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Magnesium in PDB 1xs6: Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp

Enzymatic activity of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp

All present enzymatic activity of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp:
3.5.4.13;

Protein crystallography data

The structure of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp, PDB code: 1xs6 was solved by E.Johansson, M.Fano, J.H.Bynck, J.Neuhard, S.Larsen, B.W.Sigurskjold, U.Christensen, M.Willemoes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.930, 63.073, 96.363, 90.00, 102.18, 90.00
R / Rfree (%) 25.8 / 31.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp (pdb code 1xs6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp, PDB code: 1xs6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1xs6

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Magnesium binding site 1 out of 7 in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2195

b:21.1
occ:1.00
 O3G B:DUT2194 1.9 13.9 1.0
O2B B:DUT2194 2.2 11.3 1.0
O1A B:DUT2194 2.2 14.2 1.0
PG B:DUT2194 3.1 16.3 1.0
PB B:DUT2194 3.1 14.3 1.0
PA B:DUT2194 3.3 13.9 1.0
O3B B:DUT2194 3.4 14.2 1.0
O3A B:DUT2194 3.5 15.1 1.0
O1G B:DUT2194 3.7 16.1 1.0
NH1 B:ARG174 4.2 21.2 1.0
O A:HOH2232 4.2 12.4 1.0
NH2 B:ARG126 4.3 15.2 1.0
O2G B:DUT2194 4.3 15.0 1.0
NE A:ARG110 4.3 17.7 1.0
OD1 A:ASP34 4.4 24.9 1.0
O2A B:DUT2194 4.4 15.3 1.0
NH2 A:ARG110 4.4 19.2 1.0
O5' B:DUT2194 4.4 15.3 1.0
C5' B:DUT2194 4.5 16.1 1.0
O1B B:DUT2194 4.6 12.8 1.0
OD2 A:ASP34 4.7 22.6 1.0
NH2 B:ARG174 4.8 26.3 1.0
CZ A:ARG110 4.9 18.4 1.0
CZ B:ARG174 4.9 24.6 1.0

Magnesium binding site 2 out of 7 in 1xs6

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Magnesium binding site 2 out of 7 in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3195

b:7.8
occ:1.00
 O C:HOH3243 1.8 17.7 1.0
O3G C:DUT3194 2.0 16.0 1.0
O1A C:DUT3194 2.0 6.8 1.0
O C:HOH3217 2.1 4.8 1.0
O2B C:DUT3194 2.1 14.1 1.0
PB C:DUT3194 3.0 11.0 1.0
PG C:DUT3194 3.2 16.3 1.0
PA C:DUT3194 3.3 12.3 1.0
O3B C:DUT3194 3.4 14.7 1.0
O3A C:DUT3194 3.6 11.6 1.0
O1G C:DUT3194 3.8 16.8 1.0
NH1 C:ARG174 3.9 22.4 1.0
NH2 C:ARG174 4.1 27.0 1.0
O2A C:DUT3194 4.2 14.5 1.0
NH2 C:ARG126 4.2 12.0 1.0
OD1 B:ASP34 4.3 22.7 1.0
O1B C:DUT3194 4.4 13.5 1.0
O B:HOH3228 4.4 25.7 1.0
O2G C:DUT3194 4.4 14.7 1.0
NE B:ARG110 4.4 16.1 1.0
O B:HOH3213 4.4 11.9 1.0
NH2 B:ARG110 4.5 18.4 1.0
CZ C:ARG174 4.5 24.5 1.0
O5' C:DUT3194 4.5 12.8 1.0
O C:HOH3248 4.6 15.8 1.0
C5' C:DUT3194 4.6 15.7 1.0
O B:HOH3224 4.7 19.1 1.0
CZ B:ARG110 4.9 17.8 1.0

Magnesium binding site 3 out of 7 in 1xs6

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Magnesium binding site 3 out of 7 in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1195

b:15.6
occ:1.00
 O2B A:DUT1194 2.1 12.5 1.0
O3G A:DUT1194 2.1 16.6 1.0
O A:HOH2248 2.1 13.8 1.0
O1A A:DUT1194 2.2 12.8 1.0
O A:HOH2221 2.3 19.1 1.0
PB A:DUT1194 3.1 13.6 1.0
PG A:DUT1194 3.3 18.1 1.0
PA A:DUT1194 3.3 12.1 1.0
O3B A:DUT1194 3.5 16.0 1.0
O3A A:DUT1194 3.5 13.2 1.0
O1G A:DUT1194 3.9 16.9 1.0
O A:HOH2220 4.1 10.9 1.0
O C:HOH3215 4.1 12.0 1.0
NH2 A:ARG126 4.2 14.6 1.0
NH1 A:ARG174 4.2 18.6 1.0
O2A A:DUT1194 4.3 14.1 1.0
OD1 C:ASP34 4.3 24.8 1.0
O C:HOH3225 4.3 23.4 1.0
NE C:ARG110 4.3 16.2 1.0
NH2 C:ARG110 4.4 19.6 1.0
O1B A:DUT1194 4.5 14.6 1.0
O5' A:DUT1194 4.5 14.6 1.0
O2G A:DUT1194 4.5 14.2 1.0
OD2 C:ASP34 4.6 25.4 1.0
C5' A:DUT1194 4.7 16.3 1.0
O C:HOH3241 4.8 19.8 1.0
CZ C:ARG110 4.9 17.9 1.0
CG C:ASP34 4.9 20.1 1.0

Magnesium binding site 4 out of 7 in 1xs6

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Magnesium binding site 4 out of 7 in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5195

b:24.0
occ:1.00
 O E:HOH6236 2.0 10.1 1.0
O E:HOH6229 2.1 15.5 1.0
O2B E:DUT5194 2.1 13.6 1.0
O1A E:DUT5194 2.2 15.3 1.0
O3G E:DUT5194 2.3 13.9 1.0
PB E:DUT5194 3.2 15.8 1.0
PA E:DUT5194 3.3 12.9 1.0
O3A E:DUT5194 3.6 13.5 1.0
PG E:DUT5194 3.7 14.8 1.0
O E:HOH6231 3.7 23.3 1.0
O3B E:DUT5194 3.8 16.2 1.0
O D:HOH5203 3.8 14.0 1.0
NH2 E:ARG126 4.0 13.1 1.0
OD1 D:ASP34 4.1 24.4 1.0
O2A E:DUT5194 4.1 15.4 1.0
O1G E:DUT5194 4.3 16.9 1.0
NE D:ARG110 4.4 16.3 1.0
O E:HOH6237 4.4 10.9 1.0
O5' E:DUT5194 4.5 15.3 1.0
O D:HOH5249 4.5 20.9 1.0
NH1 E:ARG174 4.5 21.9 1.0
O D:HOH5210 4.6 17.8 1.0
O1B E:DUT5194 4.6 14.3 1.0
C5' E:DUT5194 4.6 15.6 1.0
NH2 D:ARG110 4.7 18.1 1.0
OD2 D:ASP34 4.8 24.2 1.0
O2G E:DUT5194 4.9 15.1 1.0
CG D:ASP34 4.9 20.5 1.0

Magnesium binding site 5 out of 7 in 1xs6

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Magnesium binding site 5 out of 7 in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5196

b:18.7
occ:1.00
 O D:HOH5272 1.9 17.0 1.0
O E:HOH6266 1.9 19.2 1.0
O D:HOH5268 2.0 23.4 1.0
O E:HOH6264 2.0 19.2 1.0
O D:HOH5267 2.1 24.3 1.0
O E:HOH6265 2.6 31.9 1.0
OD2 D:ASP7 4.0 21.3 1.0
NH2 D:ARG6 4.1 37.3 1.0
CZ D:ARG6 4.1 35.0 1.0
OD1 D:ASP7 4.1 24.3 1.0
NH1 D:ARG6 4.3 36.0 1.0
O E:SER164 4.4 20.1 1.0
NE D:ARG6 4.5 33.8 1.0
CG D:ASP7 4.5 22.0 1.0
CA E:GLY165 4.7 19.6 1.0

