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Calcium in PDB 1s0m: Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase

Enzymatic activity of Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase

All present enzymatic activity of Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase, PDB code: 1s0m was solved by H.Ling, J.M.Sayer, F.Boudsocq, B.S.Plosky, R.Woodgate, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.60 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.029, 103.545, 106.127, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.6

Other elements in 1s0m:

The structure of Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase (pdb code 1s0m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase, PDB code: 1s0m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1s0m

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Calcium binding site 1 out of 7 in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase


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 A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca408

b:97.6
occ:1.00
 OP2 E:DG1809 1.9 61.4 1.0
O E:HOH122 2.4 72.0 1.0
O B:HOH861 2.7 39.8 1.0
P E:DG1809 2.8 62.4 1.0
OP1 E:DG1809 3.0 63.7 1.0
O B:HOH813 3.1 58.5 1.0
OD2 B:ASP294 3.4 58.9 1.0
OD1 B:ASP294 3.4 60.3 1.0
CG B:ASP294 3.7 59.4 1.0
O3' E:DG1808 3.8 58.0 1.0
C3' E:DG1808 3.9 51.3 1.0
O5' E:DG1809 4.0 59.1 1.0
O B:ILE295 4.3 53.9 1.0
C2' E:DG1808 4.3 47.0 1.0
N B:ILE295 4.5 55.8 1.0
C5' E:DG1809 4.8 58.8 1.0
CB B:ASP294 5.0 58.0 1.0

Calcium binding site 2 out of 7 in 1s0m

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Calcium binding site 2 out of 7 in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase


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 A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:36.8
occ:1.00
 O A:PHE8 2.1 31.1 1.0
O1G A:DTP803 2.2 91.1 1.0
OD2 A:ASP105 2.3 41.8 1.0
O2B A:DTP803 2.3 88.7 1.0
O1A A:DTP803 2.4 85.7 1.0
OD1 A:ASP7 2.8 36.1 1.0
OD2 A:ASP7 2.9 36.5 1.0
CG A:ASP7 3.1 32.2 1.0
PB A:DTP803 3.2 88.9 1.0
C A:PHE8 3.2 29.4 1.0
PG A:DTP803 3.3 92.1 1.0
CG A:ASP105 3.5 38.9 1.0
O3B A:DTP803 3.5 90.8 1.0
O A:HOH849 3.6 28.6 1.0
O3A A:DTP803 3.6 86.1 1.0
PA A:DTP803 3.6 83.8 1.0
N A:PHE8 3.8 29.6 1.0
CA A:PHE8 4.1 28.4 1.0
O2G A:DTP803 4.1 91.4 1.0
C A:ASP7 4.1 29.9 1.0
MG A:MG401 4.2 52.7 1.0
OD1 A:ASP105 4.2 40.0 1.0
N A:ASP9 4.2 29.7 1.0
CA A:ASP9 4.3 28.7 1.0
CB A:ASP7 4.4 31.4 1.0
N A:TYR10 4.4 27.6 1.0
CB A:ASP105 4.5 37.5 1.0
O3G A:DTP803 4.5 91.2 1.0
C A:ASP9 4.5 28.4 1.0
O A:HOH915 4.5 58.2 1.0
O A:ASP105 4.6 33.8 1.0
O A:ASP7 4.6 28.6 1.0
O1B A:DTP803 4.6 86.9 1.0
CA A:ASP7 4.6 29.8 1.0
O2A A:DTP803 4.6 85.5 1.0
NZ A:LYS159 4.7 24.3 1.0
CB A:PHE8 4.7 27.2 1.0
O A:HOH877 4.7 68.1 1.0
N A:PHE11 4.8 25.1 1.0
O5' A:DTP803 4.8 84.8 1.0

Calcium binding site 3 out of 7 in 1s0m

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Calcium binding site 3 out of 7 in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase


