Atomistry » Magnesium » PDB 4xgq-4xsz » 4xjc
Atomistry »
  Magnesium »
    PDB 4xgq-4xsz »
      4xjc »

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

Go back to Magnesium Binding Sites List in 4xjc
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

Go back to Magnesium Binding Sites List in 4xjc
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

Go back to Magnesium Binding Sites List in 4xjc
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

Go back to Magnesium Binding Sites List in 4xjc
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

Go back to Magnesium Binding Sites List in 4xjc
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

Go back to Magnesium Binding Sites List in 4xjc
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy