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Magnesium in PDB 2v9x: E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp

Enzymatic activity of E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp

All present enzymatic activity of E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp:
3.5.4.13;

Protein crystallography data

The structure of E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp, PDB code: 2v9x was solved by M.Thymark, E.Johansson, S.Larsen, M.Willemoes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.187, 71.301, 319.916, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp (pdb code 2v9x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp, PDB code: 2v9x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 2v9x

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Magnesium binding site 1 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase 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 E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1195

b:21.8
occ:1.00
 O2B A:DUT1194 2.0 16.3 1.0
O3G A:DUT1194 2.0 17.7 1.0
O1A A:DUT1194 2.1 11.8 1.0
O C:HOH2011 2.4 19.4 1.0
PB A:DUT1194 3.1 14.7 1.0
PA A:DUT1194 3.2 13.4 1.0
PG A:DUT1194 3.3 16.2 1.0
O3B A:DUT1194 3.5 15.9 1.0
O3A A:DUT1194 3.5 14.7 1.0
O1G A:DUT1194 3.9 11.7 1.0
O2A A:DUT1194 4.2 13.6 1.0
NH2 A:ARG126 4.2 17.3 1.0
NH1 A:ARG174 4.2 30.1 1.0
O C:HOH2035 4.3 7.5 1.0
OD1 C:ASP34 4.3 34.1 1.0
O A:HOH2039 4.3 32.2 1.0
O5' A:DUT1194 4.4 14.2 1.0
O2G A:DUT1194 4.4 15.4 1.0
O C:HOH2010 4.5 30.4 1.0
NE C:ARG110 4.5 26.9 1.0
O1B A:DUT1194 4.6 14.1 1.0
C5' A:DUT1194 4.6 14.5 1.0
OD2 C:ASP34 4.6 39.3 1.0
O C:HOH2009 4.6 30.5 1.0
NH2 C:ARG110 4.7 30.6 1.0
NH2 A:ARG174 4.8 34.5 1.0
CG C:ASP34 4.9 32.0 1.0
CZ A:ARG174 5.0 32.3 1.0

Magnesium binding site 2 out of 12 in 2v9x

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Magnesium binding site 2 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase 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 E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1195

b:23.7
occ:1.00
 O1A B:DUT1194 1.9 12.1 1.0
O B:HOH2045 2.0 20.6 1.0
O2B B:DUT1194 2.0 8.9 1.0
O3G B:DUT1194 2.1 13.2 1.0
O A:HOH2009 2.5 27.7 1.0
PB B:DUT1194 3.1 12.7 1.0
PA B:DUT1194 3.1 12.3 1.0
PG B:DUT1194 3.2 15.6 1.0
O3B B:DUT1194 3.5 15.5 1.0
O3A B:DUT1194 3.5 13.1 1.0
O1G B:DUT1194 3.8 22.7 1.0
O2A B:DUT1194 4.1 12.5 1.0
NH2 B:ARG126 4.2 17.5 1.0
O B:HOH2048 4.2 10.7 1.0
NH1 B:ARG174 4.2 29.6 1.0
O5' B:DUT1194 4.3 14.8 1.0
OD1 A:ASP34 4.4 34.5 1.0
O1B B:DUT1194 4.4 15.3 1.0
O2G B:DUT1194 4.5 17.3 1.0
C5' B:DUT1194 4.6 18.0 1.0
NE A:ARG110 4.6 27.2 1.0
OD2 A:ASP34 4.7 39.2 1.0
NH2 A:ARG110 4.8 30.2 1.0
NH2 B:ARG174 4.9 34.6 1.0
CZ B:ARG174 5.0 32.3 1.0
CG A:ASP34 5.0 32.2 1.0

Magnesium binding site 3 out of 12 in 2v9x

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Magnesium binding site 3 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase 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 E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1195

b:15.7
occ:1.00
 O1A C:DUT1194 2.0 11.6 1.0
O3G C:DUT1194 2.0 11.7 1.0
O2B C:DUT1194 2.1 12.1 1.0
O C:HOH2052 2.1 12.1 1.0
O B:HOH2009 2.3 19.6 1.0
PB C:DUT1194 3.1 12.9 1.0
PA C:DUT1194 3.3 13.3 1.0
PG C:DUT1194 3.3 15.0 1.0
O3B C:DUT1194 3.5 10.8 1.0
O3A C:DUT1194 3.6 15.5 1.0
O C:HOH2041 3.8 29.0 1.0
O1G C:DUT1194 3.9 18.4 1.0
NH2 C:ARG126 4.1 16.4 1.0
NH1 C:ARG174 4.1 29.8 1.0
O2A C:DUT1194 4.2 15.9 1.0
O B:HOH2025 4.2 8.8 1.0
O5' C:DUT1194 4.3 13.3 1.0
OD1 B:ASP34 4.4 34.8 1.0
O2G C:DUT1194 4.5 13.2 1.0
O1B C:DUT1194 4.5 14.9 1.0
C5' C:DUT1194 4.5 8.7 1.0
NE B:ARG110 4.8 27.2 1.0
OD2 B:ASP34 4.8 39.5 1.0
NH2 C:ARG174 4.9 34.7 1.0
NH2 B:ARG110 4.9 30.7 1.0
CZ C:ARG174 4.9 32.3 1.0

Magnesium binding site 4 out of 12 in 2v9x

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Magnesium binding site 4 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase 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 E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1195

b:26.5
occ:1.00
 O2B D:DUT1194 2.0 15.9 1.0
O3G D:DUT1194 2.0 21.7 1.0
O1A D:DUT1194 2.3 14.1 1.0
O D:HOH2035 2.3 9.0 1.0
PB D:DUT1194 3.2 13.3 1.0
PG D:DUT1194 3.3 21.6 1.0
PA D:DUT1194 3.4 12.4 1.0
O3A D:DUT1194 3.7 16.5 1.0
O3B D:DUT1194 3.7 18.6 1.0
O1G D:DUT1194 3.8 25.5 1.0
O D:HOH2030 3.9 28.3 1.0
O F:HOH2019 4.1 20.8 1.0
NH1 D:ARG174 4.1 30.4 1.0
NH2 D:ARG126 4.1 17.0 1.0
OD1 F:ASP34 4.1 34.9 1.0
O2A D:DUT1194 4.3 15.5 1.0
O5' D:DUT1194 4.4 18.8 1.0
O2G D:DUT1194 4.5 17.2 1.0
NE F:ARG110 4.5 26.8 1.0
OD2 F:ASP34 4.6 39.2 1.0
O1B D:DUT1194 4.6 18.0 1.0
C5' D:DUT1194 4.7 16.1 1.0
NH2 F:ARG110 4.7 30.3 1.0
CG F:ASP34 4.8 32.0 1.0
NH2 D:ARG174 4.8 34.5 1.0
CZ D:ARG174 4.9 32.2 1.0

Magnesium binding site 5 out of 12 in 2v9x

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Magnesium binding site 5 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase 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 E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1195

b:20.5
occ:1.00
 O2B E:DUT1194 2.0 14.2 1.0
O1A E:DUT1194 2.1 15.4 1.0
O3G E:DUT1194 2.2 13.4 1.0
O E:HOH2039 2.3 27.7 1.0
O D:HOH2007 2.3 13.1 1.0
PB E:DUT1194 3.0 11.6 1.0
PA E:DUT1194 3.2 13.7 1.0
PG E:DUT1194 3.3 13.3 1.0
O3A E:DUT1194 3.5 16.4 1.0
O3B E:DUT1194 3.5 14.7 1.0
O1G E:DUT1194 3.8 19.4 1.0
NH2 E:ARG126 4.0 17.5 1.0
O2A E:DUT1194 4.1 14.9 1.0
O D:HOH2021 4.2 7.7 1.0
NH1 E:ARG174 4.3 30.2 1.0
OD1 D:ASP34 4.3 34.4 1.0
O5' E:DUT1194 4.4 13.3 1.0
O1B E:DUT1194 4.4 16.8 1.0
NE D:ARG110 4.5 26.9 1.0
O2G E:DUT1194 4.6 16.8 1.0
C5' E:DUT1194 4.6 10.6 1.0
OD2 D:ASP34 4.7 39.4 1.0
NH2 D:ARG110 4.7 30.0 1.0
CG D:ASP34 4.9 32.1 1.0
NH2 E:ARG174 5.0 34.6 1.0

