Atomistry » Magnesium » PDB 5f7u-5fjj » 5f7u
Atomistry »
  Magnesium »
    PDB 5f7u-5fjj »
      5f7u »

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

Go back to Magnesium Binding Sites List in 5f7u
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

Go back to Magnesium Binding Sites List in 5f7u
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

Go back to Magnesium Binding Sites List in 5f7u
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

Go back to Magnesium Binding Sites List in 5f7u
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: Sun Sep 29 04:06:18 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy