1 81.2 1.0
O B:HOH808 2.1 68.4 1.0
O B:HOH802 2.2 63.9 1.0
O1P B:TRH702 2.3 73.2 1.0
CG B:ASP112 2.4 74.8 1.0
P B:TRH702 3.3 86.2 1.0
P2 B:TRH702 3.3 94.5 1.0
OPP B:TRH702 3.6 93.5 1.0
CB B:ASP112 3.9 69.0 1.0
O2P B:TRH702 3.9 86.7 1.0
OD1 B:ASP113 4.0 65.6 1.0
CB B:ASP110 4.2 68.8 1.0
NE1 B:TRP223 4.3 62.5 1.0
O3P B:TRH702 4.3 86.0 1.0
OD2 B:ASP113 4.3 63.0 1.0
O1 B:TRH702 4.3 98.8 1.0
CG B:ASP113 4.4 64.4 1.0
O B:ILE224 4.5 64.3 1.0
CD1 B:TRP223 4.6 58.8 1.0
OD2 B:ASP110 4.6 63.4 1.0
CA B:ASP112 4.7 66.7 1.0
N B:ASP112 4.7 69.4 1.0
O5' B:TRH702 4.7 84.6 1.0
CG B:ASP110 4.7 67.8 1.0
C B:ASP112 4.8 67.8 1.0

Magnesium binding site 4 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 4 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:35.5
occ:1.00
 OH D:TYR347 2.4 44.0 1.0
OH C:TYR347 2.4 47.8 1.0
O C:ASP370 2.4 43.8 1.0
O C:HOH888 2.4 44.3 1.0
O D:HOH829 2.5 43.7 1.0
O D:ASP370 2.5 43.6 1.0
OD2 C:ASP370 3.2 48.8 1.0
OD2 D:ASP370 3.4 47.2 1.0
OD1 C:ASP370 3.4 53.4 1.0
CG C:ASP370 3.4 54.0 1.0
CG D:ASP370 3.5 49.6 1.0
OD1 D:ASP370 3.5 48.2 1.0
C C:ASP370 3.6 44.2 1.0
C D:ASP370 3.7 40.6 1.0
CZ C:TYR347 3.7 45.2 1.0
CZ D:TYR347 3.7 43.1 1.0
CE2 C:TYR347 4.4 40.4 1.0
CB C:ASP370 4.4 48.3 1.0
CE2 D:TYR347 4.4 41.8 1.0
CB D:ASP370 4.4 41.4 1.0
CA C:ASP370 4.5 44.8 1.0
N C:LYS371 4.6 42.2 1.0
CA D:ASP370 4.6 41.5 1.0
CA C:LYS371 4.6 41.3 1.0
N D:LYS371 4.7 39.9 1.0
CE1 D:TYR347 4.7 42.4 1.0
CA D:LYS371 4.7 41.7 1.0
CE1 C:TYR347 4.8 41.9 1.0
O D:LYS371 4.8 40.2 1.0
O C:LYS371 4.9 41.7 1.0

Magnesium binding site 5 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 5 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:64.0
occ:1.00
 O4P C:TRH703 2.0 70.9 1.0
OD1 C:ASP112 2.0 57.0 1.0
O C:HOH834 2.0 51.1 1.0
OD2 C:ASP112 2.2 59.6 1.0
O1P C:TRH703 2.3 61.7 1.0
O C:HOH832 2.3 52.1 1.0
CG C:ASP112 2.4 54.7 1.0
P C:TRH703 3.3 69.0 1.0
P2 C:TRH703 3.3 74.2 1.0
OPP C:TRH703 3.6 76.2 1.0
CB C:ASP112 3.9 48.1 1.0
O2P C:TRH703 3.9 73.0 1.0
OD1 C:ASP113 4.0 44.4 1.0
OD2 C:ASP113 4.2 47.8 1.0
ND2 C:ASN229 4.3 104.9 1.0
O3P C:TRH703 4.3 75.1 1.0
O1 C:TRH703 4.4 84.0 1.0
OD1 C:ASN229 4.4 105.6 1.0
CG C:ASP113 4.4 47.0 1.0
NE1 C:TRP223 4.4 52.7 1.0
CB C:ASP110 4.4 50.8 1.0
O C:ILE224 4.5 52.0 1.0
CD1 C:TRP223 4.6 49.8 1.0
CA C:ASP112 4.6 49.4 1.0
N C:ASP112 4.7 51.6 1.0
O5' C:TRH703 4.7 69.5 1.0
C C:ASP112 4.7 49.6 1.0
O C:ASP112 4.8 49.4 1.0
CG C:ASN229 4.8 105.2 1.0
OD2 C:ASP110 4.8 54.6 1.0

