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Calcium in PDB 2ia6: Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap

Enzymatic activity of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap

All present enzymatic activity of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap:
2.7.7.7;

Protein crystallography data

The structure of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap, PDB code: 2ia6 was solved by J.Bauer, H.Ling, J.M.Sayer, G.Xing, H.Yagi, D.M.Jerina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.217, 102.580, 106.147, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap (pdb code 2ia6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap, PDB code: 2ia6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2ia6

Go back to Calcium Binding Sites List in 2ia6
Calcium binding site 1 out of 5 in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:36.2
occ:1.00
 OD1 A:ASP7 2.2 32.3 1.0
O2A A:ATP401 2.3 61.0 1.0
O A:PHE8 2.4 26.9 1.0
O3B A:ATP401 2.5 77.6 1.0
OD2 A:ASP105 2.7 36.4 1.0
O A:HOH564 3.1 45.5 1.0
CG A:ASP7 3.3 29.2 1.0
PB A:ATP401 3.5 69.1 1.0
PA A:ATP401 3.5 60.3 1.0
CG A:ASP105 3.6 33.5 1.0
O3G A:ATP401 3.6 88.4 1.0
C A:PHE8 3.6 26.0 1.0
PG A:ATP401 3.7 90.8 1.0
O1B A:ATP401 3.7 66.9 1.0
OD2 A:ASP7 3.7 31.7 1.0
O3A A:ATP401 3.8 68.3 1.0
O A:HOH550 3.9 23.6 1.0
OD1 A:ASP105 4.0 35.4 1.0
O5' A:ATP401 4.0 66.5 1.0
N A:PHE8 4.1 25.2 1.0
C5' A:ATP401 4.2 75.4 1.0
C A:ASP7 4.3 25.8 1.0
NZ A:LYS159 4.4 41.8 1.0
CA A:PHE8 4.4 25.2 1.0
N A:ASP9 4.5 27.2 1.0
CB A:ASP7 4.5 27.2 1.0
N A:TYR10 4.6 26.1 1.0
CA A:ASP9 4.6 25.6 1.0
CB A:ASP105 4.6 28.7 1.0
O1G A:ATP401 4.7 88.2 1.0
O1A A:ATP401 4.7 60.7 1.0
O A:ASP105 4.7 26.6 1.0
O A:ASP7 4.7 25.6 1.0
C4' A:ATP401 4.7 80.5 1.0
CA A:ASP7 4.7 26.1 1.0
O2G A:ATP401 4.8 90.1 1.0
C A:ASP9 4.8 25.4 1.0
O2B A:ATP401 4.9 67.7 1.0
N A:PHE11 4.9 24.9 1.0

Calcium binding site 2 out of 5 in 2ia6

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Calcium binding site 2 out of 5 in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:57.5
occ:1.00
 O A:ILE186 2.3 35.9 1.0
O A:ALA181 2.5 44.6 1.0
O A:HOH548 2.6 56.9 1.0
O A:HOH421 2.8 31.2 1.0
C A:ILE186 3.6 37.5 1.0
C A:ALA181 3.7 41.6 1.0
CA A:GLY187 4.2 43.0 1.0
N A:GLY187 4.3 39.1 1.0
CA A:ALA181 4.5 41.0 1.0
OP2 C:DA1813 4.6 56.3 1.0
CB A:ALA181 4.6 36.7 1.0
CA A:ILE186 4.7 34.6 1.0
N A:ASP182 4.7 42.1 1.0
C A:GLY187 4.7 47.6 1.0
CA A:ASP182 4.7 41.0 1.0
CB A:ILE186 4.7 34.1 1.0
O A:VAL183 4.7 36.5 1.0
OP1 C:DA1813 5.0 59.9 1.0
N A:ILE186 5.0 36.4 1.0

Calcium binding site 3 out of 5 in 2ia6

Go back to Calcium Binding Sites List in 2ia6
Calcium binding site 3 out of 5 in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:35.3
occ:1.00
 OD1 B:ASP7 2.2 31.1 1.0
O1B B:ATP501 2.2 49.4 1.0
OD2 B:ASP105 2.3 36.6 1.0
O B:PHE8 2.4 28.9 1.0
O1G B:ATP501 2.6 69.5 1.0
O1A B:ATP501 3.0 54.4 1.0
O5' B:ATP501 3.2 54.8 1.0
PA B:ATP501 3.3 53.1 1.0
CG B:ASP105 3.4 32.7 1.0
CG B:ASP7 3.4 29.7 1.0
PB B:ATP501 3.5 49.7 1.0
C B:PHE8 3.6 28.0 1.0
PG B:ATP501 3.8 69.3 1.0
O B:HOH756 3.9 35.2 1.0
OD1 B:ASP105 3.9 35.1 1.0
OD2 B:ASP7 4.0 32.4 1.0
O3A B:ATP501 4.0 53.6 1.0
N B:PHE8 4.1 27.3 1.0
NZ B:LYS159 4.2 42.4 1.0
O3B B:ATP501 4.2 58.9 1.0
O B:HOH627 4.2 37.5 1.0
CA B:PHE8 4.4 27.2 1.0
CB B:ASP105 4.4 30.1 1.0
C B:ASP7 4.4 26.9 1.0
N B:TYR10 4.5 26.1 1.0
N B:ASP9 4.5 28.1 1.0
C5' B:ATP501 4.6 49.2 1.0
CA B:CA503 4.6 64.4 1.0
CA B:ASP9 4.6 27.2 1.0
CB B:ASP7 4.6 29.2 1.0
O2B B:ATP501 4.7 50.4 1.0
O B:ASP105 4.7 27.1 1.0
C B:ASP9 4.7 26.7 1.0
N B:PHE11 4.8 24.4 1.0
O2G B:ATP501 4.8 66.1 1.0
O2A B:ATP501 4.8 57.5 1.0
O B:ASP7 4.8 27.9 1.0
O3G B:ATP501 4.9 67.8 1.0
CA B:ASP7 4.9 27.5 1.0
CB B:PHE8 4.9 25.9 1.0
CB B:PHE11 5.0 24.4 1.0

Calcium binding site 4 out of 5 in 2ia6

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Calcium binding site 4 out of 5 in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:64.4
occ:1.00
 O B:HOH756 2.5 35.2 1.0
OE2 B:GLU106 2.7 40.6 1.0
OD2 B:ASP7 2.7 32.4 1.0
OP1 E:DA1813 3.1 67.5 1.0
O1A B:ATP501 3.2 54.4 1.0
CD B:GLU106 3.2 37.3 1.0
O5' E:DA1813 3.2 70.9 1.0
NZ B:LYS152 3.4 38.8 1.0
CG B:ASP7 3.7 29.7 1.0
O B:HOH651 3.7 54.6 1.0
P E:DA1813 3.8 67.0 1.0
CG B:GLU106 3.8 34.0 1.0
OE1 B:GLU106 3.9 41.4 1.0
OD1 B:ASP7 4.0 31.1 1.0
NZ B:LYS159 4.0 42.4 1.0
C5' E:DA1813 4.1 74.4 1.0
O E:HOH251 4.4 66.1 1.0
PA B:ATP501 4.4 53.1 1.0
O2A B:ATP501 4.5 57.5 1.0
CE B:LYS152 4.5 37.7 1.0
CA B:CA502 4.6 35.3 1.0
OD1 B:ASP105 4.7 35.1 1.0
O B:HOH680 4.7 45.1 1.0
OP2 E:DA1813 4.8 67.7 1.0
O5' B:ATP501 4.8 54.8 1.0
O3' E:DT1812 4.9 62.4 1.0
O B:HOH677 4.9 62.4 1.0
CZ B:PHE5 5.0 27.4 1.0
CB B:ASP7 5.0 29.2 1.0

Calcium binding site 5 out of 5 in 2ia6

Go back to Calcium Binding Sites List in 2ia6
Calcium binding site 5 out of 5 in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:39.1
occ:1.00
 O B:ALA181 2.2 41.7 1.0
O B:HOH757 2.2 44.3 1.0
O B:HOH771 2.3 56.0 1.0
O E:HOH21 2.5 26.9 1.0
O E:HOH158 2.6 48.5 1.0
O B:ILE186 2.6 32.5 1.0
C B:ALA181 3.4 39.9 1.0
C B:ILE186 3.8 34.0 1.0
CA B:ALA181 4.3 40.2 1.0
N B:ASP182 4.4 41.4 1.0
CA B:GLY187 4.4 42.3 1.0
CB B:ALA181 4.4 37.1 1.0
OP1 E:DT1812 4.5 41.2 1.0
OP2 E:DT1812 4.5 41.0 1.0
CA B:ASP182 4.5 41.0 1.0
N B:GLY187 4.5 37.5 1.0
C B:GLY187 4.8 45.6 1.0
O B:HOH739 4.8 53.8 1.0
CA B:ILE186 4.9 33.7 1.0
O B:GLY187 4.9 46.1 1.0
O E:HOH277 4.9 56.2 1.0
CB B:ILE186 4.9 33.0 1.0
OD1 B:ASP182 5.0 53.9 1.0

Reference:

J.Bauer, G.Xing, H.Yagi, J.M.Sayer, D.M.Jerina, H.Ling. A Structural Gap in DPO4 Supports Mutagenic Bypass of A Major Benzo[A]Pyrene Dg Adduct in Dna Through Template Misalignment. Proc.Natl.Acad.Sci.Usa V. 104 14905 2007.
ISSN: ISSN 0027-8424
PubMed: 17848527
DOI: 10.1073/PNAS.0700717104
Page generated: Tue Jul 8 06:11:14 2025

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