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Magnesium in PDB 1xs4: Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp

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

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

Protein crystallography data

The structure of Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp, PDB code: 1xs4 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) 30.00 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.272, 97.882, 95.116, 90.00, 109.23, 90.00
R / Rfree (%) 18.5 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp (pdb code 1xs4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp, PDB code: 1xs4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1xs4

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Magnesium binding site 1 out of 6 in the Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2195

b:23.5
occ:1.00
 O1A B:DCP2194 2.0 12.0 1.0
O3G B:DCP2194 2.0 13.6 1.0
O2B B:DCP2194 2.1 14.4 1.0
O A:HOH2222 2.2 13.2 1.0
O B:HOH3221 2.2 8.4 1.0
PB B:DCP2194 3.2 13.9 1.0
PA B:DCP2194 3.3 12.0 1.0
PG B:DCP2194 3.3 16.8 1.0
O3B B:DCP2194 3.6 16.1 1.0
O3A B:DCP2194 3.7 13.8 1.0
O B:HOH3226 3.8 10.8 1.0
OD1 A:ASP34 4.1 21.9 1.0
O1G B:DCP2194 4.1 15.3 1.0
O2A B:DCP2194 4.1 13.2 1.0
O B:HOH3222 4.2 7.8 1.0
NH2 B:ARG126 4.2 15.5 1.0
NE A:ARG110 4.3 15.0 1.0
NH1 B:ARG174 4.4 27.7 1.0
O5' B:DCP2194 4.5 14.9 1.0
O2G B:DCP2194 4.5 13.8 1.0
NH2 A:ARG110 4.5 14.8 1.0
O1B B:DCP2194 4.6 12.3 1.0
C5' B:DCP2194 4.6 16.1 1.0
NH2 B:ARG174 4.7 34.3 1.0
O A:HOH2227 4.8 9.9 1.0
CZ A:ARG110 4.9 15.8 1.0
CG A:ASP34 5.0 18.7 1.0
OD2 A:ASP34 5.0 21.8 1.0

Magnesium binding site 2 out of 6 in 1xs4

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Magnesium binding site 2 out of 6 in the Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3195

b:24.3
occ:1.00
 O1A C:DCP3194 2.0 12.2 1.0
O3G C:DCP3194 2.1 13.1 1.0
O2B C:DCP3194 2.1 14.0 1.0
O B:HOH3219 2.5 13.6 1.0
PB C:DCP3194 3.2 13.9 1.0
PA C:DCP3194 3.3 12.2 1.0
PG C:DCP3194 3.3 15.4 1.0
O3B C:DCP3194 3.6 15.5 1.0
O3A C:DCP3194 3.7 13.6 1.0
O C:HOH3220 3.7 16.6 1.0
OD1 B:ASP34 4.0 21.6 1.0
O1G C:DCP3194 4.1 15.4 1.0
NH2 C:ARG126 4.2 16.1 1.0
O2A C:DCP3194 4.2 13.6 1.0
O C:HOH3206 4.2 8.6 1.0
NE B:ARG110 4.3 14.8 1.0
NH2 B:ARG110 4.4 14.4 1.0
O5' C:DCP3194 4.5 14.9 1.0
O2G C:DCP3194 4.6 13.4 1.0
NH1 C:ARG174 4.6 24.4 1.0
O1B C:DCP3194 4.6 12.0 1.0
C5' C:DCP3194 4.6 16.2 1.0
OD2 B:ASP34 4.7 22.0 1.0
NH2 C:ARG174 4.8 31.1 1.0
CG B:ASP34 4.8 18.7 1.0
CZ B:ARG110 4.9 15.8 1.0

Magnesium binding site 3 out of 6 in 1xs4

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Magnesium binding site 3 out of 6 in the Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1195

b:24.1
occ:1.00
 O2B A:DCP1194 1.9 14.1 1.0
O3G A:DCP1194 1.9 13.5 1.0
O1A A:DCP1194 1.9 12.0 1.0
O A:HOH2223 2.0 13.9 1.0
O A:HOH2200 2.2 7.3 1.0
PB A:DCP1194 3.1 14.1 1.0
PG A:DCP1194 3.2 16.4 1.0
PA A:DCP1194 3.3 11.1 1.0
O3B A:DCP1194 3.5 15.7 1.0
O3A A:DCP1194 3.6 14.2 1.0
O A:HOH2231 3.9 13.2 1.0
O A:HOH2225 3.9 12.2 1.0
O1G A:DCP1194 3.9 15.1 1.0
OD1 C:ASP34 4.1 21.5 1.0
NE C:ARG110 4.1 14.4 1.0
O2A A:DCP1194 4.2 13.6 1.0
NH2 A:ARG126 4.2 16.0 1.0
O A:HOH2226 4.3 7.0 1.0
NH2 C:ARG110 4.3 15.2 1.0
O2G A:DCP1194 4.5 13.8 1.0
O5' A:DCP1194 4.5 13.8 1.0
O1B A:DCP1194 4.5 12.3 1.0
C5' A:DCP1194 4.6 16.1 1.0
NH1 A:ARG174 4.6 26.6 1.0
CZ C:ARG110 4.7 16.1 1.0
NH2 A:ARG174 4.9 25.8 1.0
OD2 C:ASP34 4.9 22.0 1.0
CG C:ASP34 5.0 18.3 1.0

