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Magnesium in PDB 8bz7: Crystal Structure of the L. Monocytogenes Rmlt in Complex with Tdp- Rhamnose

Protein crystallography data

The structure of Crystal Structure of the L. Monocytogenes Rmlt in Complex with Tdp- Rhamnose, PDB code: 8bz7 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) 50.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.988, 291.265, 92.394, 90, 100.38, 90
R / Rfree (%) 18.7 / 21.5

Other elements in 8bz7:

The structure of Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose (pdb code 8bz7). 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 in Complex with Tdp- Rhamnose, PDB code: 8bz7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 8bz7

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Magnesium binding site 1 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:53.0
occ:1.00
 OD1 A:ASP112 2.0 46.6 1.0
O1P A:TRH701 2.1 53.9 1.0
O3P A:TRH701 2.2 64.3 1.0
O A:HOH819 2.4 47.6 1.0
O A:HOH801 2.4 44.4 1.0
OD2 A:ASP112 2.4 55.8 1.0
CG A:ASP112 2.5 49.2 1.0
P A:TRH701 3.2 61.3 1.0
P2 A:TRH701 3.3 70.0 1.0
OPP A:TRH701 3.5 63.0 1.0
O1 A:TRH701 3.8 78.0 1.0
OD1 A:ASP113 3.8 40.5 1.0
CB A:ASP110 3.9 46.5 1.0
O2P A:TRH701 3.9 61.4 1.0
OD2 A:ASP113 3.9 45.4 1.0
CB A:ASP112 4.0 48.6 1.0
CG A:ASP113 4.1 43.2 1.0
OD2 A:ASP110 4.3 51.7 1.0
CG A:ASP110 4.5 52.7 1.0
NE1 A:TRP223 4.5 48.9 1.0
O5' A:TRH701 4.5 69.2 1.0
N A:ASP112 4.6 48.3 1.0
O4P A:TRH701 4.6 65.5 1.0
CD1 A:TRP223 4.6 43.7 1.0
CA A:ASP112 4.7 44.7 1.0
O A:ILE224 4.7 48.0 1.0
C A:ASP112 4.8 47.3 1.0
C5' A:TRH701 4.9 61.3 1.0
CD2 A:HIS111 4.9 54.6 1.0

Magnesium binding site 2 out of 9 in 8bz7

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Magnesium binding site 2 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:52.5
occ:1.00
 O1P B:TRH701 2.1 49.9 1.0
OD2 B:ASP112 2.1 50.3 1.0
O3P B:TRH701 2.1 48.5 1.0
O B:HOH822 2.2 38.9 1.0
OD1 B:ASP112 2.2 46.4 1.0
CG B:ASP112 2.5 45.3 1.0
O B:HOH839 2.5 44.0 1.0
P B:TRH701 2.9 47.8 1.0
P2 B:TRH701 3.2 54.1 1.0
OPP B:TRH701 3.3 59.2 1.0
O2P B:TRH701 3.3 54.2 1.0
O1 B:TRH701 3.8 63.9 1.0
ND2 B:ASN229 4.0 88.0 1.0
CB B:ASP112 4.0 43.5 1.0
OD1 B:ASP113 4.2 40.4 1.0
O5' B:TRH701 4.4 53.8 1.0
CB B:ASP110 4.4 41.3 1.0
OD2 B:ASP113 4.5 39.9 1.0
O4P B:TRH701 4.5 62.6 1.0
CG B:ASP113 4.7 42.2 1.0
O B:ILE224 4.7 45.9 1.0
OD2 B:ASP110 4.7 45.6 1.0
NE1 B:TRP223 4.7 43.8 1.0
CA B:ASP112 4.8 45.5 1.0
N B:ASP112 4.8 45.5 1.0
CD2 B:HIS111 4.8 48.9 1.0
C5' B:TRH701 4.9 51.2 1.0
CD1 B:TRP223 4.9 41.1 1.0
CG B:ASP110 4.9 46.5 1.0

