Magnesium in PDB 8vc9: Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form

The structure of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form, PDB code: 8vc9 was solved by A.Mechaly, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.074, 102.327, 184.476, 90, 92.49, 90
R / Rfree (%)	21 / 25.4

The structure of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form also contains other interesting chemical elements:

Fluorine

(F)

18 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form (pdb code 8vc9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form, PDB code: 8vc9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:82.5 occ:1.00 OD1 A:ASP11 2.1 84.5 1.0 OD2 A:ASP56 2.1 84.5 1.0 O A:HOH505 2.1 89.2 1.0 F3 A:BEF403 2.1 78.4 1.0 O A:HOH502 2.1 82.1 1.0 O A:SER58 2.2 86.9 1.0 CG A:ASP56 3.0 79.1 1.0 CG A:ASP11 3.1 91.2 1.0 C A:SER58 3.2 84.3 1.0 BE A:BEF403 3.2 79.3 1.0 OD1 A:ASP56 3.3 80.5 1.0 OD2 A:ASP11 3.4 91.0 1.0 CA A:SER58 4.0 80.1 1.0 N A:LEU59 4.1 83.1 1.0 OE2 A:GLU10 4.1 89.2 1.0 N A:SER58 4.1 75.0 1.0 CB A:SER58 4.2 82.6 1.0 CA A:LEU59 4.2 90.1 1.0 F2 A:BEF403 4.3 75.7 1.0 CB A:ASP56 4.3 79.9 1.0 F1 A:BEF403 4.3 77.8 1.0 CB A:ASP11 4.4 92.0 1.0 OG A:SER58 4.5 88.0 1.0 N A:ASP11 4.6 82.3 1.0 NZ A:LYS106 4.6 81.3 1.0 CG A:LEU59 4.8 84.5 1.0 CD A:GLU10 4.9 87.7 1.0 CB A:LEU59 5.0 86.5 1.0

Magnesium binding site 2 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:92.7 occ:1.00 O1G A:ACP401 2.1 116.8 1.0 O A:HOH501 2.1 100.5 1.0 O1A A:ACP401 2.1 103.9 1.0 O2B A:ACP401 2.1 110.1 1.0 OD1 A:ASN274 2.1 92.9 1.0 O A:HOH503 2.1 93.2 1.0 CG A:ASN274 3.1 91.1 1.0 PB A:ACP401 3.2 83.6 1.0 PA A:ACP401 3.2 92.5 1.0 PG A:ACP401 3.3 125.2 1.0 O3A A:ACP401 3.6 97.1 1.0 ND2 A:ASN274 3.6 92.6 1.0 C3B A:ACP401 3.6 110.7 1.0 O5' A:ACP401 3.9 89.7 1.0 O2G A:ACP401 4.2 111.4 1.0 O A:ASN270 4.4 91.7 1.0 CB A:ASN274 4.4 89.3 1.0 CA A:GLY343 4.5 90.7 1.0 O3G A:ACP401 4.5 123.0 1.0 O1B A:ACP401 4.5 88.3 1.0 O2A A:ACP401 4.5 87.3 1.0 N A:ASN274 4.6 88.8 1.0 CA A:ASN274 4.6 91.2 1.0 N A:GLY343 4.8 90.8 1.0

Magnesium binding site 3 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:61.2 occ:1.00 OD2 B:ASP56 2.0 62.7 1.0 O B:HOH504 2.0 56.7 1.0 OD1 B:ASP11 2.0 58.0 1.0 F3 B:BEF403 2.1 56.6 1.0 O B:HOH506 2.1 61.9 1.0 O B:SER58 2.2 62.2 1.0 CG B:ASP56 3.0 58.3 1.0 CG B:ASP11 3.1 62.6 1.0 C B:SER58 3.2 53.1 1.0 BE B:BEF403 3.3 58.1 1.0 OD1 B:ASP56 3.4 56.6 1.0 OD2 B:ASP11 3.5 67.7 1.0 CA B:SER58 4.0 58.1 1.0 OE2 B:GLU10 4.0 64.3 1.0 N B:LEU59 4.1 56.6 1.0 F2 B:BEF403 4.2 58.3 1.0 CB B:SER58 4.2 63.3 1.0 CA B:LEU59 4.2 66.0 1.0 N B:SER58 4.2 55.4 1.0 CB B:ASP56 4.3 56.2 1.0 CB B:ASP11 4.4 51.6 1.0 N B:ASP11 4.5 60.4 1.0 OG B:SER58 4.5 63.3 1.0 F1 B:BEF403 4.5 55.9 1.0 CG B:LEU59 4.7 57.9 1.0 NZ B:LYS106 4.7 53.8 1.0 CD B:GLU10 4.8 64.0 1.0 OE1 B:GLU10 4.9 65.1 1.0 N B:SER12 4.9 59.1 1.0 CB B:LEU59 5.0 60.2 1.0 CA B:ASP11 5.0 62.1 1.0

Magnesium binding site 4 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:125.7 occ:1.00 O1G B:ACP401 2.0 138.5 1.0 OD1 B:ASN274 2.1 125.3 1.0 O2B B:ACP401 2.1 139.3 1.0 O1A B:ACP401 2.1 132.6 1.0 O B:HOH505 2.1 122.7 1.0 O B:HOH502 2.1 114.7 1.0 CG B:ASN274 3.0 127.9 1.0 PB B:ACP401 3.1 122.3 1.0 PA B:ACP401 3.2 115.3 1.0 PG B:ACP401 3.2 150.8 1.0 ND2 B:ASN274 3.4 130.5 1.0 O3A B:ACP401 3.5 126.5 1.0 C3B B:ACP401 3.5 136.4 1.0 O5' B:ACP401 3.9 118.0 1.0 O2G B:ACP401 4.1 141.2 1.0 CA B:GLY343 4.3 120.3 1.0 CB B:ASN274 4.3 121.0 1.0 O3G B:ACP401 4.4 141.1 1.0 O B:ASN270 4.4 119.3 1.0 O1B B:ACP401 4.4 123.3 1.0 CA B:ASN274 4.5 121.7 1.0 O2A B:ACP401 4.5 125.8 1.0 N B:ASN274 4.5 118.4 1.0 N B:GLY343 4.6 121.6 1.0

Magnesium binding site 5 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:60.6 occ:1.00 OD2 C:ASP56 2.0 70.7 1.0 OD1 C:ASP11 2.1 66.5 1.0 O C:SER58 2.1 64.2 1.0 F3 C:BEF403 2.1 62.6 1.0 O C:HOH501 2.1 61.2 1.0 O C:HOH505 2.1 72.1 1.0 CG C:ASP56 3.0 59.2 1.0 CG C:ASP11 3.1 67.9 1.0 C C:SER58 3.1 60.0 1.0 BE C:BEF403 3.3 63.6 1.0 OD1 C:ASP56 3.3 58.7 1.0 OD2 C:ASP11 3.5 70.3 1.0 CA C:SER58 3.9 63.8 1.0 N C:LEU59 4.0 67.2 1.0 N C:SER58 4.1 61.9 1.0 CB C:SER58 4.1 71.5 1.0 CA C:LEU59 4.2 74.0 1.0 OE2 C:GLU10 4.2 68.1 1.0 CB C:ASP56 4.3 67.7 1.0 F2 C:BEF403 4.3 56.9 1.0 F1 C:BEF403 4.3 63.9 1.0 CB C:ASP11 4.4 67.9 1.0 OG C:SER58 4.5 72.1 1.0 N C:ASP11 4.5 62.7 1.0 NZ C:LYS106 4.6 60.5 1.0 CG C:LEU59 4.6 71.8 1.0 CD C:GLU10 4.9 68.2 1.0 CB C:LEU59 4.9 72.0 1.0 OE1 C:GLU10 5.0 65.8 1.0

Magnesium binding site 6 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:87.1 occ:1.00 O1G C:ACP401 2.1 107.6 1.0 O C:HOH506 2.1 82.6 1.0 O1A C:ACP401 2.1 92.9 1.0 OD1 C:ASN274 2.1 80.2 1.0 O2B C:ACP401 2.1 94.3 1.0 O C:HOH503 2.2 84.3 1.0 CG C:ASN274 3.1 80.8 1.0 PB C:ACP401 3.2 78.3 1.0 PA C:ACP401 3.2 81.2 1.0 PG C:ACP401 3.3 126.3 1.0 O3A C:ACP401 3.5 84.3 1.0 ND2 C:ASN274 3.6 86.7 1.0 C3B C:ACP401 3.6 102.7 1.0 O5' C:ACP401 3.9 82.4 1.0 O3G C:ACP401 4.1 110.0 1.0 NZ C:LYS334 4.2 87.3 1.0 CA C:GLY343 4.3 91.3 1.0 O C:ASN270 4.4 74.9 1.0 CB C:ASN274 4.4 75.5 1.0 O1B C:ACP401 4.5 90.0 1.0 O2G C:ACP401 4.5 113.3 1.0 O2A C:ACP401 4.5 84.3 1.0 N C:ASN274 4.6 80.7 1.0 CA C:ASN274 4.6 82.6 1.0 N C:GLY343 4.7 96.2 1.0

Magnesium binding site 7 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:77.5 occ:1.00 OD2 D:ASP56 2.0 74.0 1.0 O D:SER58 2.1 80.1 1.0 F3 D:BEF403 2.1 72.3 1.0 O D:HOH501 2.1 79.5 1.0 O D:HOH507 2.1 80.7 1.0 OD1 D:ASP11 2.1 87.0 1.0 CG D:ASP56 3.0 72.6 1.0 C D:SER58 3.2 80.6 1.0 CG D:ASP11 3.2 86.7 1.0 BE D:BEF403 3.3 74.2 1.0 OD1 D:ASP56 3.4 74.0 1.0 OD2 D:ASP11 3.6 82.8 1.0 CA D:SER58 3.9 75.9 1.0 OE2 D:GLU10 4.0 77.6 1.0 N D:LEU59 4.0 83.1 1.0 CB D:SER58 4.1 81.3 1.0 N D:SER58 4.1 75.6 1.0 CA D:LEU59 4.2 92.0 1.0 CB D:ASP56 4.3 79.9 1.0 F1 D:BEF403 4.3 72.1 1.0 OG D:SER58 4.4 83.7 1.0 F2 D:BEF403 4.4 66.5 1.0 CB D:ASP11 4.5 84.5 1.0 NZ D:LYS106 4.6 65.0 1.0 N D:ASP11 4.6 77.6 1.0 CG D:LEU59 4.6 81.2 1.0 CD D:GLU10 4.8 82.0 1.0 CB D:LEU59 4.9 87.4 1.0 N D:SER12 5.0 74.9 1.0

Magnesium binding site 8 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:78.4 occ:1.00 O1G D:ACP401 2.0 94.7 1.0 O D:HOH502 2.1 85.8 1.0 O2B D:ACP401 2.1 85.9 1.0 OD1 D:ASN274 2.1 75.0 1.0 O1A D:ACP401 2.1 86.5 1.0 O D:HOH505 2.1 78.6 1.0 CG D:ASN274 3.2 75.9 1.0 PA D:ACP401 3.2 77.0 1.0 PB D:ACP401 3.2 75.3 1.0 PG D:ACP401 3.3 122.9 1.0 O3A D:ACP401 3.6 83.7 1.0 ND2 D:ASN274 3.7 70.5 1.0 C3B D:ACP401 3.8 87.8 1.0 O5' D:ACP401 3.9 77.7 1.0 O2G D:ACP401 4.3 103.7 1.0 O3G D:ACP401 4.4 120.7 1.0 CA D:GLY343 4.4 73.7 1.0 CE D:LYS334 4.4 76.9 1.0 CB D:ASN274 4.4 73.2 1.0 O D:ASN270 4.4 65.8 1.0 O1B D:ACP401 4.5 83.1 1.0 O2A D:ACP401 4.5 76.0 1.0 CA D:ASN274 4.5 69.7 1.0 N D:ASN274 4.5 71.3 1.0 NZ D:LYS334 4.7 79.0 1.0 N D:GLY343 4.7 81.5 1.0