Magnesium binding site 4 out of 6 in 1xs4

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Magnesium binding site 4 out of 6 in the Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5195

b:23.3
occ:1.00
 O1A E:DCP5194 1.9 11.7 1.0
O3G E:DCP5194 2.0 13.6 1.0
O E:HOH6216 2.1 15.7 1.0
O2B E:DCP5194 2.2 14.3 1.0
O E:HOH6228 2.2 7.7 1.0
PB E:DCP5194 3.2 13.7 1.0
PA E:DCP5194 3.3 11.9 1.0
PG E:DCP5194 3.4 16.4 1.0
O3A E:DCP5194 3.6 13.8 1.0
O3B E:DCP5194 3.7 15.6 1.0
O E:HOH6245 3.8 16.0 1.0
O1G E:DCP5194 4.0 15.4 1.0
OD1 D:ASP34 4.0 21.4 1.0
O2A E:DCP5194 4.2 13.7 1.0
O E:HOH6227 4.2 3.8 1.0
NH2 E:ARG126 4.2 15.9 1.0
NE D:ARG110 4.3 14.5 1.0
O D:HOH5232 4.4 12.2 1.0
NH2 D:ARG110 4.5 14.6 1.0
O5' E:DCP5194 4.5 14.7 1.0
NH1 E:ARG174 4.6 34.1 1.0
C5' E:DCP5194 4.6 16.0 1.0
OD2 D:ASP34 4.6 22.2 1.0
O2G E:DCP5194 4.6 13.4 1.0
NH2 E:ARG174 4.6 37.2 1.0
O1B E:DCP5194 4.7 12.0 1.0
CG D:ASP34 4.8 18.5 1.0
CZ D:ARG110 4.9 15.5 1.0

Magnesium binding site 5 out of 6 in 1xs4

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Magnesium binding site 5 out of 6 in the Dctp Deaminase From Escherichia Coli- E138A Mutant Enzyme in Complex with Dctp


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg6195

b:23.6
occ:1.00
 O2B F:DCP6194 2.0 14.0 1.0
O3G F:DCP6194 2.1 13.3 1.0
O F:HOH6197 2.1 5.1 1.0
O1A F:DCP6194 2.1 12.1 1.0
O F:HOH6212 2.3 5.7 1.0
PB F:DCP6194 3.2 13.3 1.0
PG F:DCP6194 3.3 16.4 1.0
PA F:DCP6194 3.4 11.4 1.0
O3B F:DCP6194 3.7 15.6 1.0
O3A F:DCP6194 3.7 13.8 1.0
O F:HOH6227 3.7 16.1 1.0
OD1 E:ASP34 3.9 21.8 1.0
O1G F:DCP6194 3.9 15.5 1.0
O F:HOH6211 3.9 2.0 1.0
O F:HOH6219 4.1 4.2 1.0
NE E:ARG110 4.2 14.7 1.0
NH2 F:ARG126 4.3 15.9 1.0
O2A F:DCP6194 4.3 13.5 1.0
NH2 E:ARG110 4.3 14.9 1.0
O E:HOH6197 4.5 11.4 1.0
O2G F:DCP6194 4.6 13.7 1.0
O1B F:DCP6194 4.6 12.2 1.0
O5' F:DCP6194 4.6 14.3 1.0
NH1 F:ARG174 4.7 20.8 1.0
C5' F:DCP6194 4.7 16.1 1.0
CZ E:ARG110 4.8 15.8 1.0
CG E:ASP34 4.8 18.5 1.0
OD2 E:ASP34 4.9 22.1 1.0

Magnesium binding site 6 out of 6 in 1xs4

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


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg4195

b:23.9
occ:1.00
 O3G D:DCP4194 2.0 13.4 1.0
O1A D:DCP4194 2.1 12.6 1.0
O D:HOH5208 2.2 10.8 1.0
O2B D:DCP4194 2.3 14.4 1.0
PG D:DCP4194 3.4 16.5 1.0
PB D:DCP4194 3.4 14.1 1.0
PA D:DCP4194 3.5 12.2 1.0
O3B D:DCP4194 3.8 16.0 1.0
OD1 F:ASP34 3.9 21.7 1.0
O3A D:DCP4194 3.9 14.0 1.0
O D:HOH5231 4.1 14.4 1.0
O1G D:DCP4194 4.1 15.2 1.0
NH2 D:ARG126 4.2 16.1 1.0
O F:HOH6223 4.3 14.1 1.0
O2A D:DCP4194 4.4 13.5 1.0
O D:HOH5225 4.4 9.7 1.0
NE F:ARG110 4.4 14.4 1.0
O2G D:DCP4194 4.6 13.9 1.0
NH1 D:ARG174 4.6 30.9 1.0
O5' D:DCP4194 4.6 15.2 1.0
NH2 F:ARG110 4.6 15.2 1.0
OD2 F:ASP34 4.7 21.9 1.0
C5' D:DCP4194 4.8 16.2 1.0
CG F:ASP34 4.8 18.3 1.0
O1B D:DCP4194 4.8 12.5 1.0
NH2 D:ARG174 4.9 35.2 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 18:22:49 2024

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