Magnesium in PDB 8bz6: Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose

The structure of Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose, PDB code: 8bz6 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)	44.22 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.523, 291.057, 89.824, 90, 100.08, 90
R / Rfree (%)	19.5 / 23.5

The structure of Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose (pdb code 8bz6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose, PDB code: 8bz6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose


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 Udp- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:65.5 occ:1.00 O2A A:UPG701 2.0 70.5 1.0 OD2 A:ASP112 2.1 65.8 1.0 O A:HOH809 2.1 59.4 1.0 O A:HOH891 2.2 61.9 1.0 OD1 A:ASP112 2.2 60.0 1.0 O2B A:UPG701 2.3 70.2 1.0 CG A:ASP112 2.4 64.9 1.0 PA A:UPG701 3.1 75.5 1.0 PB A:UPG701 3.3 80.1 1.0 O3A A:UPG701 3.5 80.5 1.0 O3B A:UPG701 3.7 78.5 1.0 OD1 A:ASP113 3.7 58.4 1.0 O1A A:UPG701 3.9 82.4 1.0 CB A:ASP112 3.9 58.2 1.0 NE1 A:TRP223 4.1 60.9 1.0 OD2 A:ASP113 4.2 55.4 1.0 CG A:ASP113 4.3 56.7 1.0 CB A:ASP110 4.3 61.6 1.0 CD1 A:TRP223 4.4 56.9 1.0 O5C A:UPG701 4.4 75.4 1.0 ND2 A:ASN229 4.5 84.8 1.0 O A:ILE224 4.6 56.7 1.0 OD2 A:ASP110 4.6 65.8 1.0 C5C A:UPG701 4.6 74.3 1.0 O2' A:UPG701 4.7 72.5 1.0 O1B A:UPG701 4.7 85.7 1.0 CA A:ASP112 4.8 59.5 1.0 N A:ASP112 4.8 63.3 1.0 CG A:ASP110 4.9 64.5 1.0 C1' A:UPG701 4.9 76.6 1.0 C A:ASP112 4.9 58.0 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose


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 Udp- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:66.6 occ:1.00 O1A B:UPG701 2.0 66.4 1.0 OD2 B:ASP112 2.1 69.7 1.0 O B:HOH831 2.1 60.4 1.0 OD1 B:ASP112 2.1 65.4 1.0 O B:HOH806 2.1 61.8 1.0 O2B B:UPG701 2.3 68.7 1.0 CG B:ASP112 2.4 65.9 1.0 PA B:UPG701 3.1 65.4 1.0 PB B:UPG701 3.4 69.4 1.0 O3A B:UPG701 3.4 74.5 1.0 O2A B:UPG701 3.9 72.0 1.0 CB B:ASP112 3.9 60.6 1.0 OD1 B:ASP113 4.0 58.9 1.0 O3B B:UPG701 4.0 69.0 1.0 ND2 B:ASN229 4.0 96.0 1.0 NE1 B:TRP223 4.1 61.7 1.0 OD2 B:ASP113 4.3 58.6 1.0 CB B:ASP110 4.3 63.3 1.0 CD1 B:TRP223 4.4 60.0 1.0 CG B:ASP113 4.4 60.8 1.0 O5C B:UPG701 4.5 67.5 1.0 O B:ILE224 4.5 69.1 1.0 O2' B:UPG701 4.5 71.1 1.0 OD2 B:ASP110 4.7 64.7 1.0 O1B B:UPG701 4.7 79.2 1.0 C5C B:UPG701 4.7 69.8 1.0 CA B:ASP112 4.7 65.2 1.0 N B:ASP112 4.8 67.8 1.0 C B:ASP112 4.9 65.0 1.0 CG B:ASP110 4.9 63.5 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose


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 Udp- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:58.6 occ:1.00 OD1 C:ASP112 2.1 58.9 1.0 OD2 C:ASP112 2.1 60.9 1.0 O C:HOH818 2.1 54.6 1.0 O2B C:UPG701 2.2 64.0 1.0 O2A C:UPG701 2.2 59.9 1.0 O C:HOH817 2.2 58.2 1.0 CG C:ASP112 2.4 58.1 1.0 PB C:UPG701 3.3 65.0 1.0 PA C:UPG701 3.4 64.8 1.0 O3A C:UPG701 3.6 69.1 1.0 O3B C:UPG701 3.7 68.6 1.0 OD1 C:ASP113 3.8 54.8 1.0 CB C:ASP112 3.9 56.9 1.0 OD2 C:ASP113 4.0 53.4 1.0 CB C:ASP110 4.1 59.2 1.0 CG C:ASP113 4.2 54.1 1.0 O1A C:UPG701 4.3 68.3 1.0 NE1 C:TRP223 4.3 61.5 1.0 ND2 C:ASN229 4.5 81.9 1.0 CD1 C:TRP223 4.5 59.7 1.0 OD2 C:ASP110 4.5 64.2 1.0 O5C C:UPG701 4.6 63.3 1.0 O1B C:UPG701 4.6 67.5 1.0 C5C C:UPG701 4.7 63.7 1.0 N C:ASP112 4.7 61.8 1.0 O C:ILE224 4.7 61.9 1.0 CA C:ASP112 4.7 56.1 1.0 CG C:ASP110 4.7 59.4 1.0 C C:ASP112 4.8 57.9 1.0 O2' C:UPG701 4.8 67.5 1.0 C1' C:UPG701 5.0 70.3 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose


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 Udp- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:65.2 occ:1.00 O2A D:UPG701 2.0 56.4 1.0 O D:HOH814 2.1 55.0 1.0 OD2 D:ASP112 2.1 68.2 1.0 OD1 D:ASP112 2.1 57.0 1.0 O2B D:UPG701 2.2 61.3 1.0 O D:HOH827 2.3 56.1 1.0 CG D:ASP112 2.4 64.2 1.0 PA D:UPG701 3.1 63.0 1.0 PB D:UPG701 3.2 59.5 1.0 O3A D:UPG701 3.2 59.5 1.0 O3B D:UPG701 3.8 63.4 1.0 O1A D:UPG701 3.9 70.0 1.0 CB D:ASP112 3.9 57.0 1.0 OD1 D:ASP113 4.0 57.2 1.0 ND2 D:ASN229 4.2 78.4 1.0 OD2 D:ASP113 4.2 53.9 1.0 O5C D:UPG701 4.3 60.5 1.0 CB D:ASP110 4.3 57.3 1.0 CG D:ASP113 4.4 55.8 1.0 NE1 D:TRP223 4.5 55.0 1.0 CB D:ASN229 4.6 86.4 1.0 O1B D:UPG701 4.6 62.1 1.0 C5C D:UPG701 4.6 61.0 1.0 O D:ILE224 4.7 59.9 1.0 O2' D:UPG701 4.7 62.3 1.0 CD1 D:TRP223 4.7 56.1 1.0 N D:ASP112 4.7 58.7 1.0 CG D:ASN229 4.7 82.4 1.0 CA D:ASP112 4.8 60.6 1.0 CD2 D:HIS111 4.9 67.0 1.0 C D:ASP112 4.9 61.4 1.0 C1' D:UPG701 4.9 59.9 1.0 CG D:ASP110 5.0 58.8 1.0 OD2 D:ASP110 5.0 61.6 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose


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 Udp- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg703 b:56.9 occ:1.00 O E:HOH867 2.1 53.5 1.0 OD1 E:ASP112 2.1 54.3 1.0 OD2 E:ASP112 2.1 59.3 1.0 O E:HOH806 2.1 49.0 1.0 O2B E:UPG701 2.2 60.4 1.0 O2A E:UPG701 2.2 56.8 1.0 CG E:ASP112 2.4 55.0 1.0 PB E:UPG701 3.3 64.5 1.0 PA E:UPG701 3.3 62.6 1.0 O3A E:UPG701 3.5 60.2 1.0 ND2 E:ASN229 3.7 68.1 1.0 O3B E:UPG701 3.8 61.3 1.0 CB E:ASP112 3.9 54.6 1.0 OD1 E:ASP113 4.0 51.1 1.0 O1A E:UPG701 4.1 60.9 1.0 NE1 E:TRP223 4.3 59.5 1.0 OD2 E:ASP113 4.4 54.9 1.0 CB E:ASP110 4.4 54.9 1.0 CD1 E:TRP223 4.5 53.5 1.0 O E:ILE224 4.5 52.4 1.0 CG E:ASP113 4.5 53.5 1.0 O5C E:UPG701 4.6 62.6 1.0 O1B E:UPG701 4.6 65.9 1.0 O2' E:UPG701 4.7 64.1 1.0 CA E:ASP112 4.7 56.0 1.0 N E:ASP112 4.7 53.1 1.0 C5C E:UPG701 4.8 63.5 1.0 C E:ASP112 4.8 50.0 1.0 CG E:ASN229 4.9 76.8 1.0 C1' E:UPG701 5.0 66.4 1.0 OD2 E:ASP110 5.0 57.2 1.0 O E:ASP112 5.0 51.4 1.0 CD2 E:HIS111 5.0 60.3 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp- Glucose


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 Udp- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg703 b:74.0 occ:1.00 OD2 F:ASP112 2.1 74.9 1.0 O F:HOH809 2.1 70.0 1.0 O2B F:UPG701 2.1 83.0 1.0 O F:HOH829 2.1 70.7 1.0 O2A F:UPG701 2.1 78.8 1.0 OD1 F:ASP112 2.1 71.0 1.0 CG F:ASP112 2.4 74.6 1.0 PA F:UPG701 3.1 75.0 1.0 PB F:UPG701 3.3 81.1 1.0 O3A F:UPG701 3.4 83.0 1.0 O1A F:UPG701 3.8 74.8 1.0 CB F:ASP112 3.9 76.0 1.0 ND2 F:ASN229 3.9 113.9 1.0 OD1 F:ASP113 4.0 67.2 1.0 OD2 F:ASP113 4.1 68.3 1.0 O1B F:UPG701 4.2 95.0 1.0 CB F:ASP110 4.3 72.1 1.0 NE1 F:TRP223 4.4 72.1 1.0 CG F:ASP113 4.4 70.1 1.0 CB F:ASN229 4.4 122.3 1.0 O3B F:UPG701 4.4 80.8 1.0 O5C F:UPG701 4.5 80.6 1.0 O F:ILE224 4.5 75.0 1.0 CD1 F:TRP223 4.6 65.9 1.0 CG F:ASN229 4.7 118.8 1.0 OD2 F:ASP110 4.7 74.6 1.0 CA F:ASP112 4.7 72.0 1.0 N F:ASP112 4.7 78.1 1.0 C1' F:UPG701 4.8 82.5 1.0 C5C F:UPG701 4.8 74.7 1.0 C F:ASP112 4.9 71.7 1.0 CG F:ASP110 4.9 72.0 1.0

R.Monteiro, T.B.Cereija, J.H.Morais-Cabral, D.Cabanes. Crystal Structure of the L. Monocytogenes Rmlt in Complex with Udp-Glucose To Be Published.