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Calcium in PDB 4f4y: Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh

Enzymatic activity of Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh

All present enzymatic activity of Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh:
2.7.7.7;

Protein crystallography data

The structure of Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh, PDB code: 4f4y was solved by J.D.Pata, R.C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.25 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.076, 103.390, 112.988, 90.00, 101.76, 90.00
R / Rfree (%) 22.2 / 25.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh (pdb code 4f4y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh, PDB code: 4f4y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4f4y

Go back to Calcium Binding Sites List in 4f4y
Calcium binding site 1 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:30.0
occ:1.00
O A:PHE8 2.7 33.0 1.0
OD1 A:ASP7 2.8 33.7 1.0
OD1 A:ASP105 2.8 25.6 1.0
O1B A:DCP401 2.8 29.8 1.0
O2A A:DCP401 2.9 34.4 1.0
OD2 A:ASP105 2.9 19.9 1.0
O A:HOH507 2.9 33.1 1.0
CG A:ASP105 3.2 21.1 1.0
C A:PHE8 3.4 30.4 1.0
PB A:DCP401 3.7 24.9 1.0
O A:HOH567 3.7 22.8 1.0
N A:PHE8 3.7 25.2 1.0
O3B A:DCP401 3.7 25.7 1.0
PA A:DCP401 4.0 30.3 1.0
CG A:ASP7 4.0 32.2 1.0
CA A:CA403 4.0 37.0 1.0
CA A:PHE8 4.0 33.3 1.0
C5' A:DCP401 4.2 21.7 1.0
N A:ASP9 4.2 34.6 1.0
C A:ASP7 4.2 24.4 1.0
O3A A:DCP401 4.3 0.2 1.0
NZ A:LYS160 4.4 25.0 1.0
N A:TYR10 4.4 17.5 1.0
CA A:ASP9 4.4 30.9 1.0
N A:PHE11 4.4 20.1 1.0
C A:ASP9 4.5 17.9 1.0
O5' A:DCP401 4.6 33.5 1.0
CB A:PHE8 4.6 27.7 1.0
CB A:PHE11 4.6 30.4 1.0
O A:ASP7 4.6 31.4 1.0
CB A:ASP105 4.7 26.3 1.0
OD2 A:ASP7 4.8 41.2 1.0
CA A:ASP7 4.9 19.6 1.0
O A:ASP105 4.9 24.2 1.0
CB A:ASP7 4.9 27.4 1.0
O2B A:DCP401 4.9 32.1 1.0

Calcium binding site 2 out of 4 in 4f4y

Go back to Calcium Binding Sites List in 4f4y
Calcium binding site 2 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:37.0
occ:1.00
OP1 P:DC14 2.7 32.4 1.0
OD2 A:ASP105 2.8 19.9 1.0
OE1 A:GLU106 2.9 41.9 1.0
O2A A:DCP401 2.9 34.4 1.0
OD2 A:ASP7 3.0 41.2 1.0
OD1 A:ASP7 3.2 33.7 1.0
O A:HOH546 3.2 29.9 1.0
CD A:GLU106 3.3 42.2 1.0
CG A:ASP7 3.4 32.2 1.0
OE2 A:GLU106 3.4 58.1 1.0
P P:DC14 3.9 30.0 1.0
NZ A:LYS160 3.9 25.0 1.0
CG A:ASP105 3.9 21.1 1.0
CA A:CA402 4.0 30.0 1.0
O5' P:DC14 4.1 30.8 1.0
PA A:DCP401 4.1 30.3 1.0
O1A A:DCP401 4.1 37.5 1.0
O5' A:DCP401 4.4 33.5 1.0
CG A:GLU106 4.5 36.7 1.0
CB A:GLU106 4.5 33.1 1.0
CB A:ASP105 4.6 26.3 1.0
C5' A:DCP401 4.7 21.7 1.0
OD1 A:ASP105 4.8 25.6 1.0
CB A:ASP7 4.8 27.4 1.0
OP2 P:DC14 4.8 42.9 1.0
O3' P:DG13 5.0 44.2 1.0
NZ A:LYS153 5.0 32.8 1.0

