Calcium in PDB 1s97: DPO4 with Gt Mismatch

All present enzymatic activity of DPO4 with Gt Mismatch:
2.7.7.7;

The structure of DPO4 with Gt Mismatch, PDB code: 1s97 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)	29.64 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.433, 100.644, 110.426, 90.00, 94.89, 90.00
R / Rfree (%)	21.8 / 26.9

The binding sites of Calcium atom in the DPO4 with Gt Mismatch (pdb code 1s97). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the DPO4 with Gt Mismatch, PDB code: 1s97:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the DPO4 with Gt Mismatch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 with Gt Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:25.6 occ:1.00 OD2 A:ASP7 2.3 20.8 1.0 O A:PHE8 2.6 17.9 1.0 O3A A:DCT600 2.7 47.7 1.0 O3G A:DCT600 2.7 62.4 1.0 OD2 A:ASP105 2.7 22.4 1.0 O1G A:DCT600 2.8 62.5 1.0 PG A:DCT600 3.2 61.3 1.0 O1B A:DCT600 3.2 45.6 1.0 CG A:ASP105 3.3 20.4 1.0 CG A:ASP7 3.4 21.7 1.0 PB A:DCT600 3.5 43.8 1.0 O1A A:DCT600 3.5 50.2 1.0 C A:PHE8 3.7 17.9 1.0 O3B A:DCT600 3.7 53.8 1.0 PA A:DCT600 3.7 47.4 1.0 O A:HOH756 3.8 38.5 1.0 OD1 A:ASP7 3.8 20.0 1.0 OD1 A:ASP105 3.8 20.2 1.0 N A:PHE8 4.0 18.6 1.0 CB A:ASP105 4.2 17.4 1.0 CA A:PHE8 4.4 18.3 1.0 C A:ASP7 4.4 18.2 1.0 O A:ASP105 4.4 16.3 1.0 O2G A:DCT600 4.6 63.5 1.0 N A:ASP9 4.7 17.1 1.0 O5' A:DCT600 4.7 47.2 1.0 CB A:ASP7 4.7 20.4 1.0 N A:TYR10 4.7 13.7 1.0 O A:HOH724 4.8 35.5 1.0 O2A A:DCT600 4.8 51.9 1.0 CA A:ASP9 4.8 15.8 1.0 O2B A:DCT600 4.8 47.4 1.0 CA A:ASP7 4.8 18.3 1.0 O A:ASP7 4.9 19.4 1.0 N A:PHE11 4.9 14.8 1.0 OE1 A:GLU106 4.9 26.0 1.0 CB A:PHE8 4.9 19.0 1.0 C A:ASP9 4.9 14.4 1.0 CB A:PHE11 5.0 13.9 1.0

Calcium binding site 2 out of 4 in the DPO4 with Gt Mismatch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 with Gt Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:34.5 occ:1.00 OD2 B:ASP7 2.5 26.2 1.0 O B:PHE8 2.6 20.2 1.0 O3G B:DCT601 2.8 67.8 1.0 O1G B:DCT601 2.8 65.8 1.0 O3A B:DCT601 2.8 53.5 1.0 OD2 B:ASP105 2.9 18.8 1.0 O1B B:DCT601 3.3 49.6 1.0 PG B:DCT601 3.3 66.5 1.0 CG B:ASP105 3.3 17.8 1.0 CG B:ASP7 3.3 25.3 1.0 PB B:DCT601 3.5 51.8 1.0 O1A B:DCT601 3.7 55.9 1.0 OD1 B:ASP7 3.7 25.7 1.0 C B:PHE8 3.7 17.8 1.0 O3B B:DCT601 3.8 59.8 1.0 OD1 B:ASP105 3.8 15.4 1.0 PA B:DCT601 3.9 53.6 1.0 O B:HOH725 4.0 21.0 1.0 CB B:ASP105 4.1 18.2 1.0 N B:PHE8 4.1 19.1 1.0 O B:HOH751 4.1 34.9 1.0 C B:ASP7 4.3 20.7 1.0 O B:ASP105 4.3 18.1 1.0 CB B:ASP7 4.5 22.5 1.0 CA B:PHE8 4.5 17.1 1.0 CA B:ASP7 4.7 20.4 1.0 OE1 B:GLU106 4.7 28.0 1.0 O B:ASP7 4.7 21.6 1.0 N B:ASP9 4.7 16.5 1.0 O2G B:DCT601 4.7 67.7 1.0 N B:TYR10 4.8 13.6 1.0 CA B:ASP9 4.8 15.7 1.0 O2A B:DCT601 4.8 56.5 1.0 CG B:GLU106 4.9 22.5 1.0 O2B B:DCT601 4.9 54.6 1.0 O5' B:DCT601 5.0 52.0 1.0 CB B:PHE8 5.0 16.1 1.0

Calcium binding site 3 out of 4 in the DPO4 with Gt Mismatch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 with Gt Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca703 b:37.5 occ:1.00 OD2 C:ASP7 2.5 26.5 1.0 O C:PHE8 2.6 19.0 1.0 OD2 C:ASP105 2.8 20.4 1.0 O3G C:DCT602 2.9 73.2 1.0 O1G C:DCT602 3.0 74.6 1.0 O3A C:DCT602 3.0 74.5 1.0 CG C:ASP105 3.2 17.3 1.0 CG C:ASP7 3.2 20.2 1.0 O1B C:DCT602 3.3 72.5 1.0 OD1 C:ASP7 3.4 20.8 1.0 PG C:DCT602 3.4 73.7 1.0 OD1 C:ASP105 3.5 17.4 1.0 PB C:DCT602 3.6 72.1 1.0 C C:PHE8 3.7 17.6 1.0 O3B C:DCT602 3.8 73.2 1.0 N C:PHE8 3.9 14.7 1.0 CB C:ASP105 4.1 16.2 1.0 PA C:DCT602 4.2 74.9 1.0 O C:HOH705 4.3 15.8 1.0 C C:ASP7 4.3 16.7 1.0 CA C:PHE8 4.3 14.8 1.0 O1A C:DCT602 4.4 75.0 1.0 O5' C:DCT602 4.4 71.5 1.0 O C:ASP105 4.5 15.0 1.0 CB C:ASP7 4.5 16.6 1.0 OE2 C:GLU106 4.7 26.4 1.0 CA C:ASP7 4.7 16.5 1.0 N C:ASP9 4.7 18.3 1.0 N C:TYR10 4.8 20.1 1.0 CB C:PHE8 4.8 12.9 1.0 O2G C:DCT602 4.8 74.9 1.0 O C:ASP7 4.8 17.8 1.0 CG C:GLU106 4.9 22.1 1.0 CA C:ASP9 4.9 18.7 1.0

Calcium binding site 4 out of 4 in the DPO4 with Gt Mismatch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of DPO4 with Gt Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca704 b:48.4 occ:1.00 OD2 D:ASP7 2.5 23.1 1.0 OD2 D:ASP105 2.5 17.9 1.0 O D:PHE8 2.7 20.8 1.0 O3A D:DCT603 2.8 77.9 1.0 O1G D:DCT603 2.8 74.9 1.0 CG D:ASP7 3.2 21.9 1.0 O3B D:DCT603 3.2 74.4 1.0 OD1 D:ASP7 3.3 18.7 1.0 O1A D:DCT603 3.4 80.6 1.0 PG D:DCT603 3.4 73.6 1.0 O3G D:DCT603 3.4 74.5 1.0 CG D:ASP105 3.5 16.1 1.0 PA D:DCT603 3.6 80.7 1.0 PB D:DCT603 3.6 72.5 1.0 C D:PHE8 3.9 20.8 1.0 OD1 D:ASP105 3.9 19.5 1.0 O D:HOH708 4.0 15.4 1.0 O1B D:DCT603 4.2 72.5 1.0 OE1 D:GLU106 4.2 27.9 1.0 O5' D:DCT603 4.2 80.1 1.0 N D:PHE8 4.3 19.9 1.0 C D:ASP7 4.5 21.6 1.0 CB D:ASP7 4.5 21.0 1.0 O D:ASP105 4.5 13.3 1.0 CB D:ASP105 4.6 14.0 1.0 CA D:PHE8 4.6 19.4 1.0 CG D:GLU106 4.7 22.0 1.0 CA D:ASP7 4.8 21.3 1.0 O2G D:DCT603 4.8 74.6 1.0 N D:ASP9 4.9 20.6 1.0 O2A D:DCT603 4.9 80.8 1.0 O2B D:DCT603 4.9 74.7 1.0 CD D:GLU106 4.9 24.0 1.0 N D:TYR10 4.9 15.8 1.0 O D:ASP7 4.9 22.4 1.0 CA D:ASP9 5.0 19.8 1.0 O D:HOH723 5.0 39.7 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