Calcium in PDB 6u7t: Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)

All present enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G):
3.2.2.31;

The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G), PDB code: 6u7t was solved by V.L.O'shea Murray, S.Cao, M.P.Horvath, S.S.David, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.33 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.800, 86.490, 140.580, 90.00, 90.00, 90.00
R / Rfree (%)	26.1 / 27

The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) (pdb code 6u7t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G), PDB code: 6u7t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:38.9 occ:1.00 O C:HOH103 2.2 38.5 1.0 O A:HOH538 2.3 32.4 1.0 O A:HOH507 2.3 34.0 1.0 O A:VAL123 2.4 30.7 1.0 OG A:SER118 2.7 45.6 1.0 O A:SER118 2.7 45.3 1.0 HG A:SER118 3.0 54.7 1.0 O A:HOH545 3.2 45.8 1.0 HA2 A:GLY124 3.3 34.5 1.0 HB3 A:SER118 3.4 57.8 1.0 CB A:SER118 3.5 48.2 1.0 C A:SER118 3.5 39.6 1.0 HA A:SER118 3.5 53.1 1.0 C A:VAL123 3.6 30.3 1.0 CA A:SER118 3.7 44.2 1.0 CA A:GLY124 4.2 28.8 1.0 HB A:VAL123 4.2 37.9 1.0 O A:HOH519 4.3 36.8 1.0 OP2 C:DC21 4.3 26.3 1.0 HB2 A:SER118 4.3 57.8 1.0 N A:GLY124 4.4 33.1 1.0 HG12 A:VAL123 4.4 40.4 1.0 N A:ARG119 4.6 43.4 1.0 C A:GLY124 4.7 30.2 1.0 HA A:ARG119 4.7 50.2 1.0 O A:LEU120 4.7 30.2 1.0 CA A:VAL123 4.8 26.8 1.0 CB A:VAL123 4.8 31.6 1.0 OP1 C:DC21 4.8 27.7 1.0 HA3 A:GLY124 4.9 34.5 1.0 H A:VAL123 4.9 34.4 1.0 HD3 A:PRO125 5.0 39.2 1.0

Calcium binding site 2 out of 2 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:61.7 occ:1.00 OG1 A:THR259 2.3 50.9 1.0 O A:THR259 2.3 56.3 1.0 OD2 A:ASP257 2.3 56.3 1.0 C A:THR259 3.2 46.7 1.0 CG A:ASP257 3.5 55.4 1.0 CB A:THR259 3.5 43.9 1.0 HA3 A:GLY260 3.7 53.4 1.0 HB A:THR259 3.9 52.7 1.0 CA A:THR259 3.9 49.5 1.0 H A:THR259 3.9 54.2 1.0 OD1 A:ASP257 4.1 61.4 1.0 N A:GLY260 4.2 42.5 1.0 N A:THR259 4.4 45.2 1.0 HB2 A:ASP257 4.4 57.5 1.0 CA A:GLY260 4.5 44.5 1.0 CB A:ASP257 4.6 47.9 1.0 HG23 A:THR259 4.7 61.3 1.0 CG2 A:THR259 4.7 51.0 1.0 HA A:THR259 4.8 59.4 1.0 HG21 A:THR259 4.9 61.3 1.0 H A:GLY260 5.0 51.1 1.0

R.D.Woods, V.L.O'shea, A.Chu, S.Cao, J.L.Richards, M.P.Horvath, S.S.David. Structure and Stereochemistry of the Base Excision Repair Glycosylase Muty Reveal A Mechanism Similar to Retaining Glycosidases. Nucleic Acids Res. V. 44 801 2016.
ISSN: ESSN 1362-4962
PubMed: 26673696
DOI: 10.1093/NAR/GKV1469