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

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

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

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer C 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 C Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rbd 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.852, 109.339, 100.680, 90.00, 101.12, 90.00
R / Rfree (%) 20.4 / 23.8

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 3rbd

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

b:53.1
occ:1.00
 OD1 A:ASP105 2.3 49.9 1.0
O A:HOH400 2.4 12.8 1.0
O2A A:DGT414 2.6 41.4 1.0
OD1 A:ASP7 2.9 40.9 1.0
OD2 A:ASP105 3.0 39.2 1.0
CG A:ASP105 3.0 38.3 1.0
OD2 A:ASP7 3.1 40.3 1.0
O A:HOH343 3.1 29.3 1.0
OE1 A:GLU106 3.2 37.6 1.0
CG A:ASP7 3.3 38.8 1.0
OE2 A:GLU106 3.3 44.5 1.0
CD A:GLU106 3.3 40.2 1.0
CA A:CA416 3.6 35.4 1.0
C3' D:DOC814 3.7 46.5 1.0
PA A:DGT414 3.8 36.9 1.0
OP1 D:DOC814 3.9 47.3 1.0
O1A A:DGT414 4.2 42.1 1.0
C5' D:DOC814 4.2 47.5 1.0
O5' A:DGT414 4.2 37.4 1.0
CB A:GLU106 4.2 39.5 1.0
C5' A:DGT414 4.2 34.1 1.0
C4' D:DOC814 4.3 48.1 1.0
CG A:GLU106 4.3 40.0 1.0
O5' D:DOC814 4.4 48.4 1.0
OG A:SER103 4.5 38.8 1.0
CB A:ASP105 4.5 37.9 1.0
CB A:ASP7 4.6 36.8 1.0
P D:DOC814 4.8 45.3 1.0
C A:ASP105 4.8 37.8 1.0
O A:ASP105 4.8 37.0 1.0
NZ A:LYS159 4.9 41.8 1.0

Calcium binding site 2 out of 6 in 3rbd

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

b:35.4
occ:1.00
 O A:PHE8 2.3 38.1 1.0
OD1 A:ASP7 2.3 40.9 1.0
OD2 A:ASP105 2.3 39.2 1.0
O1B A:DGT414 2.3 39.9 1.0
O2A A:DGT414 2.3 41.4 1.0
O1G A:DGT414 2.7 36.0 1.0
PG A:DGT414 3.2 35.6 1.0
PB A:DGT414 3.3 35.6 1.0
CG A:ASP7 3.5 38.8 1.0
C A:PHE8 3.5 37.7 1.0
CG A:ASP105 3.5 38.3 1.0
PA A:DGT414 3.5 36.9 1.0
CA A:CA415 3.6 53.1 1.0
O3A A:DGT414 3.8 38.0 1.0
O3B A:DGT414 3.8 37.6 1.0
N A:PHE8 4.0 37.1 1.0
OD2 A:ASP7 4.1 40.3 1.0
OD1 A:ASP105 4.2 49.9 1.0
C5' A:DGT414 4.2 34.1 1.0
O2G A:DGT414 4.3 36.3 1.0
NZ A:LYS159 4.3 41.8 1.0
O A:HOH343 4.3 29.3 1.0
CA A:PHE8 4.3 37.4 1.0
C A:ASP7 4.3 37.5 1.0
O5' A:DGT414 4.4 37.4 1.0
O3G A:DGT414 4.4 35.2 1.0
N A:ASP9 4.5 37.8 1.0
N A:TYR10 4.5 36.0 1.0
CB A:ASP7 4.5 36.8 1.0
CA A:ASP9 4.6 37.4 1.0
CB A:ASP105 4.6 37.9 1.0
O2B A:DGT414 4.6 37.5 1.0
O1A A:DGT414 4.7 42.1 1.0
C A:ASP9 4.7 37.0 1.0
O A:ASP7 4.7 38.5 1.0
CA A:ASP7 4.8 37.1 1.0
CE A:LYS159 4.8 41.6 1.0
N A:PHE11 4.8 34.2 1.0
CB A:PHE8 4.9 37.0 1.0

Calcium binding site 3 out of 6 in 3rbd

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

b:48.0
occ:1.00
 O A:HOH388 2.2 38.8 1.0
O A:ALA181 2.3 56.1 1.0
O A:ILE186 2.3 56.2 1.0
O D:HOH2 2.4 24.4 1.0
O A:HOH342 2.5 53.2 1.0
C A:ALA181 3.5 54.4 1.0
C A:ILE186 3.6 54.6 1.0
CA A:GLY187 4.1 54.1 1.0
CA A:ALA181 4.3 55.7 1.0
N A:GLY187 4.3 54.6 1.0
OP1 D:DG813 4.4 46.1 1.0
OP2 D:DG813 4.4 45.2 1.0
CB A:ALA181 4.5 55.5 1.0
N A:ASP182 4.5 54.1 1.0
C A:GLY187 4.6 56.0 1.0
CA A:ASP182 4.7 51.9 1.0
CA A:ILE186 4.7 54.6 1.0
O A:VAL183 4.8 49.3 1.0
CB A:ILE186 4.9 55.9 1.0
O A:GLY187 4.9 56.9 1.0
P D:DG813 5.0 43.9 1.0

Calcium binding site 4 out of 6 in 3rbd

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

b:64.7
occ:1.00
 O2A B:DGT1414 2.3 88.3 1.0
O H:HOH4 2.5 22.7 1.0
OD1 B:ASP1105 2.6 77.5 1.0
OE2 B:GLU1106 2.9 78.3 1.0
OD1 B:ASP1007 3.1 85.5 1.0
OD2 B:ASP1007 3.1 82.1 1.0
CD B:GLU1106 3.2 78.2 1.0
CG B:GLU1106 3.3 78.3 1.0
CG B:ASP1105 3.3 76.9 1.0
OD2 B:ASP1105 3.3 83.1 1.0
CG B:ASP1007 3.4 80.7 1.0
PA B:DGT1414 3.5 78.0 1.0
CA B:CA1416 3.5 53.3 1.0
O1A B:DGT1414 3.7 79.0 1.0
C5' H:DOC1814 3.9 90.5 1.0
C3' H:DOC1814 3.9 88.9 1.0
C5' B:DGT1414 4.0 71.5 1.0
O5' H:DOC1814 4.0 88.7 1.0
O5' B:DGT1414 4.0 75.8 1.0
OE1 B:GLU1106 4.1 78.1 1.0
O B:HOH1501 4.2 35.6 1.0
OP1 H:DOC1814 4.2 92.7 1.0
O B:HOH1502 4.4 55.7 1.0
C4' H:DOC1814 4.4 89.5 1.0
OG B:SER1103 4.4 74.7 1.0
CB B:GLU1106 4.7 79.4 1.0
P H:DOC1814 4.7 89.5 1.0
CB B:ASP1105 4.8 75.7 1.0
O3A B:DGT1414 4.8 80.5 1.0
O3G B:DGT1414 4.8 79.9 1.0
O1B B:DGT1414 4.8 84.0 1.0
CB B:ASP1007 4.9 80.8 1.0
O B:ASP1105 4.9 78.7 1.0
C B:ASP1105 4.9 77.8 1.0

Calcium binding site 5 out of 6 in 3rbd

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

b:53.3
occ:1.00
 O B:PHE1008 2.3 79.6 1.0
OD2 B:ASP1105 2.3 83.1 1.0
OD1 B:ASP1007 2.3 85.5 1.0
O1B B:DGT1414 2.3 84.0 1.0
O2A B:DGT1414 2.3 88.3 1.0
O3G B:DGT1414 2.5 79.9 1.0
PB B:DGT1414 3.3 79.5 1.0
CG B:ASP1105 3.4 76.9 1.0
CG B:ASP1007 3.4 80.7 1.0
C B:PHE1008 3.5 77.7 1.0
PA B:DGT1414 3.5 78.0 1.0
CA B:CA1415 3.5 64.7 1.0
O1G B:DGT1414 3.6 86.6 1.0
O3A B:DGT1414 3.7 80.5 1.0
O3B B:DGT1414 3.7 83.4 1.0
PG B:DGT1414 3.8 83.1 1.0
O B:HOH1501 3.8 35.6 1.0
OD1 B:ASP1105 3.9 77.5 1.0
OD2 B:ASP1007 4.0 82.1 1.0
N B:PHE1008 4.0 78.6 1.0
C5' B:DGT1414 4.2 71.5 1.0
CA B:PHE1008 4.3 78.6 1.0
O5' B:DGT1414 4.4 75.8 1.0
C B:ASP1007 4.4 80.2 1.0
N B:ASP1009 4.4 77.7 1.0
CA B:ASP1009 4.6 76.1 1.0
O2G B:DGT1414 4.6 82.1 1.0
N B:TYR1010 4.6 71.1 1.0
CB B:ASP1007 4.6 80.8 1.0
CB B:ASP1105 4.6 75.7 1.0
O2B B:DGT1414 4.6 78.5 1.0
O1A B:DGT1414 4.7 79.0 1.0
O H:HOH4 4.7 22.7 1.0
C B:ASP1009 4.7 73.3 1.0
O B:ASP1007 4.8 81.4 1.0
N B:PHE1011 4.8 64.4 1.0
CA B:ASP1007 4.9 80.6 1.0
CB B:PHE1008 4.9 77.1 1.0

Calcium binding site 6 out of 6 in 3rbd

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

b:61.4
occ:1.00
 O B:ALA1181 2.3 97.1 1.0
O B:HOH7 2.4 10.2 1.0
O B:HOH1516 2.4 26.8 1.0
O B:HOH1512 2.5 41.3 1.0
O B:HOH5 2.5 26.5 1.0
O B:ILE1186 2.6 83.3 1.0
O H:HOH1514 2.8 36.9 1.0
C B:ALA1181 3.5 94.9 1.0
C B:ILE1186 3.8 84.2 1.0
OP2 H:DG1813 4.0 79.8 1.0
OP1 H:DG1813 4.1 83.5 1.0
CA B:ASP1182 4.4 92.6 1.0
N B:ASP1182 4.4 95.1 1.0
CA B:GLY1187 4.5 84.0 1.0
CA B:ALA1181 4.5 96.0 1.0
O B:VAL1183 4.5 87.3 1.0
N B:GLY1187 4.6 84.3 1.0
P H:DG1813 4.6 79.6 1.0
CA B:ILE1186 4.8 85.3 1.0
CB B:ALA1181 4.8 96.2 1.0
C B:ASP1182 4.9 91.8 1.0
C B:GLY1187 4.9 86.2 1.0
CB B:ILE1186 5.0 86.9 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 17:59:08 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy