Calcium in PDB 4gc6: Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt

All present enzymatic activity of Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt:
2.7.7.7;

The structure of Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt, PDB code: 4gc6 was solved by R.L.Eoff, A.Ketkar, S.Banerjee, M.K.Zafar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.79 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.641, 103.357, 52.491, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 27.6

The binding sites of Calcium atom in the Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt (pdb code 4gc6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt, PDB code: 4gc6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:70.3 occ:1.00 O A:PHE8 2.7 71.9 1.0 OAH A:0OH401 2.9 81.5 1.0 OD2 A:ASP105 2.9 77.1 1.0 OD1 A:ASP7 3.0 89.8 1.0 O A:HOH526 3.2 81.3 1.0 OAC A:0OH401 3.3 64.6 1.0 OD2 A:ASP7 3.4 73.5 1.0 CG A:ASP7 3.4 80.3 1.0 C A:PHE8 3.5 63.2 1.0 CG A:ASP105 3.6 75.7 1.0 PBD A:0OH401 3.6 95.8 1.0 O A:HOH501 3.7 62.4 1.0 CA A:CA403 3.8 0.3 1.0 N A:PHE8 3.9 61.7 1.0 O A:HOH531 3.9 84.5 1.0 OD1 A:ASP105 4.0 74.8 1.0 CAL A:0OH401 4.1 83.0 1.0 CA A:PHE8 4.2 60.2 1.0 C A:ASP7 4.2 65.3 1.0 N A:ASP9 4.3 65.3 1.0 N A:TYR10 4.4 68.6 1.0 OAR A:0OH401 4.4 96.6 1.0 CA A:ASP9 4.4 72.3 1.0 C A:ASP9 4.5 70.3 1.0 CB A:ASP105 4.5 65.9 1.0 O A:ASP105 4.6 58.3 1.0 O A:ASP7 4.6 70.5 1.0 N A:PHE11 4.6 69.3 1.0 CB A:ASP7 4.7 72.2 1.0 CB A:PHE11 4.7 64.0 1.0 CA A:ASP7 4.8 64.5 1.0 CB A:PHE8 4.8 58.2 1.0 OAT A:0OH401 4.9 95.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:0.3 occ:1.00 OD2 A:ASP7 3.0 73.5 1.0 OE2 A:GLU106 3.3 78.9 1.0 OAH A:0OH401 3.3 81.5 1.0 O A:HOH505 3.4 73.8 1.0 OP1 P:DC14 3.5 0.6 1.0 O5' P:DC14 3.6 83.2 1.0 C3' P:DC14 3.8 79.8 1.0 NZ A:LYS159 3.8 82.5 0.8 CA A:CA402 3.8 70.3 1.0 P P:DC14 4.0 0.2 1.0 CD A:GLU106 4.0 74.3 1.0 CG A:ASP7 4.1 80.3 1.0 C5' P:DC14 4.1 81.9 1.0 O P:HOH108 4.1 81.4 1.0 C2' P:DC14 4.3 77.4 1.0 OD1 A:ASP105 4.3 74.8 1.0 OD1 A:ASP7 4.4 89.8 1.0 CE A:LYS159 4.5 80.8 0.7 CG A:GLU106 4.5 68.5 1.0 OP2 P:DC14 4.5 93.0 1.0 C4' P:DC14 4.5 80.8 1.0 CAL A:0OH401 4.5 83.0 1.0 O A:HOH526 4.6 81.3 1.0 O3' P:DC14 4.7 70.7 1.0 PBD A:0OH401 4.7 95.8 1.0 OD2 A:ASP105 4.7 77.1 1.0 OAR A:0OH401 4.8 96.6 1.0 OE1 A:GLU106 4.9 79.1 1.0 CG A:ASP105 4.9 75.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:91.8 occ:1.00 O A:HOH513 2.8 63.8 1.0 O A:ALA181 3.0 78.1 1.0 O A:ILE186 3.1 77.9 1.0 O A:HOH512 3.1 77.9 1.0 O A:HOH514 3.1 64.9 1.0 OP1 P:DC13 3.7 73.0 1.0 OP2 P:DC13 3.9 71.6 1.0 C A:ILE186 4.1 69.2 1.0 C A:ALA181 4.2 74.9 1.0 P P:DC13 4.3 82.3 1.0 O A:VAL183 4.3 66.0 1.0 CA A:GLY187 4.8 66.9 1.0 N A:GLY187 4.8 65.9 1.0 CA A:ASP182 4.9 69.7 1.0 C A:ASP182 5.0 67.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of DPO4 in Complex with N-Mc-Damp Opposite Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:1.0 occ:1.00 O A:HOH529 2.6 92.3 1.0 O A:HOH530 3.0 88.1 1.0 OD2 A:ASP294 3.1 96.6 1.0 OP2 P:DA10 3.2 86.6 1.0 OD1 A:ASP294 3.3 98.2 1.0 O P:HOH102 3.4 65.5 1.0 OP1 P:DA10 3.5 68.0 1.0 CG A:ASP294 3.5 99.1 1.0 P P:DA10 3.8 99.4 1.0 O A:HOH523 4.1 73.3 1.0 O3' P:DG9 4.7 88.5 1.0 C3' P:DG9 4.8 88.7 1.0

A.Ketkar, M.K.Zafar, S.Banerjee, V.E.Marquez, M.Egli, R.L.Eoff. Differential Furanose Selection in the Active Sites of Archaeal Dna Polymerases Probed By Fixed-Conformation Nucleotide Analogues. Biochemistry V. 51 9234 2012.
ISSN: ISSN 0006-2960
PubMed: 23050956
DOI: 10.1021/BI301043K