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Calcium in PDB 4fbu: DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion

Enzymatic activity of DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion

All present enzymatic activity of DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion, PDB code: 4fbu was solved by K.Kirouac, A.Basu, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.24 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.774, 181.458, 52.744, 90.00, 109.49, 90.00
R / Rfree (%) 21.7 / 26.1

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion (pdb code 4fbu). 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 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion, PDB code: 4fbu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4fbu

Go back to Calcium Binding Sites List in 4fbu
Calcium binding site 1 out of 4 in the DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:58.0
occ:1.00
 OP1 P:DC14 2.1 67.1 1.0
OD2 A:ASP7 2.6 50.7 1.0
OE2 A:GLU106 2.8 50.7 1.0
OD1 A:ASP105 3.1 35.5 1.0
OD1 A:ASP7 3.2 48.0 1.0
CG A:ASP7 3.2 46.7 1.0
OD2 A:ASP105 3.3 39.3 1.0
CD A:GLU106 3.5 48.3 1.0
CG A:GLU106 3.5 43.3 1.0
P P:DC14 3.5 71.7 1.0
CG A:ASP105 3.5 35.4 1.0
CA A:CA402 3.7 62.9 1.0
C5' P:DC14 4.2 57.5 1.0
OP2 P:DC14 4.2 63.4 1.0
O5' P:DC14 4.3 66.5 1.0
O P:HOH103 4.3 54.9 1.0
O3' P:DT13 4.5 72.6 1.0
CB A:GLU106 4.6 39.7 1.0
CB A:ASP7 4.6 41.2 1.0
O A:ASP105 4.6 29.1 1.0
OE1 A:GLU106 4.6 50.2 1.0
C A:ASP105 4.9 28.6 1.0
OG A:SER103 4.9 38.8 1.0
CB A:ASP105 4.9 32.5 1.0
NZ A:LYS159 4.9 65.0 1.0

Calcium binding site 2 out of 4 in 4fbu

Go back to Calcium Binding Sites List in 4fbu
Calcium binding site 2 out of 4 in the DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:62.9
occ:1.00
 OD2 A:ASP105 2.5 39.3 1.0
O A:PHE8 2.5 32.5 1.0
O A:HOH564 3.1 39.4 1.0
OD1 A:ASP7 3.1 48.0 1.0
O P:HOH103 3.4 54.9 1.0
O A:HOH563 3.5 48.0 1.0
CG A:ASP105 3.7 35.4 1.0
CA A:CA401 3.7 58.0 1.0
C A:PHE8 3.7 31.2 1.0
N A:TYR10 3.9 38.1 1.0
N A:PHE11 4.2 30.8 1.0
CG A:ASP7 4.3 46.7 1.0
CA A:ASP9 4.4 39.2 1.0
C A:ASP9 4.4 38.9 1.0
OD1 A:ASP105 4.4 35.5 1.0
N A:ASP9 4.5 39.0 1.0
CA A:TYR10 4.6 41.7 1.0
CB A:PHE11 4.6 30.4 1.0
O3' P:DC14 4.6 48.8 1.0
CB A:ASP105 4.6 32.5 1.0
OD2 A:ASP7 4.7 50.7 1.0
OP1 P:DC14 4.8 67.1 1.0
CA A:PHE8 4.8 31.1 1.0
N A:PHE8 4.8 31.4 1.0
O P:HOH104 4.9 39.9 1.0
NZ A:LYS159 4.9 65.0 1.0
C A:TYR10 5.0 40.2 1.0
C3' P:DC14 5.0 54.3 1.0

Calcium binding site 3 out of 4 in 4fbu

Go back to Calcium Binding Sites List in 4fbu
Calcium binding site 3 out of 4 in the DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:53.8
occ:1.00
 OP1 D:DC14 2.2 50.5 1.0
OD1 B:ASP7 2.5 37.1 1.0
OE2 B:GLU106 2.7 44.7 1.0
OD1 B:ASP105 2.8 32.9 1.0
O B:HOH510 2.8 50.0 1.0
CA B:CA402 2.9 67.0 1.0
CG B:ASP7 3.2 36.4 1.0
OD2 B:ASP7 3.3 43.3 1.0
O B:HOH558 3.4 58.4 1.0
P D:DC14 3.4 59.9 1.0
CG B:ASP105 3.5 31.3 1.0
OD2 B:ASP105 3.5 33.4 1.0
OP2 D:DC14 3.9 58.7 1.0
CD B:GLU106 3.9 42.3 1.0
O B:HOH583 4.1 45.3 1.0
C5' D:DC14 4.2 46.5 1.0
O5' D:DC14 4.3 55.9 1.0
CB B:GLU106 4.5 40.8 1.0
CG B:GLU106 4.5 39.9 1.0
O B:HOH520 4.5 35.0 1.0
O3' D:DT13 4.6 49.5 1.0
CB B:ASP7 4.6 35.0 1.0
O B:ASP105 4.7 32.9 1.0
OE1 B:GLU106 4.8 47.6 1.0
CB B:ASP105 4.9 28.6 1.0
C B:ASP105 5.0 30.1 1.0

Calcium binding site 4 out of 4 in 4fbu

Go back to Calcium Binding Sites List in 4fbu
Calcium binding site 4 out of 4 in the DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of DPO4 Polymerase Pre-Insertion Binary Complex with the N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:67.0
occ:1.00
 O B:HOH520 2.2 35.0 1.0
O B:HOH558 2.4 58.4 1.0
OD2 B:ASP7 2.6 43.3 1.0
CA B:CA401 2.9 53.8 1.0
O B:PHE8 2.9 30.1 1.0
OD2 B:ASP105 3.1 33.4 1.0
CG B:ASP7 3.2 36.4 1.0
OD1 B:ASP7 3.3 37.1 1.0
CG B:ASP105 3.6 31.3 1.0
O B:HOH541 3.6 44.9 1.0
OD1 B:ASP105 3.8 32.9 1.0
C B:PHE8 4.1 31.7 1.0
CB B:ASP105 4.5 28.6 1.0
N B:TYR10 4.6 30.7 1.0
OP1 D:DC14 4.6 50.5 1.0
N B:PHE8 4.6 29.7 1.0
CB B:ASP7 4.6 35.0 1.0
O B:HOH510 4.6 50.0 1.0
NZ B:LYS159 4.9 53.5 1.0
O B:ASP105 4.9 32.9 1.0
CA B:PHE8 4.9 32.5 1.0
C B:ASP7 4.9 32.1 1.0
N B:ASP9 5.0 35.5 1.0
CA B:ASP9 5.0 36.4 1.0
O B:HOH583 5.0 45.3 1.0

Reference:

K.N.Kirouac, A.K.Basu, H.Ling. Structural Mechanism of Replication Stalling on A Bulky Amino-Polycyclic Aromatic Hydrocarbon Dna Adduct By A Y Family Dna Polymerase. J.Mol.Biol. V. 425 4167 2013.
ISSN: ISSN 0022-2836
PubMed: 23876706
DOI: 10.1016/J.JMB.2013.07.020
Page generated: Sun Jul 14 00:16:01 2024

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