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Magnesium in PDB 4umf: Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion, Phosphate 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, Phosphate 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, Phosphate 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, Phosphate Ion and Kdo Molecule, PDB code: 4umf 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) 31.69 / 2.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.914, 46.053, 87.226, 90.00, 90.25, 90.00
R / Rfree (%) 21.426 / 28.093

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, Phosphate Ion and Kdo Molecule (pdb code 4umf). 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, Phosphate Ion and Kdo Molecule, PDB code: 4umf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4umf

Go back to Magnesium Binding Sites List in 4umf
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, Phosphate 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, Phosphate Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1175

b:40.0
occ:1.00
 O4 A:PO41174 1.8 48.2 1.0
O A:HOH2004 1.9 32.7 1.0
OD2 A:ASP17 2.1 50.2 1.0
O A:ASP19 2.2 41.1 1.0
OD1 A:ASP110 2.2 47.5 1.0
O A:HOH2005 2.2 41.6 1.0
CG A:ASP17 2.9 48.4 1.0
OD1 A:ASP17 3.1 48.8 1.0
P A:PO41174 3.2 58.2 1.0
CG A:ASP110 3.3 46.4 1.0
C A:ASP19 3.3 44.1 1.0
OD2 A:ASP110 3.8 46.4 1.0
OD2 A:ASP114 3.8 50.7 1.0
O1 A:PO41174 3.8 50.6 1.0
O3 A:PO41174 3.9 47.6 1.0
CA A:ASP19 4.0 45.7 1.0
N A:ASP19 4.1 45.7 1.0
CB A:ASP19 4.1 48.6 1.0
CB A:ASP17 4.3 47.7 1.0
O2 A:PO41174 4.3 44.4 1.0
O A:HOH2032 4.3 39.1 1.0
O7 B:KDO1176 4.4 60.3 1.0
N A:GLY20 4.4 41.2 1.0
N A:ASP110 4.5 47.5 1.0
CB A:ASP110 4.6 46.3 1.0
CA A:GLY20 4.7 42.2 1.0
CB A:ASP111 4.8 48.6 1.0
CG A:ASP114 4.8 51.2 1.0
C A:VAL18 4.9 44.0 1.0
C8 B:KDO1176 4.9 59.5 1.0
N A:ASP111 4.9 49.2 1.0
CA A:ASP110 5.0 48.2 1.0

Magnesium binding site 2 out of 4 in 4umf

Go back to Magnesium Binding Sites List in 4umf
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, Phosphate 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, Phosphate Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1175

b:51.1
occ:1.00
 OD1 B:ASP110 1.8 48.3 1.0
O B:ASP19 2.1 47.1 1.0
OD2 B:ASP17 2.2 44.6 1.0
O4 B:PO41174 2.2 55.8 1.0
O B:HOH2004 2.3 43.5 1.0
O B:HOH2005 2.4 45.6 1.0
CG B:ASP110 2.9 48.5 1.0
CG B:ASP17 3.0 46.8 1.0
OD1 B:ASP17 3.3 48.5 1.0
OD2 B:ASP110 3.3 44.3 1.0
C B:ASP19 3.3 45.4 1.0
P B:PO41174 3.6 60.5 1.0
OD2 B:ASP114 3.8 49.3 1.0
O1 B:PO41174 4.1 55.1 1.0
CA B:ASP19 4.2 45.6 1.0
N B:ASP19 4.2 44.9 1.0
CB B:ASP110 4.2 48.1 1.0
N B:ASP110 4.2 47.4 1.0
N B:GLY20 4.3 44.3 1.0
O2 B:PO41174 4.3 57.8 1.0
CB B:ASP17 4.3 46.9 1.0
CA B:GLY20 4.4 42.1 1.0
CB B:ASP19 4.5 47.5 1.0
CB B:ASP111 4.5 52.7 1.0
N B:ASP111 4.6 52.3 1.0
CG1 B:ILE21 4.6 40.5 1.0
CA B:ASP110 4.7 49.8 1.0
O3 B:PO41174 4.7 60.0 1.0
CG B:ASP114 4.9 48.3 1.0
C B:VAL18 4.9 43.6 1.0
O7 B:KDO1177 4.9 64.1 1.0
C B:GLY20 4.9 41.1 1.0
C B:ASP110 5.0 51.2 1.0

