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Magnesium in PDB 3n07: Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae

Protein crystallography data

The structure of Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae, PDB code: 3n07 was solved by W.Liu, U.A.Ramagopal, R.Toro, S.K.Burley, S.C.Almo, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.946, 77.109, 78.500, 90.00, 106.65, 90.00
R / Rfree (%) 17 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae (pdb code 3n07). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae, PDB code: 3n07:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3n07

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Magnesium binding site 1 out of 4 in the Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg200

b:21.0
occ:1.00
OD2 A:ASP29 2.0 27.4 1.0
O A:HOH279 2.1 25.3 1.0
OD1 A:ASP122 2.1 27.4 1.0
O A:ASP31 2.2 23.5 1.0
O A:HOH225 2.2 21.3 1.0
O A:HOH252 2.4 21.1 1.0
CG A:ASP29 3.0 24.0 1.0
CG A:ASP122 3.1 25.0 1.0
C A:ASP31 3.4 21.3 1.0
OD1 A:ASP29 3.5 25.4 1.0
OD2 A:ASP122 3.5 27.0 1.0
O A:HOH215 3.9 26.7 1.0
CA A:ASP31 4.1 20.1 1.0
N A:ASP31 4.1 19.9 1.0
CB A:ASP31 4.2 22.1 1.0
OD2 A:ASP126 4.2 25.2 1.0
CB A:ASP29 4.3 23.1 1.0
O A:HOH199 4.4 18.0 1.0
CB A:ASP122 4.4 21.7 1.0
N A:GLY32 4.4 20.3 1.0
O A:HOH254 4.5 28.4 1.0
CA A:GLY32 4.6 20.6 1.0
N A:ASP122 4.7 22.8 1.0
O A:HOH229 4.8 29.3 1.0
C A:VAL30 4.9 19.7 1.0
CB A:ASP123 5.0 26.8 1.0
N A:ASP123 5.0 24.2 1.0
CA A:ASP122 5.0 22.4 1.0

Magnesium binding site 2 out of 4 in 3n07

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Magnesium binding site 2 out of 4 in the Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg200

b:16.5
occ:1.00
O B:HOH238 2.0 22.5 1.0
OD2 B:ASP29 2.1 25.3 1.0
OD1 B:ASP122 2.1 21.3 1.0
O B:HOH217 2.2 19.6 1.0
O B:ASP31 2.2 18.9 1.0
O B:HOH207 2.2 19.4 1.0
CG B:ASP122 3.0 18.7 1.0
CG B:ASP29 3.1 21.8 1.0
OD2 B:ASP122 3.4 18.6 1.0
C B:ASP31 3.4 17.8 1.0
OD1 B:ASP29 3.5 23.4 1.0
O B:HOH203 4.2 28.3 1.0
OD2 B:ASP126 4.2 20.6 1.0
CA B:ASP31 4.2 17.5 1.0
O B:HOH237 4.2 24.2 1.0
O B:HOH219 4.3 17.7 1.0
N B:ASP31 4.3 17.8 1.0
CB B:ASP31 4.3 18.3 1.0
CB B:ASP29 4.4 19.8 1.0
CB B:ASP122 4.4 18.1 1.0
N B:GLY32 4.4 16.7 1.0
O B:HOH196 4.6 20.5 1.0
CA B:GLY32 4.6 17.8 1.0
OG1 D:THR53 4.6 20.1 1.0
N B:ASP122 4.7 17.3 1.0
CB B:ASP123 4.8 19.1 1.0
N B:ASP123 4.8 17.8 1.0
CA B:ASP122 4.9 16.8 1.0

Magnesium binding site 3 out of 4 in 3n07

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Magnesium binding site 3 out of 4 in the Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg200

b:21.3
occ:1.00
O C:HOH285 2.0 27.2 1.0
OD2 C:ASP29 2.1 29.5 1.0
OD1 C:ASP122 2.2 25.7 1.0
O C:ASP31 2.2 23.9 1.0
O C:HOH204 2.2 18.3 1.0
O C:HOH201 2.2 19.5 1.0
CG C:ASP122 3.1 24.2 1.0
CG C:ASP29 3.1 27.9 1.0
C C:ASP31 3.4 22.3 1.0
OD2 C:ASP122 3.4 23.2 1.0
OD1 C:ASP29 3.6 30.2 1.0
CA C:ASP31 4.1 22.4 1.0
O C:HOH215 4.1 25.8 1.0
CB C:ASP31 4.2 23.3 1.0
OD2 C:ASP126 4.2 26.2 1.0
N C:ASP31 4.2 22.2 1.0
O C:HOH250 4.4 19.8 1.0
N C:GLY32 4.4 20.9 1.0
CB C:ASP29 4.4 26.4 1.0
CB C:ASP122 4.5 21.2 1.0
O C:HOH228 4.6 25.6 1.0
CA C:GLY32 4.6 20.7 1.0
OG1 B:THR53 4.7 23.9 1.0
N C:ASP122 4.8 21.7 1.0
CB C:ASP123 4.8 23.6 1.0
N C:ASP123 4.9 22.6 1.0
C C:VAL30 5.0 22.1 1.0

Magnesium binding site 4 out of 4 in 3n07

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Magnesium binding site 4 out of 4 in the Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Putative 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg200

b:15.0
occ:0.30
O D:HOH312 1.8 11.6 0.3
OD2 D:ASP29 1.9 18.7 0.3
O D:ASP31 2.2 22.1 1.0
OD1 D:ASP122 2.2 25.1 1.0
O D:HOH213 2.4 23.7 1.0
O D:HOH204 2.5 31.9 1.0
CG D:ASP29 2.8 19.9 0.3
CG D:ASP122 3.1 21.6 1.0
OD1 D:ASP29 3.2 19.1 0.3
C D:ASP31 3.3 20.7 1.0
OD2 D:ASP122 3.4 23.8 1.0
OD1 D:ASP29 3.5 28.4 0.7
CG D:ASP29 3.7 24.2 0.7
N D:ASP31 4.0 20.9 1.0
CA D:ASP31 4.0 21.1 1.0
CB D:ASP31 4.1 22.8 1.0
OD2 D:ASP29 4.1 25.1 0.7
CB D:ASP29 4.2 21.1 0.3
CB D:ASP29 4.2 23.2 0.7
OD2 D:ASP126 4.3 23.3 1.0
O D:HOH249 4.4 28.5 1.0
N D:GLY32 4.4 19.3 1.0
CB D:ASP122 4.4 19.3 1.0
CA D:GLY32 4.7 18.9 1.0
C D:VAL30 4.7 21.1 1.0
CG2 D:VAL33 4.7 19.6 1.0
O D:HOH239 4.7 28.6 1.0
N D:ASP122 4.7 19.5 1.0
N D:VAL30 4.8 21.7 1.0

Reference:

K.D.Daughtry, H.Huang, V.Malashkevich, Y.Patskovsky, W.Liu, U.Ramagopal, J.M.Sauder, S.K.Burley, S.C.Almo, D.Dunaway-Mariano, K.N.Allen. Structural Basis For the Divergence of Substrate Specificity and Biological Function Within Had Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Biochemistry V. 52 5372 2013.
ISSN: ISSN 0006-2960
PubMed: 23848398
DOI: 10.1021/BI400659K
Page generated: Mon Dec 14 08:27:21 2020

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