Magnesium binding site 3 out of 9 in 8bz7

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Magnesium binding site 3 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:39.4
occ:1.00
 O B:ASP370 2.4 41.1 0.3
O B:ASP370 2.5 41.5 0.7
OH B:TYR347 2.5 44.7 1.0
O B:HOH947 2.8 40.1 1.0
OD2 B:ASP370 3.3 44.6 0.7
CG B:ASP370 3.5 43.1 0.7
OD1 B:ASP370 3.5 43.2 0.7
C B:ASP370 3.6 41.3 0.3
C B:ASP370 3.6 41.3 0.7
CZ B:TYR347 3.8 40.2 1.0
CB B:ASP370 4.4 40.9 0.7
CB B:ASP370 4.4 41.6 0.3
O B:HOH1007 4.4 48.3 1.0
CA B:ASP370 4.4 43.1 0.7
CA B:ASP370 4.5 41.9 0.3
CE2 B:TYR347 4.5 41.6 1.0
N B:LYS371 4.5 41.1 1.0
CA B:LYS371 4.6 39.8 1.0
CE1 B:TYR347 4.8 39.4 1.0
O B:LYS371 4.9 38.2 1.0

Magnesium binding site 4 out of 9 in 8bz7

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Magnesium binding site 4 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:49.0
occ:1.00
 O3P C:TRH701 1.9 57.7 1.0
OD2 C:ASP112 2.2 51.9 1.0
O C:HOH817 2.3 39.1 1.0
O C:HOH826 2.3 40.6 1.0
OD1 C:ASP112 2.3 41.7 1.0
O1P C:TRH701 2.4 49.5 1.0
CG C:ASP112 2.6 43.6 1.0
P2 C:TRH701 3.0 68.6 1.0
P C:TRH701 3.4 72.5 1.0
OPP C:TRH701 3.5 64.4 1.0
O4P C:TRH701 3.5 60.3 1.0
OD1 C:ASP113 4.0 39.7 1.0
O2P C:TRH701 4.1 59.0 1.0
CB C:ASP112 4.1 42.9 1.0
NE1 C:TRP223 4.2 42.4 1.0
OD2 C:ASP113 4.3 41.5 1.0
O C:ILE224 4.3 44.0 1.0
O1 C:TRH701 4.4 76.6 1.0
CB C:ASP110 4.4 41.6 1.0
CG C:ASP113 4.4 43.8 1.0
CD1 C:TRP223 4.4 39.9 1.0
ND2 C:ASN229 4.5 105.7 1.0
OD2 C:ASP110 4.5 45.3 1.0
O C:HOH803 4.6 52.7 1.0
OG1 C:THR226 4.7 77.7 1.0
O5' C:TRH701 4.8 61.0 1.0
CA C:ASP112 4.9 43.0 1.0
CG C:ASP110 5.0 46.0 1.0
N C:ASP112 5.0 42.8 1.0

Magnesium binding site 5 out of 9 in 8bz7

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Magnesium binding site 5 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:50.2
occ:1.00
 O3P D:TRH701 2.0 54.3 1.0
O D:HOH811 2.1 43.7 1.0
O1P D:TRH701 2.2 52.6 1.0
O D:HOH831 2.3 47.6 1.0
OD1 D:ASP112 2.3 48.9 1.0
OD2 D:ASP112 2.3 55.5 1.0
CG D:ASP112 2.6 50.3 1.0
P2 D:TRH701 3.1 61.9 1.0
P D:TRH701 3.2 55.6 1.0
O1 D:TRH701 3.4 66.0 1.0
OPP D:TRH701 3.5 61.7 1.0
OD1 D:ASP113 3.9 41.0 1.0
O2P D:TRH701 3.9 59.9 1.0
OD2 D:ASP113 4.0 43.9 1.0
CB D:ASP110 4.1 44.2 1.0
CB D:ASP112 4.1 50.2 1.0
CG D:ASP113 4.3 44.2 1.0
OD2 D:ASP110 4.3 44.4 1.0
NE1 D:TRP223 4.4 47.3 1.0
O D:ILE224 4.5 50.2 1.0
O4P D:TRH701 4.5 64.0 1.0
CD1 D:TRP223 4.6 44.7 1.0
O5' D:TRH701 4.6 60.2 1.0
CG D:ASP110 4.6 47.5 1.0
C1 D:TRH701 4.8 69.2 1.0
C5' D:TRH701 4.9 51.6 1.0
CA D:ASP112 4.9 47.7 1.0
N D:ASP112 4.9 48.1 1.0
C D:ASP112 4.9 48.4 1.0

