Atomistry » Calcium » PDB 3r3v-3rk2 » 3rbe
Atomistry »
  Calcium »
    PDB 3r3v-3rk2 »
      3rbe »

Calcium in PDB 3rbe: DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion

Enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rbe was solved by O.Rechkoblit, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.904, 109.860, 101.291, 90.00, 100.99, 90.00
R / Rfree (%) 22.6 / 26.6

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion (pdb code 3rbe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rbe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion


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 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:38.6
occ:1.00
 O2A A:DGT414 2.1 42.2 1.0
OD2 A:ASP7 2.4 39.0 1.0
OE2 A:GLU106 2.4 42.6 1.0
OD1 A:ASP105 2.6 38.0 1.0
OD2 A:ASP105 2.8 35.0 1.0
CG A:ASP105 3.0 36.5 1.0
CG A:ASP7 3.1 36.5 1.0
CA A:CA416 3.3 28.6 1.0
PA A:DGT414 3.4 34.1 1.0
OD1 A:ASP7 3.4 36.0 1.0
C3' D:2DT814 3.4 74.2 1.0
CD A:GLU106 3.5 40.3 1.0
O1A A:DGT414 3.8 35.8 1.0
CB A:GLU106 4.1 37.7 1.0
O5' A:DGT414 4.2 35.2 1.0
C5' A:DGT414 4.2 33.4 1.0
CG A:GLU106 4.3 39.1 1.0
CB A:ASP7 4.3 34.9 1.0
OE1 A:GLU106 4.3 40.7 1.0
NZ A:LYS159 4.3 45.3 1.0
C4' D:2DT814 4.4 74.1 1.0
C5' D:2DT814 4.4 71.3 1.0
O3A A:DGT414 4.5 35.5 1.0
O1G A:DGT414 4.5 38.2 1.0
CB A:ASP105 4.6 36.4 1.0
OG A:SER103 4.6 34.2 1.0
C2' D:2DT814 4.7 74.9 1.0
OP1 D:2DT814 4.8 61.4 1.0
O5' D:2DT814 4.9 64.4 1.0
C A:ASP105 4.9 37.3 1.0
O A:ASP105 4.9 38.1 1.0
CA A:ASP7 5.0 35.0 1.0

Calcium binding site 2 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion


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 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:28.6
occ:1.00
 OD1 A:ASP7 2.3 36.0 1.0
O A:PHE8 2.3 33.9 1.0
O1B A:DGT414 2.3 39.7 1.0
OD2 A:ASP105 2.3 35.0 1.0
O2A A:DGT414 2.3 42.2 1.0
O1G A:DGT414 2.5 38.2 1.0
PG A:DGT414 3.1 39.0 1.0
PB A:DGT414 3.2 33.5 1.0
O3A A:DGT414 3.2 35.5 1.0
CG A:ASP7 3.2 36.5 1.0
PA A:DGT414 3.3 34.1 1.0
CA A:CA415 3.3 38.6 1.0
OD2 A:ASP7 3.5 39.0 1.0
C A:PHE8 3.6 33.5 1.0
CG A:ASP105 3.6 36.5 1.0
O3B A:DGT414 3.8 37.0 1.0
NZ A:LYS159 4.0 45.3 1.0
C5' A:DGT414 4.2 33.4 1.0
N A:PHE8 4.2 33.7 1.0
O5' A:DGT414 4.2 35.2 1.0
O2G A:DGT414 4.2 38.1 1.0
OD1 A:ASP105 4.3 38.0 1.0
O3G A:DGT414 4.3 39.1 1.0
C A:ASP7 4.4 34.8 1.0
CA A:PHE8 4.4 33.7 1.0
N A:ASP9 4.5 33.8 1.0
O2B A:DGT414 4.5 31.8 1.0
O1A A:DGT414 4.5 35.8 1.0
N A:TYR10 4.6 31.8 1.0
CB A:ASP7 4.6 34.9 1.0
CA A:ASP9 4.6 33.4 1.0
CB A:ASP105 4.6 36.4 1.0
O A:ASP7 4.7 35.3 1.0
CE A:LYS159 4.7 43.7 1.0
C A:ASP9 4.8 32.7 1.0
N A:PHE11 4.9 30.7 1.0
CA A:ASP7 5.0 35.0 1.0

Calcium binding site 3 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion


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 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:51.5
occ:1.00
 O A:ALA181 2.3 63.6 1.0
O A:HOH366 2.4 23.8 1.0
O A:ILE186 2.6 49.0 1.0
C A:ALA181 3.5 61.9 1.0
C A:ILE186 3.7 49.8 1.0
CA A:GLY187 4.0 50.0 1.0
C A:GLY187 4.3 52.9 1.0
CA A:ALA181 4.3 64.0 1.0
O A:GLY187 4.3 54.8 1.0
N A:GLY187 4.3 49.8 1.0
OP1 D:DG813 4.4 44.9 1.0
CB A:ALA181 4.5 64.7 1.0
N A:ASP182 4.6 60.9 1.0
OP2 D:DG813 4.6 41.9 1.0
CA A:ASP182 4.8 57.8 1.0
CA A:ILE186 5.0 50.9 1.0

Calcium binding site 4 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:56.6
occ:1.00
 O2A B:DGT1414 2.3 0.5 1.0
OD1 B:ASP1105 2.5 82.4 1.0
OD1 B:ASP1007 2.6 93.7 1.0
CG B:GLU1106 3.0 83.6 1.0
OD2 B:ASP1105 3.1 89.0 1.0
OD2 B:ASP1007 3.1 90.6 1.0
CG B:ASP1007 3.1 89.9 1.0
CD B:GLU1106 3.2 84.7 1.0
CG B:ASP1105 3.2 81.7 1.0
CA B:CA1416 3.3 47.2 1.0
OE1 B:GLU1106 3.5 84.1 1.0
PA B:DGT1414 3.6 99.8 1.0
OE2 B:GLU1106 3.7 87.0 1.0
O1A B:DGT1414 3.7 99.9 1.0
OP1 H:2DT1814 4.1 0.7 1.0
C5' B:DGT1414 4.2 94.7 1.0
O5' B:DGT1414 4.4 97.6 1.0
CB B:GLU1106 4.4 84.2 1.0
C5' H:2DT1814 4.4 0.6 1.0
CB B:ASP1007 4.4 91.1 1.0
O5' H:2DT1814 4.4 0.7 1.0
O1B B:DGT1414 4.5 0.4 1.0
O B:ASP1105 4.5 83.4 1.0
C B:ASP1105 4.6 82.1 1.0
CB B:ASP1105 4.6 79.7 1.0
OG B:SER1103 4.7 81.7 1.0
O3A B:DGT1414 4.7 0.2 1.0
CA B:ASP1007 4.8 90.4 1.0
P H:2DT1814 4.8 0.7 1.0
N B:GLU1106 4.9 82.6 1.0
CA B:GLU1106 5.0 84.2 1.0

Calcium binding site 5 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:47.2
occ:1.00
 O2A B:DGT1414 2.3 0.5 1.0
OD2 B:ASP1105 2.3 89.0 1.0
O B:PHE1008 2.3 88.6 1.0
OD1 B:ASP1007 2.3 93.7 1.0
O1B B:DGT1414 2.3 0.4 1.0
O3B B:DGT1414 2.7 0.4 1.0
PB B:DGT1414 2.9 0.2 1.0
O3G B:DGT1414 3.2 0.2 1.0
CA B:CA1415 3.3 56.6 1.0
CG B:ASP1007 3.3 89.9 1.0
O3A B:DGT1414 3.3 0.2 1.0
O B:HOH1 3.4 45.8 1.0
PA B:DGT1414 3.4 99.8 1.0
CG B:ASP1105 3.4 81.7 1.0
C B:PHE1008 3.5 86.9 1.0
OD2 B:ASP1007 3.7 90.6 1.0
OD1 B:ASP1105 3.9 82.4 1.0
PG B:DGT1414 3.9 0.2 1.0
N B:PHE1008 4.0 87.6 1.0
CA B:PHE1008 4.3 87.2 1.0
O2B B:DGT1414 4.3 0.5 1.0
O1A B:DGT1414 4.4 99.9 1.0
O5' B:DGT1414 4.4 97.6 1.0
CB B:ASP1007 4.5 91.1 1.0
C5' B:DGT1414 4.5 94.7 1.0
C B:ASP1007 4.5 89.9 1.0
N B:ASP1009 4.5 87.4 1.0
O2G B:DGT1414 4.6 1.0 1.0
CB B:ASP1105 4.7 79.7 1.0
O1G B:DGT1414 4.7 0.1 1.0
CA B:ASP1009 4.7 86.7 1.0
N B:TYR1010 4.7 82.4 1.0
CA B:ASP1007 4.8 90.4 1.0
CB B:PHE1008 4.9 84.9 1.0
N B:PHE1011 4.9 75.9 1.0
C B:ASP1009 4.9 83.8 1.0

Calcium binding site 6 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:61.5
occ:1.00
 O B:ALA1181 2.3 0.7 1.0
O B:HOH4 2.6 5.8 1.0
O B:ILE1186 2.7 0.6 1.0
C B:ALA1181 3.4 0.6 1.0
C B:ILE1186 3.9 0.3 1.0
OP1 H:DG1813 4.1 0.8 1.0
CA B:ALA1181 4.2 0.1 1.0
O B:VAL1183 4.2 0.2 1.0
CA B:GLY1187 4.3 0.5 1.0
N B:ASP1182 4.4 0.0 1.0
CB B:ALA1181 4.5 0.9 1.0
N B:VAL1183 4.5 0.0 1.0
N B:GLY1187 4.6 0.4 1.0
CA B:ASP1182 4.6 0.8 1.0
C B:ASP1182 4.9 0.0 1.0
C B:VAL1183 5.0 0.3 1.0

Reference:

O.Rechkoblit, J.C.Delaney, J.M.Essigmann, D.J.Patel. Implications For Damage Recognition During DPO4-Mediated Mutagenic Bypass of M1G and M3C Lesions. Structure V. 19 821 2011.
ISSN: ISSN 0969-2126
PubMed: 21645853
DOI: 10.1016/J.STR.2011.03.020
Page generated: Sat Jul 13 17:59:24 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy