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Magnesium in PDB 5f7u: Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate

Protein crystallography data

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate, PDB code: 5f7u was solved by S.H.Light, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.222, 100.894, 71.812, 90.00, 104.01, 90.00
R / Rfree (%) 15.9 / 19

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate (pdb code 5f7u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate, PDB code: 5f7u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5f7u

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Magnesium binding site 1 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:11.6
occ:1.00
 O A:GLY992 2.2 22.4 1.0
O A:THR989 2.2 22.8 1.0
OD1 A:ASP1085 2.2 21.9 1.0
OE1 A:GLU970 2.2 19.6 1.0
OE1 A:GLU972 2.2 21.5 1.0
OE2 A:GLU972 2.6 21.4 1.0
O A:ASP1085 2.6 20.8 1.0
CD A:GLU972 2.8 21.2 1.0
C A:THR989 3.4 23.0 1.0
CD A:GLU970 3.4 19.2 1.0
C A:GLY992 3.4 23.1 1.0
CG A:ASP1085 3.4 22.2 1.0
C A:ASP1085 3.5 20.5 1.0
CA A:ASP1085 3.9 21.2 1.0
OG1 A:THR989 4.1 22.6 1.0
N A:THR989 4.1 23.6 1.0
N A:GLY992 4.2 23.8 1.0
OE2 A:GLU970 4.2 19.8 1.0
N A:GLY990 4.2 23.0 1.0
CB A:GLU970 4.2 18.4 1.0
CG A:GLU970 4.3 18.7 1.0
N A:PHE993 4.3 23.1 1.0
CB A:ASP1085 4.3 21.6 1.0
CG A:GLU972 4.3 21.5 1.0
CA A:THR989 4.3 23.5 1.0
OD2 A:ASP1085 4.3 22.7 1.0
CA A:GLY990 4.4 22.8 1.0
CA A:GLY992 4.4 24.2 1.0
CA A:PHE993 4.4 22.5 1.0
CB A:TYR988 4.5 24.6 1.0
N A:HIS1086 4.6 19.7 1.0
N A:ALA971 4.6 18.5 1.0
CB A:HIS1086 4.6 19.5 1.0
CA A:GLU970 4.6 18.1 1.0
C A:GLY990 4.8 23.7 1.0
N A:THR991 4.8 23.8 1.0
CB A:THR989 4.8 23.2 1.0
CB A:PHE993 4.9 22.5 1.0
CD1 A:TYR988 5.0 25.7 1.0
C A:TYR988 5.0 24.5 1.0

Magnesium binding site 2 out of 5 in 5f7u

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Magnesium binding site 2 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:14.7
occ:1.00
 O A:HOH1255 2.0 17.2 1.0
O A:HOH1250 2.0 18.7 1.0
O A:HOH1257 2.1 17.1 1.0
O A:HOH1314 2.1 15.0 1.0
O A:HOH2317 2.1 17.3 1.0
OD1 A:ASN377 2.2 16.6 1.0
CG A:ASN377 3.1 15.9 1.0
ND2 A:ASN377 3.5 16.0 1.0
O A:HOH1251 3.9 22.1 1.0
OD2 A:ASP183 4.0 20.1 1.0
OD1 A:ASP373 4.1 16.9 1.0
O A:HOH2354 4.2 40.7 1.0
OD2 A:ASP373 4.2 17.1 1.0
OD2 A:ASP185 4.2 18.7 1.0
OD2 A:ASP380 4.2 19.6 1.0
O A:HOH2369 4.2 33.4 1.0
ND2 A:ASN376 4.3 17.2 1.0
O A:HOH1850 4.3 41.5 1.0
OD1 A:ASP185 4.4 17.9 1.0
CB A:ASN377 4.5 15.1 1.0
CG A:ASP373 4.5 16.6 1.0
NZ A:LYS369 4.6 32.1 1.0
CG A:ASP185 4.7 18.2 1.0
CA A:ASN377 4.8 14.6 1.0
O A:HOH1780 5.0 51.7 1.0
O A:ASP373 5.0 14.2 1.0

Magnesium binding site 3 out of 5 in 5f7u

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Magnesium binding site 3 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:30.0
occ:1.00
 O A:ASP847 2.2 31.3 1.0
O A:HOH1640 2.2 24.3 1.0
O A:HOH2161 2.4 22.2 1.0
O A:HOH2059 2.5 20.7 1.0
O A:SER850 2.6 23.3 1.0
C A:ASP847 3.2 28.7 1.0
ND2 A:ASN833 3.5 18.5 1.0
C A:SER850 3.8 24.4 1.0
O A:HOH1738 4.0 28.6 1.0
N A:ASP847 4.1 26.4 1.0
N A:LEU848 4.1 27.1 1.0
CA A:LEU848 4.1 26.2 1.0
O A:HOH1722 4.2 15.9 1.0
CA A:ASP847 4.2 28.8 1.0
O A:HOH2206 4.3 34.2 1.0
O A:VAL844 4.5 22.5 1.0
CA A:TYR851 4.6 23.5 1.0
N A:SER850 4.6 25.8 1.0
CB A:ASP847 4.6 31.5 1.0
CG A:ASN833 4.7 18.1 1.0
N A:TYR851 4.7 23.6 1.0
C A:LEU848 4.7 26.6 1.0
C A:ASN846 4.8 24.2 1.0
CA A:SER850 4.8 25.7 1.0
OG A:SER850 4.9 28.9 1.0
CD2 A:LEU848 4.9 24.6 1.0
O A:HOH2152 5.0 10.8 1.0
O A:GLY845 5.0 21.8 1.0
N A:LYS849 5.0 26.8 1.0

Magnesium binding site 4 out of 5 in 5f7u

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Magnesium binding site 4 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:15.1
occ:1.00
 O A:HOH2010 2.2 42.2 1.0
OD1 A:ASP403 2.2 19.9 1.0
OD2 A:ASP407 2.2 19.0 1.0
O A:GLU401 2.2 17.8 1.0
O A:HOH1863 2.3 24.5 1.0
O A:HOH2190 2.3 44.3 1.0
CG A:ASP403 3.2 19.1 1.0
CG A:ASP407 3.3 18.6 1.0
C A:GLU401 3.4 16.3 1.0
OD1 A:ASP407 3.6 19.6 1.0
N A:ASP403 3.7 16.9 1.0
OD2 A:ASP403 3.9 20.0 1.0
NE A:ARG404 4.0 22.5 1.0
CB A:ASP403 4.1 18.1 1.0
CA A:TRP402 4.3 16.0 1.0
N A:TRP402 4.3 15.9 1.0
C A:TRP402 4.4 16.2 1.0
CA A:ASP403 4.4 17.3 1.0
CA A:GLU401 4.4 16.0 1.0
NH2 A:ARG404 4.4 23.8 1.0
O A:HOH1807 4.5 32.3 1.0
CB A:GLU401 4.6 16.4 1.0
CB A:ASP407 4.6 17.8 1.0
CZ A:ARG404 4.6 23.8 1.0
O A:SER693 4.8 17.9 1.0
CD A:ARG404 4.9 21.6 1.0
CG A:ARG404 4.9 20.2 1.0
C A:ASP403 5.0 17.8 1.0

Magnesium binding site 5 out of 5 in 5f7u

Go back to Magnesium Binding Sites List in 5f7u
Magnesium binding site 5 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Pentasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:24.7
occ:1.00
 O A:HOH2155 2.1 29.4 1.0
O A:TYR851 2.2 27.2 1.0
O A:ASP852 2.2 26.6 1.0
O A:HOH2139 2.4 37.0 1.0
O A:HOH2310 2.6 43.0 1.0
C A:TYR851 3.1 24.4 1.0
C A:ASP852 3.2 24.2 1.0
CA A:ASP852 3.5 24.6 1.0
N A:ASP852 3.7 23.8 1.0
O A:HOH1449 4.0 18.0 1.0
O A:HOH1477 4.1 27.4 1.0
CA A:TYR851 4.2 23.5 1.0
N A:ASN853 4.4 22.5 1.0
CB A:TYR851 4.4 22.7 1.0
N A:TYR851 4.5 23.6 1.0
O A:HOH2234 4.5 48.0 1.0
O A:HOH2558 4.6 52.5 1.0
O A:HOH2033 4.7 27.9 1.0
O A:HOH1221 4.9 24.8 1.0
OD1 A:ASP900 4.9 29.5 1.0
OD1 A:ASP852 4.9 27.1 1.0
CA A:ASN853 4.9 21.7 1.0
CB A:ASP852 5.0 24.7 1.0

Reference:

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
Page generated: Mon Dec 14 20:17:28 2020

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