Magnesium in PDB 2j4h: Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme

All present enzymatic activity of Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme:
3.5.4.13;

The structure of Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme, PDB code: 2j4h was solved by E.Johansson, M.Thymark, J.H.Bynck, M.Fanoe, S.Larsen, M.Willemoes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.545, 62.545, 342.444, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 27.3

The binding sites of Magnesium atom in the Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme (pdb code 2j4h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme, PDB code: 2j4h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1176 b:50.0 occ:1.00 O1A A:YYY1175 2.2 38.5 1.0 O1B A:YYY1175 2.5 38.1 1.0 PA A:YYY1175 3.6 38.1 1.0 PB A:YYY1175 3.7 38.4 1.0 O3A A:YYY1175 4.0 38.6 1.0 NH2 A:ARG126 4.1 25.0 1.0 O2B A:YYY1175 4.3 38.9 1.0 C5' A:YYY1175 4.3 37.1 1.0 O5' A:YYY1175 4.5 37.0 1.0 O2A A:YYY1175 4.7 38.0 1.0 O3B A:YYY1175 5.0 40.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1177 b:38.5 occ:1.00 CB A:HIS125 2.7 34.4 1.0 O A:ALA121 2.8 34.3 1.0 N A:VAL122 2.8 34.7 1.0 CG A:HIS125 2.9 36.2 1.0 C A:ALA121 3.1 33.5 1.0 ND1 A:HIS125 3.1 38.6 1.0 N A:HIS125 3.2 34.4 1.0 CA A:HIS125 3.5 33.6 1.0 C A:VAL122 3.5 36.0 1.0 CD2 A:HIS125 3.7 37.7 1.0 CA A:VAL122 3.7 35.5 1.0 N A:THR123 3.8 36.1 1.0 O A:VAL122 3.8 36.4 1.0 C A:ALA124 3.9 34.9 1.0 CE1 A:HIS125 4.0 38.4 1.0 N A:ALA124 4.2 35.1 1.0 C A:THR123 4.3 35.5 1.0 NE2 A:HIS125 4.3 38.0 1.0 CA A:ALA121 4.3 32.1 1.0 CA A:ALA124 4.5 35.0 1.0 CA A:THR123 4.5 35.7 1.0 O A:ALA124 4.6 35.2 1.0 O A:LEU107 4.6 24.5 1.0 CB A:ALA121 4.7 32.4 1.0 O A:THR123 4.7 35.5 1.0 C A:HIS125 4.8 32.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1174 b:45.7 occ:1.00 O1A B:YYY1173 2.0 38.4 1.0 O1B B:YYY1173 2.5 38.0 1.0 PA B:YYY1173 3.5 38.9 1.0 PB B:YYY1173 3.6 38.3 1.0 NH2 B:ARG126 3.9 24.8 1.0 O3A B:YYY1173 3.9 38.7 1.0 C5' B:YYY1173 4.1 37.0 1.0 O2B B:YYY1173 4.2 39.0 1.0 O5' B:YYY1173 4.3 37.2 1.0 O2A B:YYY1173 4.5 38.2 1.0 OD2 B:ASP128 4.9 27.0 1.0 O3B B:YYY1173 5.0 40.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A H121A Escherichia Coli Dctp Deaminase Mutant Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1175 b:43.1 occ:1.00 O B:ALA121 2.4 34.4 1.0 N B:VAL122 2.8 34.6 1.0 CB B:HIS125 3.0 34.7 1.0 C B:ALA121 3.0 33.4 1.0 CG B:HIS125 3.4 38.0 1.0 CD2 B:HIS125 3.5 40.2 1.0 O B:LEU107 3.5 24.5 1.0 CA B:VAL122 4.0 35.4 1.0 O B:VAL120 4.2 30.2 1.0 CA B:HIS125 4.3 34.0 1.0 ND1 B:HIS125 4.4 41.1 1.0 CA B:ALA121 4.5 32.0 1.0 C B:VAL122 4.5 35.8 1.0 NE2 B:HIS125 4.6 41.1 1.0 OD1 B:ASP108 4.6 25.7 1.0 N B:HIS125 4.6 35.1 1.0 C B:LEU107 4.7 24.7 1.0 CA B:ASP108 4.8 24.4 1.0 O B:VAL122 4.9 36.3 1.0

E.Johansson, M.Thymark, J.H.Bynck, M.Fanoe, S.Larsen, M.Willemoes. Regulation of Dctp Deaminase From Escherichia Coli By Nonallosteric Dttp Binding to An Inactive Form of the Enzyme Febs J. V. 274 4188 2007.
ISSN: ISSN 1742-464X
PubMed: 17651436
DOI: 10.1111/J.1742-4658.2007.05945.X