Magnesium binding site 6 out of 9 in 8bz7

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Magnesium binding site 6 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:31.4
occ:1.00
 O D:ASP370 2.5 37.3 0.4
OH D:TYR347 2.5 46.2 1.0
O D:ASP370 2.6 36.9 0.6
OH A:TYR347 2.8 46.7 1.0
O A:HOH911 2.8 35.9 1.0
O A:ASP370 2.8 36.2 0.6
O A:ASP370 2.8 42.1 0.4
O D:HOH890 2.9 36.2 1.0
OD2 D:ASP370 3.0 37.8 0.6
OD1 A:ASP370 3.2 38.4 0.6
CG D:ASP370 3.4 40.9 0.6
CG A:ASP370 3.6 39.6 0.6
C D:ASP370 3.7 42.1 0.4
OD1 D:ASP370 3.7 39.7 0.6
C D:ASP370 3.7 41.0 0.6
C A:ASP370 3.8 40.2 0.4
C A:ASP370 3.8 39.4 0.6
CZ D:TYR347 3.8 40.2 1.0
CZ A:TYR347 3.9 34.6 1.0
OD2 A:ASP370 4.0 41.0 0.6
CB D:ASP370 4.3 36.9 0.6
CB D:ASP370 4.4 36.5 0.4
CB A:ASP370 4.4 39.4 0.4
CE2 D:TYR347 4.5 40.9 1.0
CA D:ASP370 4.5 35.8 0.4
CB A:ASP370 4.5 39.5 0.6
CA D:ASP370 4.5 35.9 0.6
CE2 A:TYR347 4.5 38.3 1.0
CA A:ASP370 4.6 36.8 0.4
CA A:ASP370 4.6 39.7 0.6
N D:LYS371 4.6 34.4 1.0
N A:LYS371 4.6 35.2 1.0
CA A:LYS371 4.7 35.5 1.0
CA D:LYS371 4.7 32.9 1.0
CE1 D:TYR347 4.8 40.0 1.0
CE1 A:TYR347 4.9 34.8 1.0
O A:LYS371 4.9 35.7 1.0
O D:LYS371 5.0 34.5 1.0

Magnesium binding site 7 out of 9 in 8bz7

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Magnesium binding site 7 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:62.8
occ:1.00
 OD1 E:ASP112 2.1 58.2 1.0
O1P E:TRH701 2.1 66.5 1.0
O3P E:TRH701 2.2 68.1 1.0
OD2 E:ASP112 2.2 60.5 1.0
O E:HOH806 2.2 54.5 1.0
O E:HOH843 2.2 56.5 1.0
CG E:ASP112 2.4 57.9 1.0
P E:TRH701 3.0 66.0 1.0
P2 E:TRH701 3.3 65.8 1.0
O2P E:TRH701 3.4 71.5 1.0
OPP E:TRH701 3.5 68.2 1.0
O1 E:TRH701 3.8 71.3 1.0
CB E:ASP112 4.0 57.6 1.0
OD1 E:ASP113 4.0 50.5 1.0
NE1 E:TRP223 4.3 61.5 1.0
O E:ILE224 4.3 51.0 1.0
OD2 E:ASP113 4.4 53.1 1.0
CB E:ASP110 4.4 56.5 1.0
O5' E:TRH701 4.5 73.7 1.0
CG E:ASP113 4.5 53.3 1.0
CD1 E:TRP223 4.6 55.4 1.0
O4P E:TRH701 4.6 71.1 1.0
OD2 E:ASP110 4.8 58.7 1.0
CA E:ASP112 4.8 52.8 1.0
N E:ASP112 4.8 56.7 1.0
C E:ASP112 4.9 52.8 1.0
C5' E:TRH701 5.0 65.2 1.0

Magnesium binding site 8 out of 9 in 8bz7

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Magnesium binding site 8 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg703

b:27.6
occ:1.00
 O E:ASP370 2.4 38.2 0.5
O E:ASP370 2.5 37.6 0.5
OH E:TYR347 2.5 45.1 1.0
O E:HOH861 2.6 38.9 1.0
OD2 E:ASP370 3.2 43.6 0.5
CG E:ASP370 3.5 40.5 0.5
C E:ASP370 3.6 38.9 0.5
C E:ASP370 3.6 38.7 0.5
OD1 E:ASP370 3.7 37.9 0.5
CZ E:TYR347 3.8 37.5 1.0
CB E:ASP370 4.3 39.8 0.5
CB E:ASP370 4.4 39.2 0.5
CE2 E:TYR347 4.4 38.1 1.0
CA E:ASP370 4.5 38.6 0.5
CA E:ASP370 4.5 40.3 0.5
N E:LYS371 4.6 38.0 1.0
CA E:LYS371 4.6 36.5 1.0
CE1 E:TYR347 4.7 40.7 1.0
O E:LYS371 4.9 37.8 1.0

Magnesium binding site 9 out of 9 in 8bz7

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Magnesium binding site 9 out of 9 in the Crystal Structure of the L. Monocytogenes Rmlt 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 in Complex with Tdp- Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:53.4
occ:1.00
 O1P F:TRH701 2.0 62.7 1.0
O F:HOH859 2.1 52.8 1.0
OD2 F:ASP112 2.1 61.5 1.0
OD1 F:ASP112 2.2 53.4 1.0
O3P F:TRH701 2.4 53.8 1.0
O F:HOH810 2.4 46.1 1.0
CG F:ASP112 2.5 57.4 1.0
P F:TRH701 3.1 60.4 1.0
P2 F:TRH701 3.3 60.8 1.0
OPP F:TRH701 3.5 71.8 1.0
O1 F:TRH701 3.5 71.5 1.0
O2P F:TRH701 3.8 67.6 1.0
OD1 F:ASP113 4.0 51.4 1.0
CB F:ASP112 4.0 56.2 1.0
CB F:ASP110 4.0 58.1 1.0
OD2 F:ASP110 4.2 59.7 1.0
NE1 F:TRP223 4.2 54.8 1.0
OD2 F:ASP113 4.2 51.9 1.0
CG F:ASP113 4.4 55.2 1.0
CD1 F:TRP223 4.5 52.1 1.0
O5' F:TRH701 4.5 68.7 1.0
CG F:ASP110 4.5 60.1 1.0
O4P F:TRH701 4.7 73.1 1.0
O F:ILE224 4.7 57.0 1.0
C5' F:TRH701 4.8 66.0 1.0
N F:ASP112 4.8 60.5 1.0
C1 F:TRH701 4.8 73.5 1.0
CA F:ASP112 4.8 58.2 1.0
CD2 F:HIS111 5.0 60.4 1.0

Reference:

R.Monteiro, T.B.Cereija, J.H.Morais-Cabral, D.Cabanes. Crystal Structure of the L. Monocytogenes Rmlt in Complex with Tdp-Rhamnose To Be Published.
Page generated: Thu Oct 3 19:56:05 2024

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