Magnesium binding site 6 out of 12 in 2v9x

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Magnesium binding site 6 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase 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 E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1195

b:17.0
occ:1.00
 O2B F:DUT1194 2.0 16.2 1.0
O1A F:DUT1194 2.1 15.5 1.0
O3G F:DUT1194 2.1 19.7 1.0
O F:HOH2032 2.1 18.7 1.0
O E:HOH2007 2.2 24.6 1.0
O E:HOH2008 2.3 15.9 1.0
PB F:DUT1194 3.2 13.6 1.0
PG F:DUT1194 3.3 18.0 1.0
PA F:DUT1194 3.4 15.0 1.0
O3B F:DUT1194 3.5 19.7 1.0
O3A F:DUT1194 3.6 14.8 1.0
O1G F:DUT1194 4.0 24.5 1.0
OD1 E:ASP34 4.2 34.5 1.0
O F:HOH2033 4.2 8.7 1.0
NH2 F:ARG126 4.2 17.7 1.0
NH1 F:ARG174 4.2 29.8 1.0
O2A F:DUT1194 4.2 12.8 1.0
OD2 E:ASP34 4.5 39.2 1.0
O2G F:DUT1194 4.5 23.1 1.0
O1B F:DUT1194 4.5 20.4 1.0
NE E:ARG110 4.5 27.0 1.0
O5' F:DUT1194 4.6 13.1 1.0
NH2 E:ARG110 4.7 30.6 1.0
CG E:ASP34 4.8 31.9 1.0
C5' F:DUT1194 4.8 15.4 1.0
NH2 F:ARG174 4.8 34.8 1.0
CZ F:ARG174 5.0 32.3 1.0

Magnesium binding site 7 out of 12 in 2v9x

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Magnesium binding site 7 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase 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 E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1195

b:33.1
occ:1.00
 O2B G:DUT1194 2.1 23.7 1.0
O3G G:DUT1194 2.1 22.9 1.0
O1A G:DUT1194 2.2 16.5 1.0
O I:HOH2004 2.2 17.3 1.0
PB G:DUT1194 3.1 18.9 1.0
PA G:DUT1194 3.3 14.9 1.0
PG G:DUT1194 3.4 20.3 1.0
O3A G:DUT1194 3.5 18.5 1.0
O3B G:DUT1194 3.6 24.5 1.0
O1G G:DUT1194 3.9 22.7 1.0
NH2 G:ARG126 4.1 18.6 1.0
O2A G:DUT1194 4.2 15.7 1.0
O I:HOH2020 4.2 19.6 1.0
OD1 I:ASP34 4.2 34.9 1.0
NH1 G:ARG174 4.3 30.2 1.0
NE I:ARG110 4.4 27.2 1.0
O1B G:DUT1194 4.5 25.2 1.0
O5' G:DUT1194 4.5 13.7 1.0
OD2 I:ASP34 4.6 39.4 1.0
O2G G:DUT1194 4.6 22.0 1.0
NH2 I:ARG110 4.6 30.7 1.0
C5' G:DUT1194 4.7 18.7 1.0
CG I:ASP34 4.9 32.0 1.0
NH2 G:ARG174 5.0 34.8 1.0

Magnesium binding site 8 out of 12 in 2v9x

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Magnesium binding site 8 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1195

b:25.3
occ:1.00
 O2B H:DUT1194 1.9 15.8 1.0
O3G H:DUT1194 2.0 17.6 1.0
O H:HOH2044 2.1 18.2 1.0
O1A H:DUT1194 2.2 18.3 1.0
O G:HOH2002 2.2 23.2 1.0
PB H:DUT1194 3.1 15.4 1.0
PG H:DUT1194 3.2 17.9 1.0
PA H:DUT1194 3.3 12.8 1.0
O3B H:DUT1194 3.5 19.6 1.0
O3A H:DUT1194 3.5 16.0 1.0
O1G H:DUT1194 3.7 22.1 1.0
O H:HOH2032 3.8 24.7 1.0
O G:HOH2012 4.2 14.5 1.0
NH2 H:ARG126 4.2 17.9 1.0
NH1 H:ARG174 4.3 30.2 1.0
OD1 G:ASP34 4.3 34.9 1.0
O2A H:DUT1194 4.3 18.4 1.0
NE G:ARG110 4.4 27.0 1.0
O5' H:DUT1194 4.4 15.5 1.0
O2G H:DUT1194 4.4 18.9 1.0
O1B H:DUT1194 4.4 20.1 1.0
NH2 G:ARG110 4.5 30.2 1.0
OD2 G:ASP34 4.6 39.2 1.0
C5' H:DUT1194 4.7 14.8 1.0
NH2 H:ARG174 4.9 34.7 1.0
CG G:ASP34 4.9 32.0 1.0
CZ G:ARG110 5.0 28.6 1.0