Magnesium binding site 3 out of 4 in 4umf

Go back to Magnesium Binding Sites List in 4umf
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, Phosphate 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, Phosphate Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1175

b:42.2
occ:1.00
 O4 C:PO41174 2.0 52.4 1.0
O C:ASP19 2.1 44.7 1.0
OD1 C:ASP110 2.1 47.5 1.0
OD2 C:ASP17 2.1 49.3 1.0
O C:HOH2008 2.2 40.5 1.0
O A:HOH2041 2.4 39.4 1.0
CG C:ASP17 2.9 50.1 1.0
OD1 C:ASP17 3.1 52.8 1.0
CG C:ASP110 3.2 51.2 1.0
C C:ASP19 3.2 44.5 1.0
P C:PO41174 3.5 71.0 1.0
OD2 C:ASP110 3.6 50.1 1.0
CA C:ASP19 4.0 44.7 1.0
OD2 C:ASP114 4.0 52.0 1.0
N C:ASP19 4.0 43.7 1.0
CB C:ASP19 4.1 46.7 1.0
O2 C:PO41174 4.1 54.4 1.0
O7 A:KDO1176 4.3 59.5 1.0
N C:GLY20 4.3 44.1 1.0
O3 C:PO41174 4.3 63.9 1.0
CB C:ASP17 4.3 46.9 1.0
O1 C:PO41174 4.4 60.4 1.0
CB C:ASP110 4.5 50.3 1.0
C8 A:KDO1176 4.5 66.1 1.0
CA C:GLY20 4.5 44.6 1.0
O A:HOH2040 4.6 42.2 1.0
C C:VAL18 4.7 44.5 1.0
N C:ASP110 4.8 51.0 1.0
CB C:ASP111 4.9 53.5 1.0
N C:ASP111 4.9 52.0 1.0
N C:VAL18 5.0 45.2 1.0

Magnesium binding site 4 out of 4 in 4umf

Go back to Magnesium Binding Sites List in 4umf
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, Phosphate 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, Phosphate Ion and Kdo Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1175

b:39.8
occ:1.00
 O D:HOH2005 2.0 36.3 1.0
O4 D:PO41174 2.1 47.2 1.0
OD1 D:ASP110 2.1 53.2 1.0
O D:ASP19 2.1 43.5 1.0
O D:HOH2004 2.1 46.8 1.0
OD2 D:ASP17 2.3 48.6 1.0
CG D:ASP17 3.1 51.5 1.0
CG D:ASP110 3.1 54.0 1.0
C D:ASP19 3.2 44.3 1.0
OD1 D:ASP17 3.3 53.4 1.0
OD2 D:ASP110 3.5 52.5 1.0
P D:PO41174 3.5 67.6 1.0
CA D:ASP19 4.0 45.5 1.0
O C:HOH2052 4.0 52.1 1.0
OD2 D:ASP114 4.1 52.6 1.0
CB D:ASP19 4.1 46.1 1.0
N D:ASP19 4.1 48.0 1.0
O2 D:PO41174 4.2 64.5 1.0
O3 D:PO41174 4.2 65.2 1.0
N D:GLY20 4.3 44.0 1.0
CB D:ASP110 4.5 53.1 1.0
CB D:ASP17 4.5 52.7 1.0
O1 D:PO41174 4.5 59.7 1.0
CA D:GLY20 4.5 43.5 1.0
C8 C:KDO1176 4.5 81.4 1.0
CB D:ASP111 4.6 57.1 1.0
N D:ASP110 4.8 53.0 1.0
N D:ASP111 4.8 54.8 1.0
CG1 C:VAL41 4.9 56.0 1.0
O7 C:KDO1176 4.9 74.4 1.0
C D:VAL18 4.9 47.4 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 04:51:03 2024

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