Magnesium binding site 6 out of 7 in 1xs6

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Magnesium binding site 6 out of 7 in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg6195

b:18.9
occ:1.00
 O2B F:DUT6194 1.9 15.2 1.0
O3G F:DUT6194 2.0 15.5 1.0
O1A F:DUT6194 2.0 10.8 1.0
O F:HOH6222 2.1 18.2 1.0
O E:HOH6244 2.3 17.5 1.0
O E:HOH6232 2.4 11.7 1.0
PB F:DUT6194 3.1 14.5 1.0
PA F:DUT6194 3.2 14.1 1.0
PG F:DUT6194 3.2 16.2 1.0
O3B F:DUT6194 3.4 16.0 1.0
O3A F:DUT6194 3.5 14.7 1.0
O1G F:DUT6194 3.7 15.0 1.0
O2A F:DUT6194 4.1 15.4 1.0
O F:HOH6214 4.1 16.9 1.0
NH1 F:ARG174 4.2 17.9 1.0
O F:HOH6251 4.2 15.0 1.0
NH2 F:ARG126 4.2 14.3 1.0
OD1 E:ASP34 4.3 25.1 1.0
O1B F:DUT6194 4.3 13.8 1.0
O5' F:DUT6194 4.4 13.7 1.0
NE E:ARG110 4.4 15.4 1.0
OD2 E:ASP34 4.4 23.9 1.0
O2G F:DUT6194 4.5 12.4 1.0
NH2 E:ARG110 4.6 17.8 1.0
C5' F:DUT6194 4.6 15.1 1.0
O E:HOH6247 4.6 24.7 1.0
CG E:ASP34 4.8 20.0 1.0
CZ E:ARG110 5.0 16.4 1.0

Magnesium binding site 7 out of 7 in 1xs6

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Magnesium binding site 7 out of 7 in the Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Dctp Deaminase From Escherichia Coli. E138A Mutant Enzyme in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg4195

b:15.7
occ:1.00
 O1A D:DUT4194 1.7 13.5 1.0
O2B D:DUT4194 2.0 15.5 1.0
O D:HOH5243 2.1 7.2 1.0
O3G D:DUT4194 2.2 15.8 1.0
PA D:DUT4194 2.9 15.7 1.0
PB D:DUT4194 3.0 14.6 1.0
O3A D:DUT4194 3.3 16.0 1.0
PG D:DUT4194 3.4 15.3 1.0
O3B D:DUT4194 3.5 17.7 1.0
O F:HOH6203 3.7 9.7 1.0
O2A D:DUT4194 3.8 17.3 1.0
NH2 D:ARG126 4.0 12.5 1.0
O1G D:DUT4194 4.1 14.7 1.0
O5' D:DUT4194 4.1 16.0 1.0
O D:HOH5245 4.2 16.9 1.0
NE F:ARG110 4.3 16.7 1.0
OD1 F:ASP34 4.3 25.3 1.0
O D:HOH5212 4.4 12.8 1.0
O1B D:DUT4194 4.4 14.8 1.0
C5' D:DUT4194 4.4 15.6 1.0
NH1 D:ARG174 4.4 22.9 1.0
O2G D:DUT4194 4.6 15.8 1.0
NH2 F:ARG110 4.7 16.6 1.0
O F:HOH6231 4.8 22.4 1.0
CG F:ARG110 4.9 16.1 1.0
CZ F:ARG110 5.0 17.5 1.0

Reference:

E.Johansson, M.Fano, J.H.Bynck, J.Neuhard, S.Larsen, B.W.Sigurskjold, U.Christensen, M.Willemoes. Structures of Dctp Deaminase From Escherichia Coli with Bound Substrate and Product: Reaction Mechanism and Determinants of Mono- and Bifunctionality For A Family of Enzymes J.Biol.Chem. V. 280 3051 2005.
ISSN: ISSN 0021-9258
PubMed: 15539408
DOI: 10.1074/JBC.M409534200
Page generated: Tue Aug 13 18:22:50 2024

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