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Magnesium in PDB 3lpv: X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link

Protein crystallography data

The structure of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link, PDB code: 3lpv was solved by R.C.Todd, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.31 / 1.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 31.303, 35.425, 45.128, 80.06, 84.09, 81.77
R / Rfree (%) 17.2 / 19.8

Other elements in 3lpv:

The structure of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link also contains other interesting chemical elements:

Platinum (Pt) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link (pdb code 3lpv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link, PDB code: 3lpv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3lpv

Go back to Magnesium Binding Sites List in 3lpv
Magnesium binding site 1 out of 4 in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:38.9
occ:1.00
O B:HOH1056 1.9 29.9 1.0
O B:HOH1057 2.0 37.0 1.0
O B:HOH1054 2.0 37.9 1.0
O B:HOH1055 2.1 37.5 1.0
O B:HOH1058 2.1 39.0 1.0
O B:HOH1059 2.3 45.0 1.0
O B:HOH1052 3.9 43.5 1.0
N7 B:DG23 4.0 34.2 1.0
O B:HOH1046 4.1 46.9 1.0
O6 B:DG23 4.1 34.5 1.0
O B:HOH1024 4.2 38.9 1.0
N7 B:DG24 4.2 31.3 1.0
O6 B:DG24 4.3 28.2 1.0
O B:HOH1066 4.5 46.5 1.0
C5 B:DG23 4.7 31.9 1.0
C6 B:DG23 4.7 31.6 1.0
C8 B:DG23 5.0 33.0 1.0
C5 B:DG24 5.0 29.6 1.0

Magnesium binding site 2 out of 4 in 3lpv

Go back to Magnesium Binding Sites List in 3lpv
Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2004

b:50.5
occ:1.00
O B:HOH1144 2.2 50.3 1.0
O B:HOH1143 2.2 51.3 1.0
O B:HOH1148 2.2 51.6 1.0
O B:HOH1146 2.2 47.4 1.0
O B:HOH1145 2.2 49.5 1.0
O B:HOH1147 2.2 46.0 1.0
N7 B:DA20 4.0 28.4 1.0
O B:HOH1104 4.2 50.8 1.0
O B:HOH1110 4.3 39.6 1.0
N7 B:DG21 4.5 31.1 1.0
O B:HOH1045 4.5 39.9 1.0
O6 B:DG21 4.6 26.4 1.0
N6 B:DA20 4.6 26.6 1.0
C5 B:DA20 4.8 27.8 1.0
C8 B:DA20 4.8 29.4 1.0

Magnesium binding site 3 out of 4 in 3lpv

Go back to Magnesium Binding Sites List in 3lpv
Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:41.0
occ:1.00
O D:HOH1060 2.1 35.8 1.0
O D:HOH1065 2.1 60.7 1.0
O D:HOH1064 2.1 38.8 1.0
O D:HOH1061 2.1 42.2 1.0
O D:HOH1062 2.1 43.8 1.0
O D:HOH1063 2.2 36.0 1.0
N7 D:DG47 4.0 37.1 1.0
O6 D:DG47 4.1 35.7 1.0
O D:HOH1067 4.1 43.2 1.0
N7 D:DG48 4.2 32.3 1.0
O6 D:DG48 4.4 29.1 1.0
O D:HOH1092 4.6 52.8 1.0
C5 D:DG47 4.7 35.6 1.0
C6 D:DG47 4.7 33.6 1.0

Magnesium binding site 4 out of 4 in 3lpv

Go back to Magnesium Binding Sites List in 3lpv
Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:55.6
occ:1.00
O D:HOH1141 2.2 55.5 1.0
O D:HOH1138 2.2 54.0 1.0
O D:HOH1142 2.2 54.0 1.0
O D:HOH1139 2.2 51.8 1.0
O D:HOH1140 2.2 55.6 1.0
O D:HOH1137 2.2 53.0 1.0
O D:HOH1011 4.0 45.8 1.0
N7 D:DA44 4.0 29.7 1.0
O D:HOH1098 4.3 42.7 1.0
N7 D:DG45 4.5 35.1 1.0
O C:HOH1113 4.5 40.3 1.0
O6 D:DG45 4.6 29.4 1.0
O D:HOH1026 4.6 36.1 1.0
N6 D:DA44 4.6 27.9 1.0
C5 D:DA44 4.7 28.6 1.0
C8 D:DA44 4.8 30.3 1.0

Reference:

R.C.Todd, S.J.Lippard. Structure of Duplex Dna Containing the Cisplatin 1,2-{Pt(Nh(3))(2)}(2+)-D(Gpg) Cross-Link at 1.77A Resolution. J.Inorg.Biochem. V. 104 902 2010.
ISSN: ISSN 0162-0134
PubMed: 20541266
DOI: 10.1016/J.JINORGBIO.2010.04.005
Page generated: Mon Dec 14 08:24:32 2020

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