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 A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:61.0
occ:1.00
 O A:ALA181 2.3 35.0 1.0
O A:HOH914 2.3 39.5 1.0
O A:HOH805 2.5 62.5 1.0
O A:HOH878 2.5 55.3 1.0
O A:ILE186 2.6 38.8 1.0
O C:HOH269 2.7 59.9 1.0
C A:ALA181 3.6 33.2 1.0
C A:ILE186 3.8 37.2 1.0
CA A:ASP182 4.4 31.5 1.0
OP2 C:DT1813 4.4 36.3 1.0
N A:ASP182 4.4 31.5 1.0
CA A:GLY187 4.5 40.7 1.0
CA A:ALA181 4.5 33.9 1.0
O A:VAL183 4.5 28.7 1.0
N A:GLY187 4.6 38.4 1.0
C A:ASP182 4.8 30.2 1.0
CA A:ILE186 4.8 34.5 1.0
O A:HOH818 4.8 39.6 1.0
N A:VAL183 4.8 29.1 1.0
CB A:ALA181 4.9 34.1 1.0
CB A:ILE186 5.0 35.1 1.0
N A:ILE186 5.0 32.4 1.0

Calcium binding site 4 out of 7 in 1s0m

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Calcium binding site 4 out of 7 in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase


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 A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:41.7
occ:1.00
 O C:HOH127 2.3 65.6 1.0
O A:HOH873 2.5 36.8 1.0
OD2 A:ASP294 2.6 54.1 1.0
O A:HOH913 2.7 57.0 1.0
O A:HOH908 2.7 50.5 1.0
OD1 A:ASP294 2.8 56.7 1.0
O A:HOH875 2.9 34.8 1.0
CG A:ASP294 3.1 53.4 1.0
O A:HOH882 3.4 41.5 1.0
OP2 C:DA1810 3.9 40.9 1.0
O A:ILE295 4.5 41.7 1.0
CB A:ASP294 4.6 51.4 1.0
C3' C:DG1809 4.7 44.9 1.0
NH2 A:ARG328 4.9 44.8 1.0
P C:DA1810 5.0 42.3 1.0

Calcium binding site 5 out of 7 in 1s0m

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Calcium binding site 5 out of 7 in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:61.6
occ:1.00
 O2A B:DTP804 2.3 58.4 1.0
OD1 B:ASP7 2.6 39.5 1.0
OD1 B:ASP105 2.6 37.1 1.0
O E:HOH171 2.8 39.9 1.0
C5' E:DT1813 2.8 86.6 1.0
OE1 B:GLU106 2.9 49.3 1.0
CD B:GLU106 3.0 46.8 1.0
CG B:GLU106 3.0 45.8 1.0
OD2 B:ASP105 3.3 38.3 1.0
CG B:ASP105 3.3 37.2 1.0
C4' E:DT1813 3.4 87.7 1.0
C3' E:DT1813 3.5 88.0 1.0
PA B:DTP804 3.6 58.1 1.0
CG B:ASP7 3.7 36.5 1.0
OE2 B:GLU106 3.7 48.8 1.0
OP1 E:DT1813 3.8 79.7 1.0
CA B:CA404 3.9 39.2 1.0
O1A B:DTP804 4.0 56.6 1.0
O3' E:DT1813 4.0 89.3 1.0
O5' B:DTP804 4.1 57.4 1.0
O5' E:DT1813 4.1 82.4 1.0
OG B:SER103 4.1 32.7 1.0
OD2 B:ASP7 4.2 39.2 1.0
CB B:GLU106 4.3 43.1 1.0
O B:ASP105 4.5 35.5 1.0
P E:DT1813 4.6 78.5 1.0
C B:ASP105 4.7 36.5 1.0
C5' B:DTP804 4.7 56.3 1.0
CB B:ASP105 4.8 36.2 1.0
C2' E:DT1813 4.8 88.8 1.0
O4' E:DT1813 4.8 89.2 1.0
O1G B:DTP804 4.9 67.0 1.0
CB B:ASP7 4.9 36.0 1.0
O3A B:DTP804 5.0 57.7 1.0
N B:GLU106 5.0 38.5 1.0

Calcium binding site 6 out of 7 in 1s0m

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Calcium binding site 6 out of 7 in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:39.2
occ:1.00
 O B:PHE8 2.1 38.2 1.0
OD2 B:ASP105 2.2 38.3 1.0
O2A B:DTP804 2.4 58.4 1.0
O2B B:DTP804 2.7 58.6 1.0
O1G B:DTP804 2.8 67.0 1.0
OD1 B:ASP7 3.0 39.5 1.0
OD2 B:ASP7 3.1 39.2 1.0
PA B:DTP804 3.2 58.1 1.0
CG B:ASP7 3.2 36.5 1.0
C B:PHE8 3.3 36.7 1.0
O3A B:DTP804 3.3 57.7 1.0
CG B:ASP105 3.4 37.2 1.0
PB B:DTP804 3.5 58.0 1.0
PG B:DTP804 3.5 67.8 1.0
O3G B:DTP804 3.6 66.3 1.0
O3B B:DTP804 3.7 62.4 1.0
N B:PHE8 3.8 34.9 1.0
CA B:CA403 3.9 61.6 1.0
O B:HOH868 3.9 46.6 1.0
CA B:PHE8 4.1 35.1 1.0
O5' B:DTP804 4.1 57.4 1.0
OD1 B:ASP105 4.1 37.1 1.0
C B:ASP7 4.2 35.5 1.0
N B:ASP9 4.2 38.9 1.0
CA B:ASP9 4.4 39.5 1.0
N B:TYR10 4.4 38.9 1.0
CB B:ASP105 4.4 36.2 1.0
CB B:ASP7 4.5 36.0 1.0
C B:ASP9 4.5 39.3 1.0
O1A B:DTP804 4.6 56.6 1.0
C5' B:DTP804 4.6 56.3 1.0
NZ B:LYS159 4.6 41.4 1.0
N B:PHE11 4.7 35.9 1.0
O E:HOH171 4.7 39.9 1.0
CB B:PHE8 4.7 32.7 1.0
O B:ASP105 4.7 35.5 1.0
CA B:ASP7 4.7 35.5 1.0
O B:ASP7 4.7 37.1 1.0
O1B B:DTP804 4.8 56.8 1.0
CB B:PHE11 5.0 34.7 1.0
O2G B:DTP804 5.0 67.5 1.0

Calcium binding site 7 out of 7 in 1s0m

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Calcium binding site 7 out of 7 in the Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:55.0
occ:1.00
 O E:HOH272 2.0 61.7 1.0
O B:HOH851 2.1 53.2 1.0
O B:ALA181 2.3 37.6 1.0
O B:ILE186 2.6 45.5 1.0
O E:HOH175 2.9 55.1 1.0
O B:HOH853 2.9 53.1 1.0
O B:HOH889 3.0 60.7 1.0
O B:HOH852 3.0 73.7 1.0
C B:ALA181 3.6 38.5 1.0
OP2 E:DT1812 3.6 45.3 1.0
C B:ILE186 3.8 45.6 1.0
O E:HOH238 4.3 59.4 1.0
CA B:GLY187 4.4 47.4 1.0
CA B:ASP182 4.5 40.0 1.0
N B:ASP182 4.5 39.1 1.0
CA B:ALA181 4.5 38.5 1.0
O B:VAL183 4.5 35.7 1.0
N B:GLY187 4.6 46.4 1.0
CA B:ILE186 4.8 45.7 1.0
CB B:ALA181 4.8 38.7 1.0
C B:ASP182 4.9 39.3 1.0
P E:DT1812 4.9 44.5 1.0
N B:VAL183 4.9 37.9 1.0
C B:GLY187 4.9 48.4 1.0
CB B:ILE186 4.9 45.9 1.0

Reference:

H.Ling, J.M.Sayer, B.S.Plosky, H.Yagi, F.Boudsocq, R.Woodgate, D.M.Jerina, W.Yang. Crystal Structure of A Benzo[A]Pyrene Diol Epoxide Adduct in A Ternary Complex with A Dna Polymerase. Proc.Natl.Acad.Sci.Usa V. 101 2265 2004.
ISSN: ISSN 0027-8424
PubMed: 14982998
DOI: 10.1073/PNAS.0308332100
Page generated: Thu Jul 11 22:22:31 2024

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