Calcium binding site 3 out of 4 in 4f4y

Go back to Calcium Binding Sites List in 4f4y
Calcium binding site 3 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:47.5
occ:1.00
OD1 B:ASP7 2.8 29.7 1.0
O2A C:DCP101 2.8 33.3 1.0
O B:PHE8 2.8 44.3 1.0
O1B C:DCP101 2.9 34.4 1.0
OD2 B:ASP105 3.0 47.2 1.0
OD1 B:ASP105 3.1 47.2 1.0
O C:HOH210 3.2 50.0 1.0
C B:PHE8 3.4 35.6 1.0
CG B:ASP105 3.4 42.2 1.0
O3B C:DCP101 3.4 45.5 1.0
PB C:DCP101 3.5 29.0 1.0
O B:HOH502 3.5 34.1 1.0
N B:PHE8 3.8 27.5 1.0
NZ B:LYS160 3.9 30.5 1.0
PA C:DCP101 3.9 28.5 1.0
O3A C:DCP101 3.9 53.4 1.0
CG B:ASP7 3.9 46.6 1.0
CA B:CA402 4.0 35.5 1.0
N B:ASP9 4.1 29.0 1.0
CA B:PHE8 4.1 24.0 1.0
C B:ASP7 4.2 32.8 1.0
N B:TYR10 4.4 28.2 1.0
CA B:ASP9 4.4 31.8 1.0
C5' C:DCP101 4.5 31.3 1.0
C B:ASP9 4.6 31.6 1.0
CE B:LYS160 4.6 24.9 1.0
O B:ASP7 4.6 33.8 1.0
N B:PHE11 4.7 30.3 1.0
O5' C:DCP101 4.7 35.3 1.0
OD2 B:ASP7 4.7 54.8 1.0
CB B:PHE8 4.8 23.7 1.0
CB B:ASP7 4.8 48.1 1.0
O2B C:DCP101 4.8 30.6 1.0
CA B:ASP7 4.9 36.7 1.0
O1A C:DCP101 4.9 35.8 1.0
CB B:ASP105 4.9 35.2 1.0
CB B:PHE11 4.9 36.8 1.0

Calcium binding site 4 out of 4 in 4f4y

Go back to Calcium Binding Sites List in 4f4y
Calcium binding site 4 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Y-Family Dna Polymerase Chimera Dbh-DPO4-Dbh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:35.5
occ:1.00
OP1 C:DC14 2.8 37.4 1.0
O2A C:DCP101 2.8 33.3 1.0
OD2 B:ASP105 2.9 47.2 1.0
OD1 B:ASP7 2.9 29.7 1.0
OE2 B:GLU106 3.0 60.2 1.0
OD2 B:ASP7 3.2 54.8 1.0
CG B:ASP7 3.4 46.6 1.0
O B:HOH570 3.5 58.0 1.0
CD B:GLU106 3.7 57.5 1.0
CG B:GLU106 3.7 43.8 1.0
P C:DC14 3.9 43.2 1.0
O5' C:DC14 3.9 44.2 1.0
NZ B:LYS160 4.0 30.5 1.0
CA B:CA401 4.0 47.5 1.0
O1A C:DCP101 4.0 35.8 1.0
CG B:ASP105 4.0 42.2 1.0
O B:HOH537 4.0 42.7 1.0
PA C:DCP101 4.1 28.5 1.0
CB B:GLU106 4.2 45.4 1.0
NZ B:LYS153 4.7 35.6 1.0
OP2 C:DC14 4.7 44.9 1.0
CB B:ASP105 4.8 35.2 1.0
CB B:ASP7 4.8 48.1 1.0
O5' C:DCP101 4.8 35.3 1.0
OE1 B:GLU106 4.8 70.2 1.0
C5' C:DCP101 4.9 31.3 1.0
OD1 B:ASP105 4.9 47.2 1.0
CE B:LYS160 5.0 24.9 1.0
CZ B:PHE5 5.0 26.2 1.0

Reference:

R.C.Wilson, M.A.Jackson, J.D.Pata. Y-Family Polymerase Conformation Is A Major Determinant of Fidelity and Translesion Specificity. Structure V. 21 20 2013.
ISSN: ISSN 0969-2126
PubMed: 23245850
DOI: 10.1016/J.STR.2012.11.005
Page generated: Sat Dec 12 04:45:45 2020

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