Atomistry » Calcium » PDB 3r3v-3rk2 » 3rb6
Atomistry »
  Calcium »
    PDB 3r3v-3rk2 »
      3rb6 »

Calcium in PDB 3rb6: DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion

Enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer A 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rb6 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.915, 109.328, 100.828, 90.00, 101.07, 90.00
R / Rfree (%) 20.3 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion (pdb code 3rb6). 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rb6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:53.3
occ:1.00
 O2A A:DGT414 2.3 47.5 1.0
OE2 A:GLU106 2.3 55.3 1.0
OD1 A:ASP105 2.4 41.7 1.0
O D:HOH65 2.5 30.5 1.0
OD2 A:ASP105 3.0 39.1 1.0
CG A:ASP105 3.1 37.6 1.0
OD2 A:ASP7 3.1 47.2 1.0
OD1 A:ASP7 3.1 46.5 1.0
CA A:CA416 3.3 39.1 1.0
CG A:ASP7 3.4 45.1 1.0
CD A:GLU106 3.5 52.6 1.0
C3' D:2DA814 3.5 51.0 1.0
PA A:DGT414 3.6 37.5 1.0
O1A A:DGT414 3.9 39.0 1.0
C5' D:2DA814 3.9 51.3 1.0
C4' D:2DA814 4.0 52.4 1.0
O5' D:2DA814 4.1 48.4 1.0
O5' A:DGT414 4.2 37.4 1.0
OE1 A:GLU106 4.2 56.2 1.0
C5' A:DGT414 4.2 34.9 1.0
CG A:GLU106 4.4 47.8 1.0
CB A:GLU106 4.4 44.6 1.0
CB A:ASP105 4.5 39.0 1.0
OP1 D:2DA814 4.5 50.1 1.0
CB A:ASP7 4.7 42.1 1.0
NZ A:LYS159 4.7 53.0 1.0
O1B A:DGT414 4.8 43.0 1.0
OG A:SER103 4.8 41.6 1.0
O3A A:DGT414 4.8 40.8 1.0
O A:ASP105 4.9 41.1 1.0
C2' D:2DA814 4.9 51.9 1.0
C A:ASP105 4.9 40.6 1.0
P D:2DA814 5.0 48.7 1.0

Calcium binding site 2 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:39.1
occ:1.00
 O A:PHE8 2.3 41.6 1.0
OD2 A:ASP105 2.3 39.1 1.0
OD1 A:ASP7 2.3 46.5 1.0
O2A A:DGT414 2.3 47.5 1.0
O1B A:DGT414 2.3 43.0 1.0
O2G A:DGT414 2.6 42.9 1.0
PB A:DGT414 3.3 39.4 1.0
CA A:CA415 3.3 53.3 1.0
PG A:DGT414 3.4 43.2 1.0
C A:PHE8 3.4 41.8 1.0
CG A:ASP105 3.5 37.6 1.0
PA A:DGT414 3.5 37.5 1.0
CG A:ASP7 3.5 45.1 1.0
O3A A:DGT414 3.6 40.8 1.0
O3B A:DGT414 3.7 43.4 1.0
N A:PHE8 3.9 39.1 1.0
OD1 A:ASP105 4.0 41.7 1.0
OD2 A:ASP7 4.1 47.2 1.0
C5' A:DGT414 4.1 34.9 1.0
O3G A:DGT414 4.2 41.9 1.0
CA A:PHE8 4.2 40.1 1.0
NZ A:LYS159 4.3 53.0 1.0
C A:ASP7 4.3 40.5 1.0
O5' A:DGT414 4.3 37.4 1.0
N A:ASP9 4.5 41.5 1.0
CB A:ASP105 4.6 39.0 1.0
N A:TYR10 4.6 35.8 1.0
O1A A:DGT414 4.6 39.0 1.0
CA A:ASP9 4.7 40.3 1.0
O2B A:DGT414 4.7 40.0 1.0
CB A:ASP7 4.7 42.1 1.0
CE A:LYS159 4.7 51.3 1.0
O A:ASP7 4.8 41.3 1.0
C A:ASP9 4.8 38.8 1.0
O1G A:DGT414 4.8 45.9 1.0
CA A:ASP7 4.9 41.1 1.0
CB A:PHE8 4.9 40.5 1.0
N A:PHE11 4.9 35.3 1.0

Calcium binding site 3 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:58.6
occ:1.00
 O A:HOH358 2.3 60.7 1.0
O A:ALA181 2.3 61.9 1.0
O A:ILE186 2.3 61.7 1.0
O A:HOH343 2.3 65.1 1.0
O D:HOH40 2.4 57.6 1.0
O D:HOH5 2.4 43.8 1.0
C A:ALA181 3.5 58.1 1.0
C A:ILE186 3.5 56.2 1.0
CA A:GLY187 4.1 53.6 1.0
OP1 D:DG813 4.2 47.7 1.0
N A:GLY187 4.3 53.7 1.0
OP2 D:DG813 4.3 47.5 1.0
CA A:ALA181 4.4 59.2 1.0
N A:ASP182 4.5 59.1 1.0
O A:VAL183 4.6 54.5 1.0
CB A:ALA181 4.6 58.2 1.0
C A:GLY187 4.6 57.2 1.0
CA A:ILE186 4.7 56.5 1.0
CA A:ASP182 4.7 56.3 1.0
P D:DG813 4.8 46.9 1.0
O A:GLY187 4.8 59.1 1.0
CB A:ILE186 4.8 58.9 1.0

Calcium binding site 4 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:73.5
occ:1.00
 O2A B:DGT1414 2.3 0.9 1.0
OD1 B:ASP1105 2.3 94.3 1.0
OD2 B:ASP1007 2.3 96.9 1.0
O B:HOH6 2.7 53.4 1.0
CG B:ASP1007 3.0 91.2 1.0
OE2 B:GLU1106 3.0 87.9 1.0
OD1 B:ASP1007 3.0 94.3 1.0
CG B:ASP1105 3.1 86.2 1.0
OD2 B:ASP1105 3.1 90.2 1.0
CG B:GLU1106 3.2 85.8 1.0
CD B:GLU1106 3.3 87.6 1.0
CA B:CA1416 3.3 63.9 1.0
C3' H:2DA1814 3.6 0.2 1.0
PA B:DGT1414 3.7 91.8 1.0
C5' H:2DA1814 3.9 0.6 1.0
O5' H:2DA1814 4.0 0.9 1.0
O1A B:DGT1414 4.1 93.7 1.0
C4' H:2DA1814 4.2 0.0 1.0
OE1 B:GLU1106 4.2 87.5 1.0
C5' B:DGT1414 4.2 87.7 1.0
O5' B:DGT1414 4.3 90.6 1.0
CB B:ASP1007 4.4 89.6 1.0
OG B:SER1103 4.5 82.3 1.0
CB B:GLU1106 4.5 85.0 1.0
CB B:ASP1105 4.6 83.3 1.0
O1B B:DGT1414 4.6 0.3 1.0
O B:ASP1105 4.7 83.5 1.0
C B:ASP1105 4.7 83.0 1.0
OP1 H:2DA1814 4.8 0.1 1.0
O3A B:DGT1414 4.9 96.5 1.0
N B:GLU1106 4.9 84.5 1.0
C2' H:2DA1814 5.0 0.6 1.0

Calcium binding site 5 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:63.9
occ:1.00
 OD1 B:ASP1007 2.3 94.3 1.0
OD2 B:ASP1105 2.3 90.2 1.0
O2A B:DGT1414 2.3 0.9 1.0
O B:PHE1008 2.3 85.0 1.0
O1B B:DGT1414 2.3 0.3 1.0
O3G B:DGT1414 2.8 95.0 1.0
O3B B:DGT1414 3.1 99.9 1.0
PB B:DGT1414 3.1 96.7 1.0
CA B:CA1415 3.3 73.5 1.0
PA B:DGT1414 3.4 91.8 1.0
CG B:ASP1007 3.4 91.2 1.0
CG B:ASP1105 3.4 86.2 1.0
O3A B:DGT1414 3.5 96.5 1.0
C B:PHE1008 3.5 81.2 1.0
PG B:DGT1414 3.8 97.8 1.0
OD2 B:ASP1007 3.9 96.9 1.0
OD1 B:ASP1105 3.9 94.3 1.0
C5' B:DGT1414 4.1 87.7 1.0
N B:PHE1008 4.2 82.5 1.0
O5' B:DGT1414 4.2 90.6 1.0
O1G B:DGT1414 4.3 0.4 1.0
CA B:PHE1008 4.4 82.0 1.0
O2B B:DGT1414 4.5 96.6 1.0
N B:ASP1009 4.5 82.2 1.0
O2G B:DGT1414 4.5 95.3 1.0
C B:ASP1007 4.5 85.5 1.0
O1A B:DGT1414 4.6 93.7 1.0
N B:TYR1010 4.6 78.1 1.0
O B:HOH6 4.6 53.4 1.0
CA B:ASP1009 4.6 82.4 1.0
CB B:ASP1105 4.7 83.3 1.0
CB B:ASP1007 4.7 89.6 1.0
C B:ASP1009 4.8 80.0 1.0
N B:PHE1011 4.9 72.7 1.0
O B:ASP1007 5.0 86.8 1.0

Calcium binding site 6 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:68.8
occ:1.00
 O B:ALA1181 2.3 0.4 1.0
O B:ILE1186 2.3 99.5 1.0
O H:HOH3 2.5 44.4 1.0
O B:HOH9 2.5 53.9 1.0
O B:HOH8 2.6 57.0 1.0
O B:HOH1 3.1 73.7 1.0
C B:ALA1181 3.4 0.5 1.0
C B:ILE1186 3.5 94.7 1.0
OP1 H:DG1813 3.8 98.0 1.0
CA B:ALA1181 4.0 0.0 1.0
CA B:GLY1187 4.1 93.9 1.0
N B:GLY1187 4.3 94.7 1.0
CB B:ALA1181 4.3 0.6 1.0
N B:ASP1182 4.5 1.0 1.0
C B:GLY1187 4.6 96.8 1.0
O B:VAL1183 4.6 89.4 1.0
CA B:ILE1186 4.6 94.0 1.0
CB B:ILE1186 4.7 94.6 1.0
O B:GLY1187 4.8 99.6 1.0
CA B:ASP1182 4.8 100.0 1.0
P H:DG1813 4.9 95.2 1.0
OP2 H:DG1813 4.9 95.1 1.0
CG2 B:ILE1186 4.9 96.1 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 17:57:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy