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Mercury in PDB 4r6m: Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs

Protein crystallography data

The structure of Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs, PDB code: 4r6m was solved by C.Y.Xu, F.Yu, L.H.Wang, Y.Zhao, T.Lin, C.H.Fan, J.H.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.66 / 2.36
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 70.785, 70.785, 108.037, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 24

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs (pdb code 4r6m). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs, PDB code: 4r6m:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 4r6m

Go back to Mercury Binding Sites List in 4r6m
Mercury binding site 1 out of 6 in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg101

b:57.0
occ:0.75
N3 A:DT5 2.2 56.4 1.0
N3 B:DT6 2.2 61.8 1.0
O2 A:DT5 2.8 57.1 1.0
C2 A:DT5 2.9 52.8 1.0
O2 B:DT6 3.0 61.7 1.0
C2 B:DT6 3.0 68.2 1.0
O6 B:DG7 3.1 50.2 1.0
C4 B:DT6 3.2 72.9 1.0
C4 A:DT5 3.2 58.0 1.0
O4 B:DT5 3.3 72.9 1.0
O4 B:DT6 3.3 64.2 1.0
O4 A:DT5 3.5 61.8 1.0
C6 B:DG7 3.5 58.7 1.0
HG B:HG102 3.6 56.3 0.9
C4 B:DT5 3.7 59.5 1.0
N3 B:DT5 3.8 69.6 1.0
N4 A:DC4 3.9 56.8 1.0
O4 A:DT6 4.0 66.3 1.0
N1 B:DG7 4.2 53.3 1.0
N1 A:DT5 4.2 67.8 1.0
C5 B:DG7 4.2 64.4 1.0
N1 B:DT6 4.3 76.7 1.0
C4 A:DT6 4.4 66.9 1.0
C4 A:DC4 4.4 57.8 1.0
N3 A:DC4 4.4 60.8 1.0
N3 A:DT6 4.5 68.9 1.0
C5 B:DT6 4.5 71.7 1.0
C5 A:DT5 4.5 61.1 1.0
N7 B:DG7 4.6 66.9 1.0
C5 B:DT5 4.8 72.5 1.0
C6 A:DT5 4.8 60.6 1.0
C6 B:DT6 4.8 77.9 1.0
C2 B:DT5 4.9 67.7 1.0

Mercury binding site 2 out of 6 in 4r6m

Go back to Mercury Binding Sites List in 4r6m
Mercury binding site 2 out of 6 in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg102

b:56.3
occ:0.86
N3 A:DT6 2.1 68.9 1.0
N3 B:DT5 2.3 69.6 1.0
O2 B:DT5 2.8 56.3 1.0
O4 A:DT6 2.8 66.3 1.0
C4 A:DT6 2.8 66.9 1.0
C2 B:DT5 2.9 67.7 1.0
O2 B:DT6 2.9 61.7 1.0
O6 B:DG4 3.1 48.9 1.0
C2 A:DT6 3.1 46.7 1.0
C4 B:DT5 3.3 59.5 1.0
O2 A:DT6 3.3 43.8 1.0
C6 B:DG4 3.4 50.1 1.0
C2 B:DT6 3.4 68.2 1.0
N1 B:DG4 3.5 55.5 1.0
HG B:HG101 3.6 57.0 0.8
O4 B:DT5 3.6 72.9 1.0
N3 B:DT6 3.8 61.8 1.0
N3 A:DC7 3.9 40.4 1.0
OP2 F:DC1 4.0 63.3 0.0
N1 B:DT6 4.2 76.7 1.0
C5 A:DT6 4.2 54.7 1.0
N1 B:DT5 4.2 68.2 1.0
C4 A:DC7 4.2 59.5 1.0
N4 A:DC7 4.2 51.6 1.0
C5 B:DG4 4.3 64.7 1.0
N1 A:DT6 4.3 63.5 1.0
C2 B:DG4 4.4 61.8 1.0
C2 A:DC7 4.5 60.0 1.0
C1' B:DT6 4.6 72.8 1.0
C5 B:DT5 4.6 72.5 1.0
N3 A:DT5 4.7 56.4 1.0
C6 A:DT6 4.7 62.9 1.0
O2 A:DC7 4.8 65.5 1.0
C4 B:DT6 4.9 72.9 1.0
C6 B:DT5 4.9 68.1 1.0
N2 B:DG4 4.9 45.2 1.0
C4 B:DG4 5.0 62.6 1.0

Mercury binding site 3 out of 6 in 4r6m

Go back to Mercury Binding Sites List in 4r6m
Mercury binding site 3 out of 6 in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg101

b:68.9
occ:0.75
N3 C:DT6 2.2 71.5 1.0
N3 D:DT5 2.4 86.4 1.0
O4 C:DT6 2.5 66.7 1.0
C4 C:DT6 2.7 74.9 1.0
O2 D:DT6 2.8 86.2 1.0
C4 D:DT5 3.1 75.1 1.0
O4 D:DT5 3.1 71.8 1.0
O6 D:DG4 3.2 74.6 1.0
HG D:HG102 3.3 77.1 0.8
C2 D:DT5 3.3 97.1 1.0
C2 C:DT6 3.3 75.7 1.0
O2 D:DT5 3.4 88.4 1.0
C2 D:DT6 3.4 80.0 1.0
C6 D:DG4 3.5 83.2 1.0
O2 C:DT6 3.6 74.9 1.0
N3 D:DT6 3.6 69.7 1.0
N3 C:DC7 3.6 62.9 1.0
N1 D:DG4 3.8 77.0 1.0
N3 C:DT5 4.0 54.5 1.0
N4 C:DC7 4.1 67.9 1.0
C4 C:DC7 4.1 85.3 1.0
C5 C:DT6 4.1 62.9 1.0
C2 C:DC7 4.3 74.5 1.0
O4 C:DT5 4.4 76.8 1.0
C5 D:DG4 4.4 92.6 1.0
N1 C:DT6 4.4 73.6 1.0
N1 D:DT6 4.4 88.3 1.0
C5 D:DT5 4.5 81.5 1.0
N1 D:DT5 4.5 90.2 1.0
O2 C:DC7 4.5 73.3 1.0
N4 B:DC1 4.5 77.2 1.0
C4 C:DT5 4.6 70.3 1.0
C6 C:DT6 4.7 63.2 1.0
C2 D:DG4 4.7 78.5 1.0
C4 D:DT6 4.7 80.9 1.0
C2 C:DT5 4.8 74.2 1.0
O2 C:DT5 4.8 62.2 1.0
C6 D:DT5 5.0 90.4 1.0
C1' D:DT6 5.0 81.5 1.0

Mercury binding site 4 out of 6 in 4r6m

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Mercury binding site 4 out of 6 in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg102

b:77.1
occ:0.76
N3 C:DT5 2.2 54.5 1.0
N3 D:DT6 2.2 69.7 1.0
C2 C:DT5 3.0 74.2 1.0
C4 C:DT5 3.0 70.3 1.0
C4 D:DT6 3.0 80.9 1.0
C2 D:DT6 3.1 80.0 1.0
O2 C:DT5 3.1 62.2 1.0
O4 D:DT6 3.1 74.3 1.0
O4 C:DT5 3.1 76.8 1.0
O6 D:DG7 3.1 65.7 1.0
O2 D:DT6 3.2 86.2 1.0
HG D:HG101 3.3 68.9 0.8
O4 D:DT5 3.5 71.8 1.0
C6 D:DG7 3.7 65.0 1.0
N4 C:DC4 3.7 71.5 1.0
C4 D:DT5 3.8 75.1 1.0
O4 C:DT6 3.8 66.7 1.0
N3 D:DT5 4.0 86.4 1.0
N4 B:DC1 4.2 77.2 1.0
C4 C:DT6 4.2 74.9 1.0
N3 C:DT6 4.2 71.5 1.0
C5 D:DG7 4.2 69.2 1.0
N1 C:DT5 4.3 61.0 1.0
N1 D:DT6 4.4 88.3 1.0
C5 C:DT5 4.4 73.6 1.0
N1 D:DG7 4.4 53.1 1.0
C5 D:DT6 4.4 88.9 1.0
C4 C:DC4 4.4 70.0 1.0
N7 D:DG7 4.5 74.7 1.0
N3 C:DC4 4.7 65.9 1.0
C5 D:DT5 4.8 81.5 1.0
C6 C:DT5 4.8 70.2 1.0
C6 D:DT6 4.8 84.3 1.0
C2 D:DT5 5.0 97.1 1.0

