Atomistry » Magnesium » PDB 1xoq-1xyc » 1xs4
Atomistry »
  Magnesium »
    PDB 1xoq-1xyc »
      1xs4 »

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

Go back to Magnesium Binding Sites List in 1xs4
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

Go back to Magnesium Binding Sites List in 1xs4
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

Go back to Magnesium Binding Sites List in 1xs4
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

Go back to Magnesium Binding Sites List in 1xs4
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

Go back to Magnesium Binding Sites List in 1xs4
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

Go back to Magnesium Binding Sites List in 1xs4
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy