Magnesium in PDB 4kmq: 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E

The structure of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E, PDB code: 4kmq was solved by A.S.Halavaty, G.Minasov, E.V.Filippova, I.Dubrovska, J.Winsor, L.Shuvalova, S.Peterson, W.F.Anderson, Center For Structural Genomicsof Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.66 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.858, 102.359, 74.334, 90.00, 104.86, 90.00
R / Rfree (%)	15.1 / 18.4

The binding sites of Magnesium atom in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E (pdb code 4kmq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E, PDB code: 4kmq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:33.8 occ:1.00 O A:HOH2196 2.0 32.1 1.0 O A:HOH2197 2.0 27.3 1.0 OD1 A:ASN377 2.0 28.2 1.0 O A:HOH2097 2.1 29.8 1.0 O A:HOH2124 2.1 30.2 1.0 O A:HOH1354 2.3 31.6 1.0 CG A:ASN377 3.0 28.4 1.0 ND2 A:ASN377 3.4 28.4 1.0 O A:HOH1450 4.0 32.8 1.0 OD2 A:ASP380 4.0 34.9 1.0 OD2 A:ASP183 4.1 34.2 1.0 OD1 A:ASP373 4.1 30.2 1.0 OD2 A:ASP185 4.1 32.8 1.0 ND2 A:ASN376 4.2 33.6 1.0 OD2 A:ASP373 4.2 30.4 1.0 O A:HOH2098 4.3 45.6 1.0 OD1 A:ASP185 4.3 30.4 1.0 CB A:ASN377 4.3 25.3 1.0 CG A:ASP373 4.5 30.0 1.0 CG A:ASP185 4.7 31.1 1.0 CA A:ASN377 4.7 26.1 1.0 NZ A:LYS369 4.8 48.4 1.0 N A:ASN377 5.0 25.0 1.0 O A:ASP373 5.0 27.2 1.0

Magnesium binding site 2 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:37.8 occ:1.00 O A:HOH2142 2.1 37.9 1.0 O A:HOH1953 2.2 42.3 1.0 O A:GLU401 2.2 30.6 1.0 O A:HOH2139 2.2 40.4 1.0 OD1 A:ASP403 2.3 37.6 1.0 OD2 A:ASP407 2.3 36.9 1.0 CG A:ASP403 3.3 35.8 1.0 CG A:ASP407 3.4 35.7 1.0 C A:GLU401 3.4 31.0 1.0 OD1 A:ASP407 3.7 39.7 1.0 N A:ASP403 3.9 30.9 1.0 OD2 A:ASP403 4.0 38.4 1.0 NE A:ARG404 4.2 39.7 1.0 CB A:ASP403 4.2 33.4 1.0 N A:TRP402 4.3 30.1 1.0 CA A:GLU401 4.3 30.8 1.0 CA A:TRP402 4.3 30.4 1.0 CB A:GLU401 4.4 31.0 1.0 NH2 A:ARG404 4.5 44.8 1.0 C A:TRP402 4.5 31.2 1.0 CA A:ASP403 4.6 32.5 1.0 CB A:ASP407 4.7 34.1 1.0 CZ A:ARG404 4.7 42.5 1.0 O A:SER693 4.7 34.6 1.0 OD1 A:ASP694 4.7 44.0 1.0 CG A:GLU401 5.0 30.5 1.0

Magnesium binding site 3 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:32.2 occ:1.00 OD1 A:ASP1085 1.8 56.1 1.0 O A:THR989 1.9 55.1 1.0 OE2 A:GLU972 2.1 29.3 1.0 OE1 A:GLU970 2.3 44.7 1.0 OE1 A:GLU972 2.4 50.1 1.0 O A:GLY992 2.6 61.9 1.0 CD A:GLU972 2.6 44.5 1.0 O A:ASP1085 2.9 49.4 1.0 C A:THR989 3.0 54.8 1.0 CG A:ASP1085 3.0 54.0 1.0 CD A:GLU970 3.3 41.1 1.0 OG1 A:THR989 3.4 54.3 1.0 N A:THR989 3.6 57.9 1.0 C A:ASP1085 3.6 50.5 1.0 C A:GLY992 3.7 63.4 1.0 CA A:THR989 3.8 56.3 1.0 OD2 A:ASP1085 3.8 54.3 1.0 N A:GLY990 3.9 54.0 1.0 OE2 A:GLU970 3.9 42.6 1.0 CA A:ASP1085 3.9 53.6 1.0 CB A:ASP1085 4.1 54.7 1.0 CA A:GLY990 4.1 53.6 1.0 CG A:GLU972 4.2 42.4 1.0 CB A:THR989 4.2 53.3 1.0 N A:GLY992 4.4 62.5 1.0 CG A:GLU970 4.4 40.7 1.0 CB A:TYR988 4.4 64.8 1.0 CB A:GLU970 4.5 41.1 1.0 C A:TYR988 4.6 61.4 1.0 C A:GLY990 4.6 56.6 1.0 N A:PHE993 4.6 65.0 1.0 CA A:GLY992 4.6 65.0 1.0 CB A:HIS1086 4.6 47.5 1.0 ND1 A:HIS1086 4.6 51.0 1.0 N A:HIS1086 4.7 49.5 1.0 CA A:PHE993 4.7 64.2 1.0 CD1 A:TYR988 4.7 67.6 1.0 N A:THR991 4.8 57.3 1.0 CA A:GLU970 4.9 41.4 1.0 CA A:TYR988 4.9 63.9 1.0

Magnesium binding site 4 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:49.5 occ:1.00 O A:HOH2164 2.0 55.9 1.0 O A:HOH2081 2.1 44.5 1.0 O A:HOH2165 2.1 51.1 1.0 O A:HOH2166 2.2 52.8 1.0 O A:HOH1536 2.2 43.1 1.0 O A:HOH1476 2.2 39.8 1.0 ND2 A:ASN606 4.0 36.3 1.0 OD1 A:ASP560 4.2 34.1 1.0 CG A:ASN606 4.3 34.6 1.0 OD1 A:ASN606 4.4 31.4 1.0 O A:HOH1243 4.4 34.3 1.0 O A:HOH1309 4.4 45.5 1.0 O A:GLY558 4.5 33.1 1.0 O A:HOH2117 4.8 45.6 1.0 CE1 A:HIS475 4.9 33.4 1.0

Magnesium binding site 5 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1105 b:50.0 occ:1.00 O A:HOH1580 2.0 47.1 1.0 O A:HOH2127 2.0 46.5 1.0 O A:HOH2138 2.0 51.5 1.0 O A:HOH1659 2.1 53.5 1.0 O A:HOH2159 2.2 40.0 1.0 O A:HOH2012 2.2 52.6 1.0 O A:HOH1472 3.4 54.7 1.0 O A:HOH1660 3.8 37.0 1.0 O A:HOH1331 4.2 29.7 1.0 O A:HOH1414 4.3 35.4 1.0 O A:HOH2161 4.3 52.2 1.0 NZ A:LYS643 4.3 29.8 1.0 OD2 A:ASP765 4.5 32.6 1.0 CE A:LYS643 5.0 30.9 1.0

Magnesium binding site 6 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1106 b:64.9 occ:1.00 O A:HOH2141 1.9 52.1 1.0 O A:HOH2168 2.0 59.5 1.0 O A:HOH2145 2.1 76.4 1.0 O A:HOH2131 2.2 74.7 1.0 OD1 A:ASP836 3.8 48.4 1.0 OD1 A:ASN853 4.1 41.3 1.0 OD2 A:ASP836 4.1 53.3 1.0 O A:HOH1585 4.3 46.3 1.0 CG A:ASP836 4.4 48.5 1.0 O A:HOH1797 4.5 56.8 1.0 OE2 A:GLU901 4.5 55.7 1.0 O A:ASN931 4.5 59.1 1.0

Magnesium binding site 7 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1107 b:60.6 occ:1.00 O A:HOH2156 1.9 70.0 1.0 O A:HOH2155 2.0 57.9 1.0 O A:HOH2213 2.0 71.0 1.0 O A:HOH2154 2.2 51.6 1.0 O A:GLU884 4.0 38.1 1.0 OD1 A:ASP863 4.0 43.2 1.0 O A:HOH1658 4.2 43.4 1.0 CG A:ASP863 4.6 42.8 1.0 O A:HOH1448 4.6 47.7 1.0 OD2 A:ASP863 4.6 48.3 1.0 CA A:GLY862 4.8 38.1 1.0

Magnesium binding site 8 out of 8 in the 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 1.9 Angstrom Resolution Crystal Structure of Uncharacterized Protein LMO2446 From Listeria Monocytogenes Egd-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1108 b:65.2 occ:1.00 O A:HOH2201 2.0 66.6 1.0 O A:HOH2200 2.0 59.5 1.0 O A:HOH1568 2.0 49.8 1.0 O A:HOH1590 2.2 53.3 1.0 O A:HOH2210 3.7 49.4 1.0 O A:HOH1770 4.0 53.5 1.0 O A:HOH2049 4.2 56.4 1.0 O A:HOH1321 4.2 40.2 1.0 O A:GLY510 4.4 45.8 1.0 O A:HOH2150 4.6 60.1 1.0 O A:HOH1631 5.0 53.8 1.0

S.H.Light, L.A.Cahoon, A.S.Halavaty, N.E.Freitag, W.F.Anderson. Structure to Function of An Alpha-Glucan Metabolic Pathway That Promotes Listeria Monocytogenes Pathogenesis. Nat Microbiol V. 2 16202 2016.
ISSN: ESSN 2058-5276
PubMed: 27819654
DOI: 10.1038/NMICROBIOL.2016.202