Magnesium binding site 6 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 6 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:55.6
occ:1.00
 O4P D:TRH702 1.8 66.7 1.0
OD1 D:ASP112 2.0 52.9 1.0
OD2 D:ASP112 2.1 57.1 1.0
O D:HOH807 2.1 45.1 1.0
CG D:ASP112 2.3 52.4 1.0
O D:HOH801 2.3 52.6 1.0
O1P D:TRH702 2.3 55.5 1.0
P2 D:TRH702 3.1 72.0 1.0
P D:TRH702 3.3 60.5 1.0
OPP D:TRH702 3.5 73.3 1.0
CB D:ASP112 3.8 47.9 1.0
O2P D:TRH702 3.8 68.8 1.0
OD1 D:ASP113 4.1 45.1 1.0
O1 D:TRH702 4.1 75.0 1.0
O3P D:TRH702 4.2 65.5 1.0
OD2 D:ASP113 4.2 43.9 1.0
CB D:ASP110 4.3 51.0 1.0
CG D:ASP113 4.4 48.3 1.0
O D:ILE224 4.5 47.1 1.0
N D:ASP112 4.6 50.1 1.0
CA D:ASP112 4.6 45.7 1.0
NE1 D:TRP223 4.6 47.2 1.0
O5' D:TRH702 4.7 69.3 1.0
C D:ASP112 4.7 48.0 1.0
OD2 D:ASP110 4.7 53.7 1.0
CD1 D:TRP223 4.8 44.5 1.0
CD2 D:HIS111 4.9 50.8 1.0
CG D:ASP110 4.9 50.1 1.0
O D:ASP112 5.0 47.3 1.0

Magnesium binding site 7 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 7 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:33.6
occ:1.00
 O F:HOH818 2.2 41.1 1.0
O E:ASP370 2.3 44.1 0.5
O E:ASP370 2.4 45.5 0.5
O E:HOH838 2.5 47.9 1.0
O F:ASP370 2.5 44.9 1.0
OH E:TYR347 2.5 44.8 1.0
OH F:TYR347 2.5 44.8 1.0
OD2 F:ASP370 3.0 49.1 1.0
OD2 E:ASP370 3.2 45.2 0.5
CG F:ASP370 3.3 51.2 1.0
CG E:ASP370 3.5 46.3 0.5
OD1 F:ASP370 3.5 48.9 1.0
C E:ASP370 3.5 46.1 0.5
C E:ASP370 3.5 46.5 0.5
C F:ASP370 3.7 42.1 1.0
OD1 E:ASP370 3.8 47.4 0.5
CZ F:TYR347 3.8 43.1 1.0
CZ E:TYR347 3.8 40.6 1.0
CB E:ASP370 4.3 47.6 0.5
CB F:ASP370 4.3 39.9 1.0
CB E:ASP370 4.3 47.1 0.5
CA E:ASP370 4.4 46.2 0.5
CA E:ASP370 4.4 49.6 0.5
N E:LYS371 4.4 43.7 1.0
CA F:ASP370 4.5 40.7 1.0
CA E:LYS371 4.5 43.5 1.0
CE2 E:TYR347 4.5 42.6 1.0
CE2 F:TYR347 4.6 45.4 1.0
N F:LYS371 4.6 40.8 1.0
CA F:LYS371 4.7 40.0 1.0
CE1 F:TYR347 4.7 45.3 1.0
CE1 E:TYR347 4.8 40.2 1.0
O E:LYS371 4.9 48.9 1.0