Mercury binding site 5 out of 6 in 4r6m

Go back to Mercury Binding Sites List in 4r6m
Mercury binding site 5 out of 6 in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg101

b:84.2
occ:0.63
O E:HOH201 2.3 53.4 1.0
O2 F:DT6 2.3 65.2 1.0
N3 E:DT5 2.3 82.6 1.0
N3 F:DT6 2.4 70.2 1.0
C2 F:DT6 2.7 71.8 1.0
O4 E:DT5 3.0 80.5 1.0
C4 E:DT5 3.0 84.9 1.0
O F:HOH201 3.1 57.7 1.0
HG F:HG101 3.1 66.7 0.7
C2 E:DT5 3.3 90.1 1.0
O6 F:DG7 3.4 63.1 1.0
O2 E:DT5 3.4 87.8 1.0
C4 F:DT6 3.6 73.5 1.0
C6 F:DG7 3.6 73.1 1.0
O4 F:DT5 3.7 68.8 1.0
N3 F:DT5 3.8 56.3 1.0
N3 E:DT6 3.9 60.9 1.0
O4 E:DT6 3.9 67.5 1.0
C4 F:DT5 4.0 69.2 1.0
N4 E:DC4 4.0 77.7 1.0
O4 F:DT6 4.0 78.7 1.0
N1 F:DT6 4.0 77.5 1.0
C4 E:DT6 4.1 60.7 1.0
C5 F:DG7 4.1 75.9 1.0
N1 F:DG7 4.2 84.2 1.0
C4 E:DC4 4.4 88.3 1.0
C5 E:DT5 4.4 90.4 1.0
N3 E:DC4 4.4 93.2 1.0
N7 F:DG7 4.5 82.5 1.0
N1 E:DT5 4.5 88.8 1.0
C2 F:DT5 4.6 70.0 1.0
C2 E:DT6 4.7 78.8 1.0
C5 F:DT6 4.7 74.6 1.0
C6 F:DT6 4.9 63.7 1.0
O2 F:DT5 4.9 61.9 1.0
C6 E:DT5 5.0 93.4 1.0
C1' F:DT6 5.0 83.2 1.0
C4 F:DG7 5.0 80.6 1.0

Mercury binding site 6 out of 6 in 4r6m

Go back to Mercury Binding Sites List in 4r6m
Mercury binding site 6 out of 6 in the Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Dna Duplex Containing Two Consecutive Mercury- Mediated Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Hg101

b:66.7
occ:0.71
N3 F:DT5 2.3 56.3 1.0
N3 E:DT6 2.3 60.9 1.0
O F:HOH201 2.4 57.7 1.0
O2 F:DT5 2.8 61.9 1.0
O4 E:DT6 2.9 67.5 1.0
C2 F:DT5 2.9 70.0 1.0
C4 E:DT6 3.0 60.7 1.0
O6 F:DG4 3.1 53.5 1.0
HG E:HG101 3.1 84.2 0.6
O2 F:DT6 3.2 65.2 1.0
C6 F:DG4 3.3 56.8 1.0
C2 E:DT6 3.3 78.8 1.0
C4 F:DT5 3.3 69.2 1.0
N1 F:DG4 3.5 59.7 1.0
O2 E:DT6 3.5 78.7 1.0
O4 F:DT5 3.6 68.8 1.0
C2 F:DT6 3.8 71.8 1.0
N3 E:DC7 3.9 72.4 1.0
N4 E:DC7 4.0 58.3 1.0
C4 E:DC7 4.0 71.3 1.0
N3 F:DT6 4.0 70.2 1.0
C5 F:DG4 4.1 60.6 1.0
N1 F:DT5 4.2 67.1 1.0
N3 E:DT5 4.3 82.6 1.0
C2 F:DG4 4.4 58.9 1.0
C5 E:DT6 4.4 74.5 1.0
O4 E:DT5 4.4 80.5 1.0
C2 E:DC7 4.5 75.0 1.0
N1 E:DT6 4.5 80.7 1.0
C5 F:DT5 4.6 73.3 1.0
O E:HOH201 4.6 53.4 1.0
C4 E:DT5 4.7 84.9 1.0
N1 F:DT6 4.8 77.5 1.0
N7 F:DG4 4.8 60.2 1.0
C4 F:DG4 4.8 58.3 1.0
C5 E:DC7 4.9 53.4 1.0
C6 F:DT5 4.9 60.8 1.0
O2 E:DC7 4.9 76.2 1.0
C6 E:DT6 4.9 77.4 1.0
N2 F:DG4 5.0 62.9 1.0

Reference:

C.Y.Xu, F.Yu, L.H.Wang, Y.Zhao, T.Lin, C.H.Fan, J.H.He. Crystal Structure of Dna Duplex Containing Two Consecutive Mercury-Mediated Base Pairs To Be Published.
Page generated: Sun Dec 13 19:11:55 2020

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