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Magnesium in PDB 4xjc: Dctp Deaminase-Dutpase From Bacillus Halodurans

Enzymatic activity of Dctp Deaminase-Dutpase From Bacillus Halodurans

All present enzymatic activity of Dctp Deaminase-Dutpase From Bacillus Halodurans:
3.5.4.13;

Protein crystallography data

The structure of Dctp Deaminase-Dutpase From Bacillus Halodurans, PDB code: 4xjc was solved by C.Oehlenschlaeger, M.Loevgreen, M.Willemoes, P.Harris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.81 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.720, 55.630, 95.600, 90.00, 97.36, 90.00
R / Rfree (%) 20.7 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dctp Deaminase-Dutpase From Bacillus Halodurans (pdb code 4xjc). 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-Dutpase From Bacillus Halodurans, PDB code: 4xjc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4xjc

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Magnesium binding site 1 out of 6 in the Dctp Deaminase-Dutpase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dctp Deaminase-Dutpase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:18.5
occ:1.00
 O3G C:TTP201 1.8 17.8 1.0
O A:HOH314 2.0 22.1 1.0
O2B C:TTP201 2.1 15.4 1.0
O A:HOH313 2.1 17.5 1.0
O2A C:TTP201 2.2 20.7 1.0
O C:HOH308 2.2 20.1 1.0
PG C:TTP201 3.1 19.3 1.0
PB C:TTP201 3.2 18.0 1.0
PA C:TTP201 3.3 18.1 1.0
O3B C:TTP201 3.5 18.8 1.0
O3A C:TTP201 3.6 20.3 1.0
O A:HOH321 3.6 16.0 1.0
O1G C:TTP201 3.7 16.3 1.0
OE1 A:GLN28 3.9 27.4 1.0
O1A C:TTP201 4.0 16.6 1.0
O C:HOH329 4.2 20.5 1.0
CD A:GLN28 4.2 28.1 1.0
O2G C:TTP201 4.3 14.6 1.0
NE A:ARG98 4.3 21.1 1.0
CG A:GLN28 4.3 27.6 1.0
OD1 A:ASP33 4.4 23.3 1.0
OD2 A:ASP33 4.4 23.9 1.0
OD2 C:ASP115 4.5 21.0 1.0
O5' C:TTP201 4.5 17.4 1.0
NH2 A:ARG98 4.6 22.6 1.0
OE1 A:GLN144 4.6 23.0 1.0
O1B C:TTP201 4.6 17.5 1.0
C5' C:TTP201 4.6 17.9 1.0
O C:HOH315 4.7 13.4 1.0
CE1 C:TYR157 4.8 24.2 1.0
CG A:ASP33 4.8 23.8 1.0
OD1 C:ASP115 4.9 20.0 1.0
CZ A:ARG98 4.9 21.9 1.0

Magnesium binding site 2 out of 6 in 4xjc

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Magnesium binding site 2 out of 6 in the Dctp Deaminase-Dutpase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dctp Deaminase-Dutpase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:21.5
occ:1.00
 O2A E:TTP202 1.9 16.3 1.0
O2B E:TTP202 2.0 18.3 1.0
O E:HOH322 2.0 24.5 1.0
O C:HOH309 2.1 16.9 1.0
O3G E:TTP202 2.2 18.6 1.0
O E:HOH321 2.2 20.0 1.0
PB E:TTP202 3.1 19.3 1.0
PA E:TTP202 3.2 17.2 1.0
PG E:TTP202 3.3 17.6 1.0
O3A E:TTP202 3.5 17.6 1.0
O3B E:TTP202 3.6 20.8 1.0
O1G E:TTP202 3.9 16.9 1.0
OE1 C:GLN28 4.1 23.2 1.0
O1A E:TTP202 4.1 19.1 1.0
OD1 C:ASP33 4.1 19.6 1.0
O C:HOH311 4.1 14.5 1.0
NE C:ARG98 4.2 23.5 1.0
O E:HOH324 4.2 20.9 1.0
CD C:GLN28 4.3 24.1 1.0
OD2 C:ASP33 4.3 21.9 1.0
OE1 C:GLN144 4.3 18.8 1.0
CG C:GLN28 4.4 23.1 1.0
O5' E:TTP202 4.4 15.2 1.0
O1B E:TTP202 4.5 20.8 1.0
O E:HOH336 4.5 17.8 1.0
C5' E:TTP202 4.6 16.8 1.0
O2G E:TTP202 4.6 21.4 1.0
NH2 C:ARG98 4.6 25.4 1.0
OD2 E:ASP115 4.6 21.7 1.0
CG C:ASP33 4.7 20.5 1.0
CZ C:ARG98 4.9 24.9 1.0
CG C:ARG98 4.9 20.9 1.0
NE2 C:GLN144 4.9 17.8 1.0
CD C:GLN144 4.9 18.2 1.0
OD1 E:ASP115 5.0 21.3 1.0

Magnesium binding site 3 out of 6 in 4xjc

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Magnesium binding site 3 out of 6 in the Dctp Deaminase-Dutpase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dctp Deaminase-Dutpase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:25.8
occ:1.00
 O3G A:TTP201 1.9 22.3 1.0
O E:HOH320 2.0 19.6 1.0
O2A A:TTP201 2.0 25.0 1.0
O2B A:TTP201 2.1 23.5 1.0
O A:HOH312 2.3 16.2 1.0
O E:HOH319 2.3 13.9 1.0
PB A:TTP201 3.1 24.3 1.0
PG A:TTP201 3.1 22.6 1.0
PA A:TTP201 3.2 23.1 1.0
O3B A:TTP201 3.3 23.6 1.0
O3A A:TTP201 3.5 22.1 1.0
O1G A:TTP201 3.7 20.4 1.0
O E:HOH330 3.8 15.6 1.0
OE1 E:GLN28 4.0 23.4 1.0
O1A A:TTP201 4.2 20.7 1.0
O A:HOH333 4.3 19.8 1.0
CD E:GLN28 4.3 22.4 1.0
O2G A:TTP201 4.3 22.1 1.0
OD1 E:ASP33 4.4 21.4 1.0
NE E:ARG98 4.4 20.9 1.0
CG E:GLN28 4.4 21.5 1.0
O5' A:TTP201 4.4 22.6 1.0
O1B A:TTP201 4.5 23.2 1.0
C5' A:TTP201 4.5 21.6 1.0
OD2 E:ASP33 4.5 22.4 1.0
OE1 E:GLN144 4.5 22.0 1.0
OD2 A:ASP115 4.5 22.6 1.0
NH2 E:ARG98 4.7 22.4 1.0
CE1 A:TYR157 4.7 23.9 1.0
O A:HOH324 4.8 16.1 1.0
OD1 A:ASP115 4.8 21.1 1.0
CG E:ASP33 4.9 21.2 1.0

Magnesium binding site 4 out of 6 in 4xjc

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Magnesium binding site 4 out of 6 in the Dctp Deaminase-Dutpase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dctp Deaminase-Dutpase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:17.8
occ:1.00
 O B:HOH317 1.9 14.9 1.0
O1A D:TTP201 2.0 17.2 1.0
O D:HOH318 2.1 22.0 1.0
O1G D:TTP201 2.1 26.9 1.0
O B:HOH318 2.3 13.1 1.0
O1B D:TTP201 2.4 18.9 1.0
PB D:TTP201 3.3 21.9 1.0
PA D:TTP201 3.3 18.7 1.0
PG D:TTP201 3.3 23.3 1.0
O3A D:TTP201 3.6 19.4 1.0
O3B D:TTP201 3.7 21.8 1.0
O D:HOH333 3.7 25.4 1.0
O3G D:TTP201 3.8 22.8 1.0
OE1 B:GLN28 3.8 30.1 1.0
CD B:GLN28 4.1 29.6 1.0
O D:HOH320 4.2 14.2 1.0
CG B:GLN28 4.2 28.3 1.0
OD1 B:ASP33 4.2 24.6 1.0
OD2 B:ASP33 4.3 28.4 1.0
O2A D:TTP201 4.3 19.7 1.0
NE B:ARG98 4.3 21.9 1.0
OE1 B:GLN144 4.5 23.7 1.0
O5' D:TTP201 4.5 17.6 1.0
OD2 D:ASP115 4.5 28.6 1.0
O2G D:TTP201 4.6 22.1 1.0
C5' D:TTP201 4.6 19.9 1.0
NH2 B:ARG98 4.6 24.4 1.0
O2B D:TTP201 4.7 24.9 1.0
CG B:ASP33 4.7 25.1 1.0
O D:HOH326 4.7 15.0 1.0
CE1 D:TYR157 4.7 33.2 1.0
NE2 B:GLN28 4.9 30.8 1.0
OD1 D:ASP115 4.9 27.4 1.0
CZ B:ARG98 5.0 23.0 1.0