Magnesium binding site 8 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 8 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:74.0
occ:1.00
 OD2 E:ASP112 2.1 74.1 1.0
OD1 E:ASP112 2.1 72.8 1.0
O E:HOH801 2.1 61.7 1.0
O4P E:TRH703 2.2 84.7 1.0
O E:HOH812 2.2 65.2 1.0
O1P E:TRH703 2.3 80.9 1.0
CG E:ASP112 2.3 70.3 1.0
P E:TRH703 3.4 86.3 1.0
P2 E:TRH703 3.4 89.5 1.0
OPP E:TRH703 3.6 87.5 1.0
OD1 E:ASP113 3.7 56.4 1.0
CB E:ASP112 3.8 64.3 1.0
NE1 E:TRP223 3.9 63.0 1.0
O1 E:TRH703 4.1 97.0 1.0
O2P E:TRH703 4.1 86.4 1.0
OD2 E:ASP113 4.1 58.8 1.0
CD1 E:TRP223 4.2 57.7 1.0
CG E:ASP113 4.2 58.2 1.0
O E:ILE224 4.2 53.3 1.0
CB E:ASP110 4.3 67.3 1.0
OD2 E:ASP110 4.4 70.9 1.0
O3P E:TRH703 4.6 90.1 1.0
CA E:ASP112 4.6 62.0 1.0
N E:ASP112 4.7 66.8 1.0
O5' E:TRH703 4.7 86.7 1.0
C E:ASP112 4.7 59.8 1.0
O E:ASP112 4.9 57.9 1.0
CG2 E:THR226 4.9 68.3 1.0
CG E:ASP110 4.9 69.2 1.0
C5' E:TRH703 5.0 83.0 1.0

Magnesium binding site 9 out of 9 in 8bz8

Go back to Magnesium Binding Sites List in 8bz8
Magnesium binding site 9 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose


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 the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg701

b:75.5
occ:1.00
 OD1 F:ASP112 2.1 72.0 1.0
OD2 F:ASP112 2.1 83.0 1.0
O F:HOH802 2.1 67.0 1.0
O F:HOH801 2.1 70.1 1.0
O4P F:TRH702 2.2 83.7 1.0
O1P F:TRH702 2.3 85.2 1.0
CG F:ASP112 2.4 77.7 1.0
P F:TRH702 3.3 88.0 1.0
P2 F:TRH702 3.3 84.7 1.0
OPP F:TRH702 3.5 94.4 1.0
CB F:ASP112 3.9 75.1 1.0
O1 F:TRH702 3.9 96.2 1.0
O2P F:TRH702 3.9 90.4 1.0
OD1 F:ASP113 4.0 68.7 1.0
O F:ILE224 4.3 72.2 1.0
CB F:ASP110 4.4 73.8 1.0
OD2 F:ASP113 4.4 67.0 1.0
CG F:ASP113 4.5 68.2 1.0
NE1 F:TRP223 4.6 68.5 1.0
OD2 F:ASP110 4.6 71.4 1.0
O3P F:TRH702 4.6 88.5 1.0
N F:ASP112 4.7 73.4 1.0
CA F:ASP112 4.7 73.3 1.0
O5' F:TRH702 4.7 85.8 1.0
C F:ASP112 4.8 72.3 1.0
CD1 F:TRP223 4.8 64.5 1.0
CD2 F:HIS111 4.9 79.6 1.0
O F:ASP112 5.0 66.5 1.0

Reference:

R.Monteiro, T.B.Cereija, J.H.Morais-Cabral, D.Cabanes. Crystal Structure of the L. Monocytogenes Rmlt D198A Variant in Complex with Tdp-Rhamnose To Be Published.
Page generated: Thu Oct 3 19:56:06 2024

Last articles

Cl in 5XUJ
Cl in 5XU7
Cl in 5XTU
Cl in 5XNP
Cl in 5XPF
Cl in 5XS2
Cl in 5XRB
Cl in 5XR5
Cl in 5XQE
Cl in 5XQD
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy