Atomistry » Calcium » PDB 4eoy-4fb1 » 4f4y
Atomistry »
  Calcium »
    PDB 4eoy-4fb1 »
      4f4y »

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: Sun Jul 14 00:08:28 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy