Calcium in PDB 1s9f: Dpo with at Matched

All present enzymatic activity of Dpo with at Matched:
2.7.7.7;

The structure of Dpo with at Matched, PDB code: 1s9f was solved by J.Trincao, R.E.Johnson, W.T.Wolfle, C.R.Escalante, S.Prakash, L.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.800, 100.300, 110.800, 90.00, 95.20, 90.00
R / Rfree (%)	20.5 / 23.9

The structure of Dpo with at Matched also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Dpo with at Matched (pdb code 1s9f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Dpo with at Matched, PDB code: 1s9f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4001 b:22.9 occ:1.00 O1A A:DDY4010 2.3 21.8 1.0 O A:PHE8 2.4 20.9 1.0 OD2 A:ASP7 2.4 27.0 1.0 O1B A:DDY4010 2.5 27.3 1.0 OD2 A:ASP105 2.5 25.1 1.0 O A:HOH4080 2.7 22.6 1.0 PA A:DDY4010 3.4 25.1 1.0 CG A:ASP7 3.4 27.9 1.0 O3A A:DDY4010 3.5 25.0 1.0 PB A:DDY4010 3.5 27.4 1.0 CG A:ASP105 3.6 24.3 1.0 C A:PHE8 3.6 22.6 1.0 OD1 A:ASP7 3.8 30.1 1.0 O A:HOH4013 3.8 22.7 1.0 C5' A:DDY4010 4.0 32.1 1.0 OD1 A:ASP105 4.0 25.3 1.0 O5' A:DDY4010 4.0 29.8 1.0 N A:PHE8 4.2 21.1 1.0 O A:HOH4056 4.2 23.1 1.0 O3B A:DDY4010 4.3 27.1 1.0 NZ A:LYS159 4.3 30.4 1.0 C A:ASP7 4.4 19.9 1.0 N A:TYR10 4.4 20.5 1.0 CA A:PHE8 4.4 21.4 1.0 N A:ASP9 4.5 20.7 1.0 CA A:ASP9 4.6 22.6 1.0 O A:ASP7 4.7 19.9 1.0 O2A A:DDY4010 4.7 26.6 1.0 C A:ASP9 4.7 20.8 1.0 CB A:ASP7 4.7 22.8 1.0 O A:ASP105 4.7 20.4 1.0 O2B A:DDY4010 4.7 26.1 1.0 CB A:ASP105 4.8 20.6 1.0 N A:PHE11 4.8 17.8 1.0 CA A:ASP7 4.9 21.2 1.0 CB A:PHE8 5.0 20.8 1.0

Calcium binding site 2 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:44.3 occ:1.00 O1B B:DDY4011 2.5 47.6 1.0 O B:PHE8 2.5 27.4 1.0 O B:HOH4170 2.6 38.2 1.0 OD2 B:ASP7 2.6 33.1 1.0 O1A B:DDY4011 2.7 47.3 1.0 OD2 B:ASP105 2.7 36.0 1.0 CG B:ASP7 3.3 33.9 1.0 CG B:ASP105 3.3 31.7 1.0 O5' B:DDY4011 3.4 47.4 1.0 OD1 B:ASP7 3.4 35.1 1.0 PA B:DDY4011 3.5 44.1 1.0 PB B:DDY4011 3.6 43.6 1.0 C B:PHE8 3.7 27.3 1.0 OD1 B:ASP105 3.8 32.6 1.0 O3A B:DDY4011 4.0 46.6 1.0 O B:HOH4034 4.1 32.9 1.0 N B:PHE8 4.2 26.4 1.0 O2B B:DDY4011 4.2 46.0 1.0 CB B:ASP105 4.2 27.3 1.0 O B:HOH4039 4.3 50.7 1.0 O B:ASP105 4.4 27.6 1.0 C5' B:DDY4011 4.5 48.4 1.0 C B:ASP7 4.5 27.7 1.0 CA B:PHE8 4.5 26.5 1.0 N B:TYR10 4.6 24.9 1.0 CB B:ASP7 4.6 30.3 1.0 N B:ASP9 4.7 26.7 1.0 CA B:ASP9 4.8 26.7 1.0 OE1 B:GLU106 4.8 39.3 1.0 NZ B:LYS159 4.8 40.3 1.0 N B:PHE11 4.9 23.1 1.0 CA B:ASP7 4.9 28.2 1.0 C B:ASP9 4.9 24.5 1.0 O2A B:DDY4011 4.9 41.7 1.0 O3B B:DDY4011 4.9 47.3 1.0 O B:ASP7 4.9 28.0 1.0 CB B:PHE8 5.0 24.4 1.0

Calcium binding site 3 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca4003 b:26.2 occ:1.00 O1B C:DDY4012 2.3 29.0 1.0 O C:PHE8 2.4 21.7 1.0 O1A C:DDY4012 2.4 23.6 1.0 OD2 C:ASP105 2.4 27.9 1.0 OD2 C:ASP7 2.6 28.0 1.0 O C:HOH4106 2.6 25.4 1.0 CG C:ASP7 3.3 27.6 1.0 PB C:DDY4012 3.5 27.4 1.0 CG C:ASP105 3.5 23.7 1.0 PA C:DDY4012 3.5 24.7 1.0 C C:PHE8 3.6 21.9 1.0 OD1 C:ASP7 3.6 31.0 1.0 O3A C:DDY4012 3.6 26.2 1.0 O C:HOH4022 3.8 23.1 1.0 C5' C:DDY4012 3.9 28.0 1.0 OD1 C:ASP105 3.9 24.0 1.0 N C:PHE8 4.1 21.2 1.0 O5' C:DDY4012 4.1 28.7 1.0 O3B C:DDY4012 4.2 26.8 1.0 O C:HOH4035 4.3 24.3 1.0 C C:ASP7 4.3 22.6 1.0 CA C:PHE8 4.4 20.9 1.0 NZ C:LYS159 4.4 30.6 1.0 N C:TYR10 4.5 21.7 1.0 N C:ASP9 4.6 21.3 1.0 CB C:ASP7 4.6 25.4 1.0 O C:ASP105 4.6 19.5 1.0 CA C:ASP9 4.6 22.4 1.0 O C:ASP7 4.7 24.7 1.0 CB C:ASP105 4.7 23.3 1.0 O2B C:DDY4012 4.7 31.4 1.0 O C:HOH4126 4.7 44.0 1.0 C C:ASP9 4.8 22.0 1.0 CA C:ASP7 4.8 24.2 1.0 N C:PHE11 4.8 19.8 1.0 O2A C:DDY4012 4.8 23.8 1.0 CE C:LYS159 4.8 34.4 1.0 CB C:PHE8 4.9 19.2 1.0 OE1 C:GLU106 5.0 35.6 1.0

Calcium binding site 4 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4004 b:19.9 occ:1.00 O1A D:DDY4013 2.3 17.3 1.0 O1B D:DDY4013 2.4 22.0 1.0 OD2 D:ASP7 2.4 16.6 1.0 O D:PHE8 2.4 17.4 1.0 OD2 D:ASP105 2.4 19.9 1.0 O D:HOH4118 2.6 21.8 1.0 PA D:DDY4013 3.4 19.0 1.0 CG D:ASP105 3.4 19.0 1.0 CG D:ASP7 3.5 22.2 1.0 PB D:DDY4013 3.5 23.4 1.0 C D:PHE8 3.6 16.5 1.0 O3A D:DDY4013 3.6 22.1 1.0 O D:HOH4014 3.6 24.2 1.0 OD1 D:ASP105 3.8 21.7 1.0 OD1 D:ASP7 4.0 20.8 1.0 C5' D:DDY4013 4.0 26.9 1.0 O5' D:DDY4013 4.1 25.4 1.0 N D:PHE8 4.1 18.4 1.0 O D:HOH4018 4.1 21.6 1.0 NZ D:LYS159 4.2 21.6 1.0 C D:ASP7 4.3 18.0 1.0 O3B D:DDY4013 4.3 19.1 1.0 CA D:PHE8 4.4 18.4 1.0 N D:TYR10 4.4 18.4 1.0 O D:HOH4205 4.5 54.0 1.0 N D:ASP9 4.5 16.8 1.0 CA D:ASP9 4.6 17.1 1.0 O D:ASP7 4.6 19.7 1.0 CB D:ASP7 4.7 18.6 1.0 O2B D:DDY4013 4.7 27.0 1.0 O2A D:DDY4013 4.7 20.4 1.0 C D:ASP9 4.7 16.3 1.0 CB D:ASP105 4.7 17.4 1.0 O D:ASP105 4.7 17.3 1.0 CA D:ASP7 4.8 19.5 1.0 N D:PHE11 4.8 16.4 1.0 CB D:PHE8 4.9 16.3 1.0 CE D:LYS159 5.0 23.1 1.0 OE1 D:GLU106 5.0 27.8 1.0

J.Trincao, R.E.Johnson, W.T.Wolfle, C.R.Escalante, S.Prakash, L.Prakash, A.K.Aggarwal. DPO4 Is Hindered in Extending A G.T Mismatch By A Reverse Wobble Nat.Struct.Mol.Biol. V. 11 457 2004.
ISSN: ISSN 1545-9993
PubMed: 15077104
DOI: 10.1038/NSMB755