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Magnesium in PDB 4ume: Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

Enzymatic activity of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

All present enzymatic activity of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule:
3.1.3.45;

Protein crystallography data

The structure of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule, PDB code: 4ume was solved by S.Dhindwal, S.Tomar, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.38 / 2.09
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 86.610, 86.610, 41.400, 90.00, 90.00, 90.00
R / Rfree (%) 19.015 / 25.844

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule (pdb code 4ume). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule, PDB code: 4ume:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ume

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Magnesium binding site 1 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule


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 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1175

b:17.6
occ:1.00
 OD2 A:ASP17 2.0 15.2 1.0
OD1 A:ASP110 2.0 14.8 1.0
O A:HOH2007 2.1 14.9 1.0
O A:HOH2009 2.1 12.8 1.0
O A:HOH2006 2.1 17.1 1.0
O A:ASP19 2.2 13.1 1.0
CG A:ASP17 3.0 14.5 1.0
CG A:ASP110 3.1 15.2 1.0
C A:ASP19 3.3 13.3 1.0
OD1 A:ASP17 3.4 14.2 1.0
OD2 A:ASP110 3.5 14.6 1.0
OD2 A:ASP114 4.0 12.4 1.0
CA A:ASP19 4.1 14.0 1.0
N A:ASP19 4.2 13.5 1.0
CB A:ASP19 4.2 14.6 1.0
O A:HOH2082 4.3 23.6 1.0
CB A:ASP17 4.3 14.0 1.0
CB A:ASP110 4.4 14.9 1.0
N A:GLY20 4.4 13.0 1.0
O A:HOH2048 4.5 12.9 1.0
N A:ASP110 4.5 14.3 1.0
O8 A:KDO1174 4.5 33.0 1.0
O A:HOH2008 4.6 6.2 1.0
C8 A:KDO1174 4.6 33.2 1.0
CA A:GLY20 4.6 12.7 1.0
N A:ASP111 4.8 15.6 1.0
CB A:ASP111 4.8 15.3 1.0
CA A:ASP110 4.9 15.1 1.0
C A:VAL18 4.9 13.4 1.0
CG1 A:ILE21 5.0 12.2 1.0

Magnesium binding site 2 out of 4 in 4ume

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Magnesium binding site 2 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule


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 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1176

b:16.2
occ:0.25
 O A:HOH2085 2.3 18.9 1.0
O A:HOH2086 2.5 42.9 1.0
O A:HOH2084 3.3 30.6 1.0
OE1 A:GLN26 4.6 17.4 1.0
NE2 A:GLN26 4.9 17.7 1.0

Magnesium binding site 3 out of 4 in 4ume

Go back to Magnesium Binding Sites List in 4ume
Magnesium binding site 3 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule


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 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1177

b:85.3
occ:0.25
 O A:HOH2084 2.8 30.6 1.0
MG A:MG1178 3.1 25.8 0.2
CG2 A:THR36 5.0 12.3 1.0

Magnesium binding site 4 out of 4 in 4ume

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Magnesium binding site 4 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule


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 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1178

b:25.8
occ:0.25
 MG A:MG1177 3.1 85.3 0.2
O A:HOH2021 3.2 11.7 1.0
OG1 A:THR36 4.5 12.1 1.0
CG2 A:THR36 4.8 12.3 1.0

Reference:

S.Dhindwal, P.Priyadarshini, D.N.Patil, S.Tapas, P.Kumar, S.Tomar, P.Kumar. Ligand-Bound Structures of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Moraxella Catarrhalis Reveal A Water Channel Connecting to the Active Site For the Second Step of Catalysis Acta Crystallogr.,Sect.D V. 71 239 2015.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714025218
Page generated: Tue Aug 20 04:50:59 2024

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