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Calcium in PDB 3gii: DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation

Enzymatic activity of DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation

All present enzymatic activity of DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation, PDB code: 3gii was solved by O.Rechkoblit, L.Malinina, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.761, 111.646, 52.708, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26.5

Other elements in 3gii:

The structure of DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation (pdb code 3gii). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation, PDB code: 3gii:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3gii

Go back to Calcium Binding Sites List in 3gii
Calcium binding site 1 out of 3 in the DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:45.3
occ:1.00
OD1 A:ASP7 2.3 45.2 1.0
O2A A:DGT414 2.3 42.1 1.0
OE2 A:GLU106 2.3 48.4 1.0
OD1 A:ASP105 2.4 44.3 1.0
O A:HOH599 2.8 31.6 1.0
CG A:ASP105 3.1 45.3 1.0
OD2 A:ASP105 3.2 43.3 1.0
PA A:DGT414 3.5 36.3 1.0
CG A:ASP7 3.5 43.5 1.0
CD A:GLU106 3.5 50.1 1.0
CA A:CA416 3.6 41.4 1.0
O1A A:DGT414 3.7 37.0 1.0
O5' A:DGT414 3.9 36.9 1.0
C5' A:DGT414 4.1 36.9 1.0
OD2 A:ASP7 4.1 43.6 1.0
CG A:GLU106 4.3 47.9 1.0
OG A:SER103 4.3 49.3 1.0
CB A:GLU106 4.4 46.5 1.0
OE1 A:GLU106 4.5 53.6 1.0
CB A:ASP105 4.6 45.2 1.0
O A:HOH597 4.6 50.6 1.0
CB A:ASP7 4.6 42.5 1.0
O A:ASP105 4.7 45.5 1.0
C A:ASP105 4.8 45.5 1.0
O3A A:DGT414 4.8 36.4 1.0
NZ A:LYS159 5.0 53.8 1.0

Calcium binding site 2 out of 3 in 3gii

Go back to Calcium Binding Sites List in 3gii
Calcium binding site 2 out of 3 in the DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:41.4
occ:1.00
OD2 A:ASP105 2.3 43.3 1.0
O2A A:DGT414 2.3 42.1 1.0
O A:PHE8 2.3 42.3 1.0
OD2 A:ASP7 2.3 43.6 1.0
O1B A:DGT414 2.3 38.8 1.0
O1G A:DGT414 2.7 33.7 1.0
OD1 A:ASP7 2.9 45.2 1.0
CG A:ASP7 2.9 43.5 1.0
PG A:DGT414 3.2 35.2 1.0
PB A:DGT414 3.4 33.3 1.0
PA A:DGT414 3.4 36.3 1.0
C A:PHE8 3.5 42.4 1.0
CG A:ASP105 3.5 45.3 1.0
O3A A:DGT414 3.6 36.4 1.0
CA A:CA415 3.6 45.3 1.0
O3B A:DGT414 3.9 34.8 1.0
N A:PHE8 3.9 42.0 1.0
NZ A:LYS159 4.0 53.8 1.0
C5' A:DGT414 4.1 36.9 1.0
OD1 A:ASP105 4.1 44.3 1.0
O2G A:DGT414 4.2 35.0 1.0
O5' A:DGT414 4.3 36.9 1.0
C A:ASP7 4.3 42.2 1.0
CA A:PHE8 4.3 42.4 1.0
CB A:ASP7 4.3 42.5 1.0
O3G A:DGT414 4.5 30.9 1.0
N A:ASP9 4.5 42.5 1.0
O1A A:DGT414 4.6 37.0 1.0
CA A:ASP9 4.6 42.5 1.0
O A:ASP7 4.6 41.7 1.0
N A:TYR10 4.6 43.2 1.0
CB A:ASP105 4.7 45.2 1.0
O2B A:DGT414 4.7 34.1 1.0
CA A:ASP7 4.8 42.5 1.0
C A:ASP9 4.8 42.7 1.0
O A:ASP105 4.9 45.5 1.0
CE A:LYS159 4.9 54.5 1.0
CB A:PHE8 5.0 42.7 1.0

Calcium binding site 3 out of 3 in 3gii

Go back to Calcium Binding Sites List in 3gii
Calcium binding site 3 out of 3 in the DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 Extension Ternary Complex with Disordered A Opposite An Oxog in Anti Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:61.4
occ:1.00
O A:ILE186 2.3 52.4 1.0
O A:ALA181 2.3 56.8 1.0
O D:HOH582 2.4 42.5 1.0
O A:HOH576 2.5 41.4 1.0
O A:VAL183 3.0 50.5 1.0
OP1 D:DG813 3.2 42.6 1.0
C A:ILE186 3.3 51.5 1.0
C A:ALA181 3.4 54.9 1.0
C A:VAL183 4.0 50.7 1.0
N A:ILE186 4.0 50.7 1.0
OP2 D:DG813 4.0 45.2 1.0
CA A:ILE186 4.0 51.1 1.0
P D:DG813 4.0 44.4 1.0
N A:VAL183 4.2 51.8 1.0
N A:GLY187 4.2 51.5 1.0
CB A:ILE186 4.2 51.0 1.0
C A:ASP182 4.3 52.7 1.0
CA A:ALA181 4.3 55.0 1.0
N A:ASP182 4.3 54.2 1.0
CA A:ASP182 4.3 53.2 1.0
CA A:GLY187 4.4 51.5 1.0
CA A:VAL183 4.7 50.8 1.0
N A:PRO184 4.8 50.2 1.0
CA A:PRO184 4.8 50.1 1.0
N A:GLY185 4.8 50.0 1.0
O A:ASP182 4.8 52.8 1.0
CG2 A:ILE186 4.9 50.0 1.0
CB A:ALA181 5.0 54.7 1.0
O3' D:DA812 5.0 43.6 1.0

Reference:

O.Rechkoblit, L.Malinina, Y.Cheng, N.E.Geacintov, S.Broyde, D.J.Patel. Impact of Conformational Heterogeneity of Oxog Lesions and Their Pairing Partners on Bypass Fidelity By Y Family Polymerases. Structure V. 17 725 2009.
ISSN: ISSN 0969-2126
PubMed: 19446528
DOI: 10.1016/J.STR.2009.03.011
Page generated: Sat Dec 12 04:12:58 2020

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