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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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