Magnesium binding site 9 out of 12 in 2v9x

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Magnesium binding site 9 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1195

b:24.3
occ:1.00
 O3G I:DUT1194 1.9 16.6 1.0
O1A I:DUT1194 2.0 16.8 1.0
O2B I:DUT1194 2.0 15.7 1.0
O I:HOH2040 2.3 18.9 1.0
PG I:DUT1194 3.2 14.1 1.0
PB I:DUT1194 3.2 13.4 1.0
PA I:DUT1194 3.3 14.4 1.0
O3B I:DUT1194 3.5 16.0 1.0
O3A I:DUT1194 3.6 15.5 1.0
O1G I:DUT1194 3.8 17.2 1.0
O I:HOH2034 4.0 26.9 1.0
NH1 I:ARG174 4.1 30.2 1.0
NH2 I:ARG126 4.2 17.7 1.0
OD1 H:ASP34 4.2 34.2 1.0
O H:HOH2027 4.2 20.2 1.0
O2A I:DUT1194 4.3 8.8 1.0
O5' I:DUT1194 4.3 13.3 1.0
O2G I:DUT1194 4.4 17.1 1.0
NE H:ARG110 4.5 26.4 1.0
O1B I:DUT1194 4.5 18.3 1.0
NH2 H:ARG110 4.6 30.2 1.0
OD2 H:ASP34 4.6 39.6 1.0
C5' I:DUT1194 4.6 17.5 1.0
NH2 I:ARG174 4.8 35.0 1.0
CG H:ASP34 4.9 32.1 1.0
CZ I:ARG174 4.9 32.0 1.0

Magnesium binding site 10 out of 12 in 2v9x

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Magnesium binding site 10 out of 12 in the E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E138D Variant of Escherichia Coli Dctp Deaminase in Complex with Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1195

b:29.1
occ:1.00
 O1A J:DUT1194 2.0 19.6 1.0
O2B J:DUT1194 2.1 23.0 1.0
O L:HOH2002 2.2 28.9 1.0
O3G J:DUT1194 2.2 30.9 1.0
PB J:DUT1194 3.2 23.5 1.0
PA J:DUT1194 3.2 20.5 1.0
PG J:DUT1194 3.4 38.1 1.0
O3A J:DUT1194 3.5 20.9 1.0
O3B J:DUT1194 3.7 28.0 1.0
O2A J:DUT1194 4.1 19.1 1.0
OD2 L:ASP34 4.1 42.0 1.0
NH2 J:ARG126 4.1 20.6 1.0
O1G J:DUT1194 4.2 33.1 1.0
O J:HOH2032 4.3 21.4 1.0
OD1 L:ASP34 4.4 39.8 1.0
O5' J:DUT1194 4.4 18.6 1.0
O1B J:DUT1194 4.5 24.5 1.0
NE L:ARG110 4.5 31.7 1.0
NH2 L:ARG110 4.5 34.4 1.0
O2G J:DUT1194 4.6 35.3 1.0
C5' J:DUT1194 4.6 19.3 1.0
CG L:ASP34 4.8 36.3 1.0

Reference:

M.Thymark, E.Johansson, S.Larsen, M.Willemoes. Mutational Analysis of the Nucleotide Binding Site of Escherichia Coli Dctp Deaminase. Arch.Biochem.Biophys. V. 470 20 2008.
ISSN: ISSN 0003-9861
PubMed: 17996716
DOI: 10.1016/J.ABB.2007.10.013
Page generated: Mon Dec 14 07:41:19 2020

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