Calcium in PDB 4qwb: Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp

All present enzymatic activity of Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp:
2.7.7.7;

The structure of Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp, PDB code: 4qwb was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.27 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.950, 102.340, 52.730, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.1

The binding sites of Calcium atom in the Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp (pdb code 4qwb). 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 Linker Region P236A Mutant with An Incoming D-Dcdp, PDB code: 4qwb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp


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 Linker Region P236A Mutant with An Incoming D-Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:16.4 occ:1.00 OD2 A:ASP105 2.2 15.8 1.0 O1A A:YYY401 2.2 17.7 1.0 O1B A:YYY401 2.2 18.0 1.0 OD1 A:ASP7 2.3 17.0 1.0 O A:PHE8 2.3 16.8 1.0 O A:HOH501 2.4 18.4 1.0 CG A:ASP105 3.4 16.5 1.0 PB A:YYY401 3.4 17.7 1.0 PA A:YYY401 3.5 18.2 1.0 CG A:ASP7 3.5 17.3 1.0 C A:PHE8 3.5 16.7 1.0 O A:HOH504 3.7 17.2 1.0 O3A A:YYY401 3.8 18.3 1.0 C5' A:YYY401 4.0 17.0 1.0 OD2 A:ASP7 4.0 17.9 1.0 N A:PHE8 4.0 16.6 1.0 O3B A:YYY401 4.0 19.7 1.0 OD1 A:ASP105 4.1 15.8 1.0 O5' A:YYY401 4.1 18.0 1.0 O A:HOH503 4.2 16.5 1.0 O A:HOH502 4.3 20.5 1.0 O A:HOH505 4.3 20.5 1.0 CA A:PHE8 4.4 17.1 1.0 C A:ASP7 4.4 17.5 1.0 NZ A:LYS159 4.4 22.3 1.0 CB A:ASP105 4.5 16.5 1.0 O A:HOH547 4.5 30.6 1.0 N A:ASP9 4.5 16.6 1.0 N A:TYR10 4.5 16.5 1.0 CA A:ASP9 4.6 17.0 1.0 C A:ASP9 4.7 16.6 1.0 N A:PHE11 4.7 15.8 1.0 O2B A:YYY401 4.7 18.0 1.0 CB A:ASP7 4.7 17.1 1.0 CB A:PHE11 4.8 16.1 1.0 O2A A:YYY401 4.8 18.7 1.0 O A:ASP7 4.8 17.8 1.0 CA A:ASP7 4.9 17.2 1.0 CA A:CA403 5.0 18.5 1.0 CB A:PHE8 5.0 17.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp


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 Linker Region P236A Mutant with An Incoming D-Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:18.5 occ:1.00 OD2 A:ASP7 2.3 17.9 1.0 O A:HOH504 2.3 17.2 1.0 OE2 A:GLU106 2.3 17.9 1.0 O B:HOH201 2.3 16.3 1.0 OP1 B:DOC13 2.3 22.0 1.0 O A:HOH505 2.4 20.5 1.0 CD A:GLU106 3.3 18.8 1.0 CG A:ASP7 3.4 17.3 1.0 P B:DOC13 3.6 21.3 1.0 CG A:GLU106 3.9 18.5 1.0 C5' B:DOC13 3.9 22.1 1.0 O5' B:DOC13 3.9 22.2 1.0 OD1 A:ASP7 3.9 17.0 1.0 O1A A:YYY401 4.0 17.7 1.0 NZ A:LYS159 4.0 22.3 1.0 OE1 A:GLU106 4.1 19.1 1.0 NZ A:LYS152 4.2 20.5 1.0 O B:HOH212 4.2 33.9 1.0 CE A:LYS152 4.3 20.9 1.0 CZ A:PHE5 4.4 17.8 1.0 OP2 B:DOC13 4.5 21.8 1.0 CB A:ASP7 4.6 17.1 1.0 O A:HOH518 4.6 30.7 1.0 O A:HOH621 4.7 30.7 1.0 O3' B:DT12 4.7 23.2 1.0 OD1 A:ASP105 4.8 15.8 1.0 C4' B:DOC13 5.0 21.9 1.0 CA A:CA402 5.0 16.4 1.0 CE2 A:PHE5 5.0 17.9 1.0 PA A:YYY401 5.0 18.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp


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 Linker Region P236A Mutant with An Incoming D-Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:27.3 occ:1.00 O B:HOH204 2.3 27.3 1.0 O A:HOH541 2.3 39.5 1.0 O A:ALA181 2.3 29.0 1.0 O A:HOH542 2.4 45.8 1.0 O A:ILE186 2.5 20.6 1.0 O A:HOH520 2.6 28.2 1.0 C A:ALA181 3.5 28.6 1.0 C A:ILE186 3.7 20.7 1.0 CA A:GLY187 4.2 24.1 1.0 CA A:ALA181 4.4 29.9 1.0 N A:GLY187 4.4 23.0 1.0 N A:ASP182 4.4 27.7 1.0 CA A:ASP182 4.5 28.1 1.0 OP1 B:DT12 4.6 24.8 1.0 CB A:ALA181 4.6 30.2 1.0 O A:VAL183 4.7 19.5 1.0 C A:GLY187 4.7 26.4 1.0 OP2 B:DT12 4.8 25.5 1.0 CA A:ILE186 4.8 20.1 1.0 CB A:ILE186 4.9 19.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of DPO4 Linker Region P236A Mutant with An Incoming D-Dcdp


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 Linker Region P236A Mutant with An Incoming D-Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:64.3 occ:1.00 O B:HOH223 2.7 45.7 1.0 N3 B:DG1 3.0 26.0 1.0 O4' B:DG2 3.5 41.1 1.0 N2 B:DG1 3.6 26.4 1.0 C2 B:DG1 3.7 25.4 1.0 C1' B:DG1 3.7 29.4 1.0 C4 B:DG1 3.9 25.6 1.0 C4' B:DG2 4.1 40.8 1.0 C5' B:DG2 4.1 39.6 1.0 N9 B:DG1 4.3 26.2 1.0 O4' B:DG1 4.3 30.4 1.0 C2' B:DG1 4.7 30.6 1.0 O3' B:DG1 4.8 36.3 1.0 C1' B:DG2 4.8 40.7 1.0 C4' B:DG1 4.9 32.0 1.0

V.Gaur, R.Vyas, J.D.Fowler, G.Efthimiopoulos, J.Y.Feng, Z.Suo. Structural and Kinetic Insights Into Binding and Incorporation of L-Nucleotide Analogs By A Y-Family Dna Polymerase. Nucleic Acids Res. V. 42 9984 2014.
ISSN: ISSN 0305-1048
PubMed: 25104018
DOI: 10.1093/NAR/GKU709