Atomistry » Calcium » PDB 3m0c-3mip » 3m9o
Atomistry »
  Calcium »
    PDB 3m0c-3mip »
      3m9o »

Calcium in PDB 3m9o: Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion

Enzymatic activity of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion

All present enzymatic activity of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 3m9o was solved by J.H.Y.Wong, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.238, 103.683, 51.968, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 23.5

Other elements in 3m9o:

The structure of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion also contains other interesting chemical elements:

Platinum (Pt) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion (pdb code 3m9o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 3m9o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3m9o

Go back to Calcium Binding Sites List in 3m9o
Calcium binding site 1 out of 4 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4001

b:24.3
occ:1.00
O3G B:ATP2001 2.2 40.5 1.0
O2B B:ATP2001 2.4 25.0 1.0
OD2 B:ASP105 2.4 25.6 1.0
O B:PHE8 2.4 19.4 1.0
OD1 B:ASP7 2.4 26.9 1.0
O1A B:ATP2001 2.4 25.9 1.0
PG B:ATP2001 3.5 47.4 1.0
O B:HOH353 3.5 18.4 1.0
CG B:ASP105 3.5 27.0 1.0
PB B:ATP2001 3.5 30.3 1.0
CG B:ASP7 3.5 25.6 1.0
C B:PHE8 3.6 21.0 1.0
PA B:ATP2001 3.7 28.1 1.0
O3B B:ATP2001 3.8 31.3 1.0
C5' B:ATP2001 4.0 27.0 1.0
O3A B:ATP2001 4.0 28.2 1.0
OD2 B:ASP7 4.0 25.6 1.0
O B:HOH356 4.0 25.6 1.0
OD1 B:ASP105 4.1 21.5 1.0
N B:PHE8 4.2 20.4 1.0
O5' B:ATP2001 4.3 26.5 1.0
NZ B:LYS159 4.3 34.6 1.0
C B:ASP7 4.4 22.1 1.0
O2G B:ATP2001 4.4 38.1 1.0
CA B:PHE8 4.4 20.0 1.0
O B:HOH372 4.5 29.9 1.0
O1G B:ATP2001 4.5 40.3 1.0
N B:ASP9 4.5 21.4 1.0
CA B:ASP9 4.6 22.3 1.0
CB B:ASP105 4.6 23.9 1.0
N B:TYR10 4.7 22.4 1.0
O B:ASP7 4.7 21.5 1.0
CB B:ASP7 4.7 24.5 1.0
C B:ASP9 4.8 22.2 1.0
N B:PHE11 4.9 23.1 1.0
O B:ASP105 4.9 25.7 1.0
O1B B:ATP2001 4.9 26.5 1.0
CA B:CA4003 4.9 31.0 1.0
CA B:ASP7 4.9 22.3 1.0
CB B:PHE8 4.9 19.2 1.0
O2A B:ATP2001 5.0 25.8 1.0
CB B:PHE11 5.0 19.1 1.0

Calcium binding site 2 out of 4 in 3m9o

Go back to Calcium Binding Sites List in 3m9o
Calcium binding site 2 out of 4 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4002

b:39.2
occ:1.00
O B:ALA181 2.4 37.5 1.0
O B:ILE186 2.6 29.4 1.0
O B:HOH405 2.7 34.9 1.0
O P:HOH14 2.7 41.5 1.0
O P:HOH15 2.7 31.4 1.0
O P:HOH100 2.7 40.2 1.0
C B:ALA181 3.5 37.1 1.0
C B:ILE186 3.9 31.1 1.0
CA B:ALA181 4.3 37.5 1.0
CA B:GLY187 4.4 34.9 1.0
N B:ASP182 4.5 36.0 1.0
CB B:ALA181 4.5 37.7 1.0
CA B:ASP182 4.5 36.2 1.0
OP2 P:DC12 4.5 32.2 1.0
N B:GLY187 4.6 31.9 1.0
OP1 P:DC12 4.6 31.2 1.0
C B:GLY187 4.8 37.6 1.0
O B:VAL183 4.8 26.9 1.0
OD1 B:ASP182 4.9 43.2 1.0
CA B:ILE186 4.9 28.8 1.0
CB B:ILE186 4.9 29.9 1.0
O B:GLY187 5.0 37.7 1.0

Calcium binding site 3 out of 4 in 3m9o

Go back to Calcium Binding Sites List in 3m9o
Calcium binding site 3 out of 4 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4003

b:31.0
occ:1.00
O B:HOH371 2.4 38.2 1.0
OP1 P:DC13 2.4 31.7 1.0
O B:HOH372 2.5 29.9 1.0
OE2 B:GLU106 2.5 23.5 1.0
O B:HOH353 2.5 18.4 1.0
OD2 B:ASP7 2.6 25.6 1.0
CD B:GLU106 3.4 27.1 1.0
NZ B:LYS152 3.5 39.6 1.0
CG B:ASP7 3.6 25.6 1.0
P P:DC13 3.7 32.1 1.0
CG B:GLU106 3.9 26.8 1.0
NZ B:LYS159 3.9 34.6 1.0
O5' P:DC13 4.0 30.4 1.0
OD1 B:ASP7 4.1 26.9 1.0
O1A B:ATP2001 4.1 25.9 1.0
C5' P:DC13 4.1 29.6 1.0
OE1 B:GLU106 4.3 28.1 1.0
O B:HOH373 4.4 35.6 1.0
CZ B:PHE5 4.5 22.2 1.0
OP2 P:DC13 4.6 33.4 1.0
O P:HOH123 4.7 44.7 1.0
CE B:LYS152 4.7 37.8 1.0
CB B:ASP7 4.8 24.5 1.0
O3' P:DC12 4.8 32.1 1.0
O B:HOH374 4.8 37.9 1.0
O B:HOH467 4.8 42.5 1.0
CE2 B:PHE5 4.9 23.4 1.0
CA B:CA4001 4.9 24.3 1.0
C3' P:DC13 4.9 28.7 1.0
OD1 B:ASP105 5.0 21.5 1.0

Calcium binding site 4 out of 4 in 3m9o

Go back to Calcium Binding Sites List in 3m9o
Calcium binding site 4 out of 4 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca4004

b:52.7
occ:1.00
O T:HOH221 2.6 44.9 1.0
O2 T:DC18 2.6 67.5 1.0
O T:HOH20 2.7 47.5 1.0
O P:HOH135 3.1 56.8 1.0
O2 T:DC14 3.8 34.2 1.0
C2 T:DC18 3.8 67.8 1.0
O2 T:DC17 4.2 55.5 1.0
N2 P:DG3 4.3 30.5 1.0
N3 T:DC17 4.3 52.2 1.0
N3 T:DC18 4.4 65.5 1.0
C2 T:DC17 4.6 54.4 1.0
C5' T:DC15 4.7 39.3 1.0
N3 P:DA4 4.7 34.5 1.0
N1 T:DC18 4.8 69.8 1.0
C1' T:DC18 4.9 72.8 1.0
C1' T:DC14 4.9 35.6 1.0
C2 T:DC14 4.9 34.1 1.0
O4' T:DC15 4.9 35.1 1.0
C4' T:DC15 5.0 38.9 1.0

Reference:

J.H.Wong, J.A.Brown, Z.Suo, P.Blum, T.Nohmi, H.Ling. Structural Insight Into Dynamic Bypass of the Major Cisplatin-Dna Adduct By Y-Family Polymerase DPO4. Embo J. V. 29 2059 2010.
ISSN: ISSN 0261-4189
PubMed: 20512114
DOI: 10.1038/EMBOJ.2010.101
Page generated: Sat Dec 12 04:20:37 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy