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Calcium in PDB 3m9m: 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: 3m9m 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) 45.00 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 98.576, 101.193, 52.418, 90.00, 90.00, 90.00
R / Rfree (%) 28.5 / 30.9

Other elements in 3m9m:

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 3m9m). 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: 3m9m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3m9m

Go back to Calcium Binding Sites List in 3m9m
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:Ca353

b:68.8
occ:1.00
 OE2 B:GLU106 2.8 49.0 1.0
O5' B:CTP2001 3.0 59.1 1.0
OD1 B:ASP105 3.1 42.1 1.0
O1A B:CTP2001 3.2 59.1 1.0
C5' B:CTP2001 3.3 56.6 1.0
CD B:GLU106 3.3 47.6 1.0
O B:HOH377 3.5 51.0 1.0
O B:HOH378 3.5 56.2 1.0
CA B:CA354 3.7 35.7 1.0
PA B:CTP2001 3.8 60.4 1.0
CG B:GLU106 3.8 44.5 1.0
OD2 B:ASP105 3.8 41.0 1.0
OD2 B:ASP7 3.8 35.0 1.0
CG B:ASP105 3.8 40.5 1.0
OE1 B:GLU106 4.1 49.0 1.0
P P:DG13 4.2 74.2 1.0
OG B:SER103 4.3 33.4 1.0
OD1 B:ASP7 4.4 37.3 1.0
CG B:ASP7 4.4 34.8 1.0
C4' B:CTP2001 4.4 54.9 1.0
OP2 P:DG13 4.4 74.0 1.0
O2A B:CTP2001 4.5 60.3 1.0
OP1 P:DG13 4.5 74.1 1.0
O B:ASP105 4.7 39.1 1.0
CB B:GLU106 4.8 40.6 1.0
O4' B:CTP2001 5.0 54.5 1.0

Calcium binding site 2 out of 4 in 3m9m

Go back to Calcium Binding Sites List in 3m9m
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:Ca354

b:35.7
occ:1.00
 OD1 B:ASP7 2.3 37.3 1.0
O B:PHE8 2.5 33.4 1.0
O2B B:CTP2001 2.5 62.3 1.0
OD2 B:ASP105 2.6 41.0 1.0
O1A B:CTP2001 3.1 59.1 1.0
O1G B:CTP2001 3.2 68.5 1.0
CG B:ASP7 3.4 34.8 1.0
C5' B:CTP2001 3.6 56.6 1.0
CG B:ASP105 3.6 40.5 1.0
C B:PHE8 3.6 33.5 1.0
CA B:CA353 3.7 68.8 1.0
O3G B:CTP2001 3.7 68.2 1.0
OD2 B:ASP7 3.8 35.0 1.0
PB B:CTP2001 3.8 61.6 1.0
PG B:CTP2001 4.0 68.0 1.0
PA B:CTP2001 4.0 60.4 1.0
O5' B:CTP2001 4.0 59.1 1.0
OD1 B:ASP105 4.1 42.1 1.0
C B:ASP7 4.2 33.3 1.0
N B:PHE8 4.2 31.7 1.0
O B:ASP7 4.3 31.8 1.0
NZ B:LYS159 4.3 45.5 1.0
O3B B:CTP2001 4.3 65.3 1.0
O3A B:CTP2001 4.3 61.5 1.0
O B:ASP105 4.4 39.1 1.0
CA B:PHE8 4.5 32.3 1.0
N B:ASP9 4.6 37.9 1.0
CB B:ASP7 4.6 34.3 1.0
CA B:ASP9 4.6 43.6 1.0
CA B:ASP7 4.7 35.9 1.0
CB B:ASP105 4.7 38.9 1.0
N B:TYR10 4.8 44.2 1.0
C B:ASP9 4.8 42.4 1.0
C4' B:CTP2001 4.9 54.9 1.0
CB B:PHE11 4.9 28.9 1.0
N B:PHE11 5.0 37.2 1.0

Calcium binding site 3 out of 4 in 3m9m

Go back to Calcium Binding Sites List in 3m9m
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:Ca355

b:74.3
occ:1.00
 O B:ALA181 2.7 49.8 1.0
O B:ILE186 2.8 51.6 1.0
C B:ALA181 3.9 50.9 1.0
C B:ILE186 4.0 54.4 1.0
CA B:GLY187 4.1 61.0 1.0
OP2 P:DA12 4.3 72.9 1.0
N B:GLY187 4.5 56.2 1.0
C B:GLY187 4.6 62.3 1.0
CA B:ALA181 4.7 51.2 1.0
ND2 B:ASN188 4.8 92.1 1.0
CB B:ALA181 4.8 53.4 1.0
N B:ASP182 4.9 50.7 1.0
CA B:ASP182 4.9 52.4 1.0
O B:GLY187 4.9 62.0 1.0
OP1 P:DA12 5.0 73.1 1.0

Calcium binding site 4 out of 4 in 3m9m

Go back to Calcium Binding Sites List in 3m9m
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
B:Ca356

b:73.2
occ:1.00
 OD2 B:ASP156 3.6 50.4 1.0
OP1 P:DG13 3.9 74.1 1.0
OD1 B:ASP156 4.2 50.8 1.0
CG B:ASP156 4.3 48.6 1.0
OP2 P:DG13 4.4 74.0 1.0
P P:DG13 4.5 74.2 1.0
OP1 P:DA12 4.6 73.1 1.0
CE B:LYS152 4.7 45.0 1.0
CA B:PRO184 5.0 40.5 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: Tue Jul 8 14:32:55 2025

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