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Magnesium in PDB 4um7: Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion

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

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

Protein crystallography data

The structure of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion, PDB code: 4um7 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) 27.16 / 1.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.264, 43.562, 87.552, 90.00, 91.18, 90.00
R / Rfree (%) 19.698 / 22.831

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion (pdb code 4um7). 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 (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion, PDB code: 4um7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4um7

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Magnesium binding site 1 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium 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 (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg175

b:17.9
occ:1.00
 OD2 A:ASP17 1.9 17.8 1.0
O A:HOH2031 2.0 27.4 1.0
OD1 A:ASP110 2.0 19.2 1.0
O A:ASP19 2.2 14.4 1.0
O A:HOH2034 2.2 24.6 1.0
O A:HOH2033 2.3 29.7 1.0
CG A:ASP17 3.0 16.9 1.0
CG A:ASP110 3.1 19.0 1.0
C A:ASP19 3.4 14.3 1.0
OD1 A:ASP17 3.5 17.1 1.0
OD2 A:ASP110 3.5 19.8 1.0
OD2 A:ASP114 3.9 16.3 1.0
CA A:ASP19 4.1 14.5 1.0
N A:ASP19 4.1 14.5 1.0
O A:HOH2030 4.3 25.3 1.0
CB A:ASP17 4.3 16.3 1.0
CB A:ASP19 4.3 15.0 1.0
CB A:ASP110 4.4 18.4 1.0
N A:GLY20 4.4 14.0 1.0
N A:ASP110 4.6 16.7 1.0
O A:HOH2032 4.6 18.0 1.0
CA A:GLY20 4.6 14.0 1.0
N A:ASP111 4.7 16.8 1.0
O A:HOH2147 4.7 21.9 1.0
O A:HOH2036 4.7 38.9 1.0
C A:VAL18 4.8 14.3 1.0
CB A:ASP111 4.9 16.0 1.0
CA A:ASP110 4.9 17.5 1.0
CG A:ASP114 4.9 16.0 1.0
N A:VAL18 5.0 14.5 1.0

Magnesium binding site 2 out of 4 in 4um7

Go back to Magnesium Binding Sites List in 4um7
Magnesium binding site 2 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium 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 (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg175

b:15.6
occ:1.00
 O B:HOH2023 2.0 19.3 1.0
OD1 B:ASP110 2.0 19.0 1.0
OD2 B:ASP17 2.0 18.1 1.0
O B:HOH2019 2.1 27.3 1.0
O B:ASP19 2.1 15.3 1.0
O B:HOH2018 2.2 21.3 1.0
CG B:ASP110 3.1 18.6 1.0
CG B:ASP17 3.1 17.5 1.0
C B:ASP19 3.3 15.1 1.0
OD2 B:ASP110 3.4 19.7 1.0
OD1 B:ASP17 3.5 18.1 1.0
OD2 B:ASP114 4.0 15.8 1.0
CA B:ASP19 4.1 15.6 1.0
N B:ASP19 4.1 15.4 1.0
CB B:ASP19 4.2 16.2 1.0
O B:HOH2005 4.3 25.6 1.0
N B:GLY20 4.4 14.7 1.0
CB B:ASP110 4.4 18.0 1.0
CB B:ASP17 4.4 16.8 1.0
O B:HOH2021 4.4 26.6 1.0
O B:HOH2139 4.6 18.5 1.0
N B:ASP110 4.6 16.6 1.0
CA B:GLY20 4.6 14.2 1.0
N B:ASP111 4.6 16.1 1.0
O B:HOH2020 4.8 24.6 1.0
NZ B:LYS87 4.8 22.8 1.0
CB B:ASP111 4.8 15.3 1.0
C B:VAL18 4.9 15.4 1.0
CA B:ASP110 4.9 17.1 1.0
O B:HOH2025 5.0 41.3 1.0
CG B:ASP114 5.0 15.2 1.0

Magnesium binding site 3 out of 4 in 4um7

Go back to Magnesium Binding Sites List in 4um7
Magnesium binding site 3 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium 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 (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg175

b:19.5
occ:1.00
 O C:HOH2014 1.9 18.3 0.1
OD2 C:ASP17 2.0 16.4 1.0
OD1 C:ASP110 2.0 20.2 1.0
O C:ASP19 2.1 16.1 1.0
O C:HOH2018 2.2 25.8 1.0
O C:HOH2017 2.4 27.1 1.0
CG C:ASP17 3.1 16.0 1.0
CG C:ASP110 3.1 19.5 1.0
C C:ASP19 3.3 15.8 1.0
OD1 C:ASP17 3.5 16.3 1.0
OD2 C:ASP110 3.5 20.5 1.0
OD2 C:ASP114 4.0 15.1 1.0
CA C:ASP19 4.0 15.9 1.0
N C:ASP19 4.1 15.5 1.0
O C:HOH2015 4.2 20.1 1.0
CB C:ASP19 4.2 16.3 1.0
N C:GLY20 4.3 15.4 1.0
CB C:ASP17 4.3 15.9 1.0
CB C:ASP110 4.4 18.9 1.0
CA C:GLY20 4.5 15.0 1.0
O C:HOH2021 4.5 27.4 1.0
O B:HOH2071 4.6 20.3 1.0
O C:HOH2016 4.6 16.4 1.0
N C:ASP111 4.7 16.9 1.0
N C:ASP110 4.7 17.2 1.0
CB C:ASP111 4.8 16.1 1.0
C C:VAL18 4.9 15.4 1.0
CA C:ASP110 4.9 17.8 1.0
CG C:ASP114 5.0 15.0 1.0

Magnesium binding site 4 out of 4 in 4um7

Go back to Magnesium Binding Sites List in 4um7
Magnesium binding site 4 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium 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 (Kdsc) From Moraxella Catarrhalis in Complex with Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg175

b:19.3
occ:1.00
 OD2 D:ASP17 2.0 16.3 1.0
O D:HOH2017 2.0 29.5 1.0
O D:HOH2020 2.0 21.0 1.0
OD1 D:ASP110 2.0 18.1 1.0
O D:ASP19 2.1 14.7 1.0
O D:HOH2019 2.4 28.4 1.0
CG D:ASP110 3.1 18.0 1.0
CG D:ASP17 3.1 15.7 1.0
C D:ASP19 3.3 14.2 1.0
OD2 D:ASP110 3.5 18.9 1.0
OD1 D:ASP17 3.5 15.9 1.0
OD2 D:ASP114 4.0 15.4 1.0
CA D:ASP19 4.1 14.6 1.0
N D:ASP19 4.2 14.2 1.0
CB D:ASP19 4.2 15.1 1.0
O D:HOH2018 4.3 23.2 1.0
N D:GLY20 4.4 14.0 1.0
CB D:ASP17 4.4 15.0 1.0
CB D:ASP110 4.4 17.3 1.0
O D:HOH2108 4.4 18.8 1.0
CA D:GLY20 4.6 13.6 1.0
O D:HOH2016 4.6 16.9 1.0
N D:ASP110 4.7 16.0 1.0
N D:ASP111 4.7 15.4 1.0
CB D:ASP111 4.8 14.9 1.0
O D:HOH2022 4.8 39.0 1.0
CG1 A:VAL41 4.9 14.8 1.0
CA D:ASP110 4.9 16.4 1.0
C D:VAL18 4.9 14.2 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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