Magnesium binding site 9 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:104.5 occ:1.00 F3 E:BEF403 2.1 93.7 1.0 OD2 E:ASP56 2.1 113.5 1.0 O E:HOH503 2.1 108.3 1.0 O E:HOH506 2.1 120.0 1.0 OD1 E:ASP11 2.1 118.4 1.0 O E:SER58 2.2 113.5 1.0 CG E:ASP56 2.9 110.7 1.0 CG E:ASP11 3.2 120.6 1.0 C E:SER58 3.2 111.4 1.0 BE E:BEF403 3.2 100.6 1.0 OD1 E:ASP56 3.2 114.9 1.0 OD2 E:ASP11 3.6 108.1 1.0 CA E:SER58 4.0 103.4 1.0 N E:LEU59 4.0 119.8 1.0 OE2 E:GLU10 4.1 110.0 1.0 CA E:LEU59 4.1 122.7 1.0 N E:SER58 4.2 99.5 1.0 F1 E:BEF403 4.2 101.8 1.0 CB E:ASP56 4.2 97.4 1.0 F2 E:BEF403 4.3 97.1 1.0 CB E:SER58 4.3 104.0 1.0 CB E:ASP11 4.5 120.9 1.0 CG E:LEU59 4.6 116.0 1.0 OG E:SER58 4.6 107.0 1.0 N E:ASP11 4.7 110.4 1.0 NZ E:LYS106 4.7 100.6 1.0 CB E:LEU59 4.9 119.4 1.0 CD E:GLU10 4.9 112.1 1.0 OE1 E:GLU10 5.0 116.8 1.0

Magnesium binding site 10 out of 12 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg404 b:122.5 occ:1.00 OD1 E:ASN274 2.1 118.3 1.0 O1G E:ACP401 2.1 131.8 1.0 O1A E:ACP401 2.1 119.7 1.0 O E:HOH501 2.1 126.4 1.0 O E:HOH502 2.1 109.0 1.0 O2B E:ACP401 2.1 126.8 1.0 CG E:ASN274 3.0 116.8 1.0 PB E:ACP401 3.2 116.8 1.0 PA E:ACP401 3.2 107.1 1.0 PG E:ACP401 3.3 143.9 1.0 O3A E:ACP401 3.5 115.1 1.0 ND2 E:ASN274 3.5 110.4 1.0 C3B E:ACP401 3.7 127.7 1.0 O5' E:ACP401 3.9 110.9 1.0 O E:ASN270 4.2 107.8 1.0 O2G E:ACP401 4.3 142.6 1.0 CB E:ASN274 4.3 110.5 1.0 CA E:GLY343 4.4 112.2 1.0 O3G E:ACP401 4.4 132.0 1.0 N E:ASN274 4.5 107.0 1.0 CA E:ASN274 4.5 106.6 1.0 O1B E:ACP401 4.5 111.1 1.0 O2A E:ACP401 4.5 109.1 1.0 N E:GLY343 4.7 122.2 1.0

E.Agustoni, A.Mechaly, J.Dalla Rizza, P.Isaikina, F.Trajtenberg, T.Muntener, E.Wunder, A.I.Ko, T.Schirmer, A.Buschiazzo, S.Hiller. Coiled Coil Formation and Symmetry Breaking Activates the Leptospira Virulence Regulator Lvrb, A Hybrid Response Regulator To Be Published.