Magnesium binding site 5 out of 6 in 4xjc

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Magnesium binding site 5 out of 6 in the Dctp Deaminase-Dutpase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dctp Deaminase-Dutpase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:38.8
occ:1.00
 O F:HOH308 1.9 23.2 1.0
O1G F:TTP202 1.9 38.2 1.0
O1B F:TTP202 2.0 41.4 1.0
O1A F:TTP202 2.0 37.1 1.0
O D:HOH356 2.0 40.7 1.0
O D:HOH319 2.2 31.6 1.0
PB F:TTP202 3.1 41.7 1.0
PG F:TTP202 3.2 45.0 1.0
PA F:TTP202 3.2 39.7 1.0
O3B F:TTP202 3.5 42.9 1.0
O3A F:TTP202 3.6 41.7 1.0
O F:HOH332 3.7 26.5 1.0
O3G F:TTP202 3.8 37.9 1.0
O F:HOH320 3.9 39.0 1.0
O2A F:TTP202 3.9 40.9 1.0
NE D:ARG98 4.0 41.6 1.0
OE1 D:GLN28 4.1 38.9 1.0
OD1 D:ASP33 4.2 36.8 1.0
OD2 D:ASP33 4.2 41.6 1.0
NH2 D:ARG98 4.3 44.5 1.0
CD D:GLN28 4.4 39.3 1.0
O2G F:TTP202 4.4 36.5 1.0
O5' F:TTP202 4.5 37.0 1.0
CG D:GLN28 4.5 37.8 1.0
O2B F:TTP202 4.5 45.5 1.0
OE1 D:GLN144 4.6 31.9 1.0
C5' F:TTP202 4.6 43.5 1.0
CG D:ASP33 4.7 38.8 1.0
CZ D:ARG98 4.7 43.4 1.0
OD2 F:ASP115 4.7 34.2 1.0
O F:HOH310 4.8 18.0 1.0
CG D:ARG98 4.8 38.8 1.0
CD D:ARG98 4.9 40.3 1.0

Magnesium binding site 6 out of 6 in 4xjc

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Magnesium binding site 6 out of 6 in the Dctp Deaminase-Dutpase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dctp Deaminase-Dutpase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:15.2
occ:1.00
 O F:HOH307 2.0 7.7 1.0
O1A B:TTP201 2.1 18.2 1.0
O1G B:TTP201 2.1 18.3 1.0
O F:HOH306 2.2 16.0 1.0
O B:HOH316 2.3 13.6 1.0
O1B B:TTP201 2.4 17.8 1.0
PA B:TTP201 3.4 14.7 1.0
PB B:TTP201 3.4 16.8 1.0
PG B:TTP201 3.5 19.9 1.0
O3B B:TTP201 3.7 18.7 1.0
OE1 F:GLN28 3.8 23.1 1.0
O3A B:TTP201 3.8 19.1 1.0
CD F:GLN28 4.0 23.1 1.0
CG F:GLN28 4.1 22.0 1.0
O F:HOH316 4.1 19.0 1.0
OD1 F:ASP33 4.1 20.2 1.0
O2A B:TTP201 4.1 15.0 1.0
O3G B:TTP201 4.1 18.3 1.0
OE1 F:GLN144 4.2 18.4 1.0
OD2 F:ASP33 4.3 20.4 1.0
OD2 B:ASP115 4.3 19.7 1.0
NE F:ARG98 4.5 19.4 1.0
O B:HOH319 4.6 27.0 1.0
O F:HOH318 4.6 11.2 1.0
O5' B:TTP201 4.6 14.7 1.0
O2G B:TTP201 4.6 14.8 1.0
CG F:ASP33 4.6 20.8 1.0
C5' B:TTP201 4.7 14.4 1.0
O2B B:TTP201 4.8 21.3 1.0
CB F:GLN28 4.8 21.3 1.0
OD1 B:ASP115 4.8 18.3 1.0
CD F:GLN144 4.8 18.8 1.0
CE1 B:TYR157 4.9 19.4 1.0
NE2 F:GLN28 4.9 24.4 1.0
NE2 F:GLN144 4.9 19.3 1.0
NH2 F:ARG98 4.9 21.1 1.0
CG B:ASP115 5.0 19.5 1.0

Reference:

C.B.Oehlenschlger, M.N.Lvgreen, E.Reinauer, E.Lehtinen, M.L.Pind, P.Harris, J.Martinussen, M.Willemoes. Bacillus Halodurans Strain C125 Encodes and Synthesizes Enzymes From Both Known Pathways to Form Dump Directly From Cytosine Deoxyribonucleotides. Appl.Environ.Microbiol. 2015.
ISSN: ESSN 1098-5336
PubMed: 25746996
DOI: 10.1128/AEM.00268-15
Page generated: Tue Aug 20 15:32:35 2024

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