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Magnesium in PDB 4um5: Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Phosphate Ion

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

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 Phosphate Ion:
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 Phosphate Ion, PDB code: 4um5 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) 31.68 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.795, 45.770, 87.801, 90.00, 90.32, 90.00
R / Rfree (%) 18.789 / 24.578

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 Phosphate Ion (pdb code 4um5). 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 Phosphate Ion, PDB code: 4um5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4um5

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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 Phosphate Ion


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 Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1174

b:29.8
occ:1.00
 O4 A:PO41175 1.9 55.9 1.0
OD2 A:ASP17 1.9 40.4 1.0
O A:ASP19 2.0 38.2 1.0
O A:HOH2001 2.1 31.5 1.0
O A:HOH2002 2.1 33.5 1.0
OD1 A:ASP110 2.2 40.2 1.0
CG A:ASP17 2.9 42.4 1.0
C A:ASP19 3.2 38.9 1.0
OD1 A:ASP17 3.2 44.1 1.0
CG A:ASP110 3.3 42.8 1.0
P A:PO41175 3.4 66.4 1.0
OD2 A:ASP110 3.8 41.9 1.0
CA A:ASP19 3.9 38.6 1.0
OD2 A:ASP114 4.0 40.9 1.0
N A:ASP19 4.0 37.8 1.0
O3 A:PO41175 4.1 60.7 1.0
CB A:ASP19 4.1 40.5 1.0
O1 A:PO41175 4.2 63.1 1.0
N A:GLY20 4.2 37.1 1.0
CB A:ASP17 4.3 40.8 1.0
O2 A:PO41175 4.3 60.9 1.0
O A:HOH2019 4.4 35.4 1.0
CA A:GLY20 4.5 38.0 1.0
CB A:ASP110 4.5 42.1 1.0
C A:VAL18 4.7 36.8 1.0
N A:ASP110 4.8 41.2 1.0
N A:ASP111 4.9 41.1 1.0

Magnesium binding site 2 out of 4 in 4um5

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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 Phosphate Ion


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 Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1174

b:39.6
occ:1.00
 OD1 B:ASP110 1.9 49.7 1.0
OD2 B:ASP17 1.9 56.4 1.0
O B:HOH2004 2.1 32.6 1.0
O B:ASP19 2.1 38.5 1.0
O4 B:PO41175 2.4 62.6 1.0
O B:HOH2005 2.5 44.0 1.0
CG B:ASP110 3.0 48.2 1.0
CG B:ASP17 3.1 55.9 1.0
C B:ASP19 3.4 40.4 1.0
OD2 B:ASP110 3.6 46.7 1.0
OD1 B:ASP17 3.7 58.6 1.0
P B:PO41175 3.8 74.2 1.0
OD2 B:ASP114 3.9 47.8 1.0
CA B:ASP19 4.2 40.6 1.0
N B:ASP19 4.2 41.3 1.0
CB B:ASP110 4.2 47.7 1.0
CB B:ASP17 4.2 50.8 1.0
N B:ASP110 4.3 46.1 1.0
O2 B:PO41175 4.3 69.0 1.0
N B:GLY20 4.3 38.3 1.0
O1 B:PO41175 4.4 66.8 1.0
CA B:GLY20 4.5 36.6 1.0
CB B:ASP19 4.5 42.3 1.0
O B:HOH2013 4.6 36.3 1.0
N B:ASP111 4.6 46.9 1.0
CA B:ASP110 4.7 47.3 1.0
CB B:ASP111 4.7 46.6 1.0
CG1 B:ILE21 4.7 34.5 1.0
O3 B:PO41175 4.8 63.2 1.0
C B:ASP110 4.9 47.1 1.0
CG B:ASP114 4.9 48.0 1.0
C B:VAL18 5.0 40.8 1.0

Magnesium binding site 3 out of 4 in 4um5

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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 Phosphate Ion


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 Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1174

b:38.2
occ:1.00
 O4 C:PO41175 1.9 59.9 1.0
O C:HOH2005 2.0 37.0 1.0
O C:HOH2004 2.1 32.3 1.0
OD2 C:ASP17 2.2 39.2 1.0
OD1 C:ASP110 2.2 48.4 1.0
O C:ASP19 2.4 43.5 1.0
CG C:ASP17 3.1 41.5 1.0
OD1 C:ASP17 3.3 43.8 1.0
CG C:ASP110 3.3 48.4 1.0
P C:PO41175 3.4 74.2 1.0
C C:ASP19 3.5 39.7 1.0
OD2 C:ASP110 3.7 48.9 1.0
OD2 C:ASP114 3.9 47.0 1.0
O3 C:PO41175 4.1 65.8 1.0
O1 C:PO41175 4.2 60.0 1.0
CA C:ASP19 4.3 39.8 1.0
CB C:ASP19 4.3 39.5 1.0
O2 C:PO41175 4.3 62.0 1.0
N C:ASP19 4.4 40.3 1.0
CB C:ASP17 4.5 42.2 1.0
O C:HOH2017 4.5 44.4 1.0
N C:GLY20 4.6 38.5 1.0
CB C:ASP110 4.6 46.3 1.0
N C:ASP110 4.7 45.1 1.0
CB C:ASP111 4.8 44.0 1.0
CA C:GLY20 4.9 37.6 1.0
N C:ASP111 4.9 48.0 1.0
CG C:ASP114 4.9 48.0 1.0

Magnesium binding site 4 out of 4 in 4um5

Go back to Magnesium Binding Sites List in 4um5
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 Phosphate Ion


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 Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1174

b:42.2
occ:1.00
 O D:HOH2002 1.9 35.6 1.0
O4 D:PO41175 2.0 83.9 1.0
OD2 D:ASP17 2.0 53.6 1.0
OD1 D:ASP110 2.1 42.6 1.0
O D:ASP19 2.2 40.3 1.0
O D:HOH2003 2.4 55.1 1.0
CG D:ASP17 3.1 52.2 1.0
CG D:ASP110 3.2 45.6 1.0
C D:ASP19 3.4 40.2 1.0
OD1 D:ASP17 3.4 54.0 1.0
P D:PO41175 3.4 94.5 1.0
OD2 D:ASP110 3.7 42.7 1.0
OD2 D:ASP114 3.8 52.3 1.0
O3 D:PO41175 3.9 90.4 1.0
N D:ASP19 4.0 39.5 1.0
CA D:ASP19 4.0 39.9 1.0
O2 D:PO41175 4.3 84.4 1.0
CB D:ASP19 4.3 40.3 1.0
CB D:ASP17 4.4 48.7 1.0
O1 D:PO41175 4.4 85.1 1.0
CB D:ASP110 4.4 45.7 1.0
O D:HOH2012 4.4 45.7 1.0
N D:GLY20 4.4 38.5 1.0
N D:ASP110 4.6 44.2 1.0
CA D:GLY20 4.7 38.4 1.0
CG D:ASP114 4.8 51.8 1.0
N D:ASP111 4.8 49.3 1.0
CB D:ASP111 4.8 50.6 1.0
C D:VAL18 4.8 40.1 1.0
OD1 D:ASP114 4.9 53.7 1.0
CA D:ASP110 5.0 45.8 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 04:50:17 2024

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