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Cadmium in PDB 488d: Catalytic Rna Enzyme-Product Complex

Protein crystallography data

The structure of Catalytic Rna Enzyme-Product Complex, PDB code: 488d was solved by J.B.Murray, H.Szoke, A.Szoke, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.60 / 3.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.503, 65.503, 136.484, 90.00, 90.00, 120.00
R / Rfree (%) 25.8 / 30.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Catalytic Rna Enzyme-Product Complex (pdb code 488d). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Catalytic Rna Enzyme-Product Complex, PDB code: 488d:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 488d

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Cadmium binding site 1 out of 8 in the Catalytic Rna Enzyme-Product Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1

b:79.9
occ:1.00
N7 A:G23 2.1 35.0 1.0
C5 A:G23 3.0 29.9 1.0
O6 A:G23 3.1 36.7 1.0
C8 A:G23 3.2 31.5 1.0
C6 A:G23 3.3 30.1 1.0
C5 A:U24 3.9 25.9 1.0
C4 A:U24 4.0 25.2 1.0
N7 A:G22 4.0 27.6 1.0
C4 A:G23 4.2 26.3 1.0
O4 A:U24 4.2 33.3 1.0
N9 A:G23 4.3 30.0 1.0
C6 A:U24 4.4 25.4 1.0
N3 A:U24 4.5 24.2 1.0
C8 A:G22 4.7 31.0 1.0
OP2 A:G23 4.7 51.7 1.0
N1 A:G23 4.7 27.3 1.0
N1 A:U24 4.9 23.6 1.0
C5 A:G22 4.9 29.7 1.0
O6 A:G22 4.9 40.9 1.0
C2 A:U24 4.9 24.1 1.0

Cadmium binding site 2 out of 8 in 488d

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Cadmium binding site 2 out of 8 in the Catalytic Rna Enzyme-Product Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2

b:24.9
occ:1.00
N7 A:G50 2.0 38.9 1.0
C5 A:G50 2.9 41.7 1.0
O6 A:G50 3.0 53.3 1.0
C8 A:G50 3.1 37.6 1.0
C6 A:G50 3.3 46.9 1.0
C4 A:G50 4.1 39.7 1.0
N9 A:G50 4.2 38.0 1.0
N6 A:A60 4.4 42.6 1.0
OP1 A:G50 4.5 48.1 1.0
O2' A:U40 4.5 36.2 1.0
N1 A:G50 4.6 46.7 1.0
O3' A:U40 4.7 43.1 1.0

Cadmium binding site 3 out of 8 in 488d

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Cadmium binding site 3 out of 8 in the Catalytic Rna Enzyme-Product Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3

b:26.7
occ:1.00
N7 B:G164 2.0 19.3 0.4
N7 D:G164 2.0 13.3 0.6
C5 B:G164 2.9 20.0 0.4
C5 D:G164 2.9 14.7 0.6
O6 B:G164 3.0 29.4 0.4
O6 D:G164 3.0 29.2 0.6
C8 B:G164 3.0 23.1 0.4
C8 D:G164 3.0 19.5 0.6
C6 B:G164 3.3 23.1 0.4
C6 D:G164 3.3 19.8 0.6
C4 B:G164 4.1 21.6 0.4
C4 D:G164 4.1 17.6 0.6
N9 B:G164 4.2 23.9 0.4
N9 D:G164 4.2 21.2 0.6
OP2 B:A34L 4.4 37.6 0.4
OP2 D:A34L 4.4 40.7 0.6
N1 B:G164 4.7 23.1 0.4
N1 D:G164 4.7 20.1 0.6
OP1 B:A34L 4.7 39.0 0.4
OP1 D:A34L 4.7 42.8 0.6
N7 B:A163 4.7 23.0 0.4
N7 D:A163 4.7 21.3 0.6
P B:A34L 4.9 40.2 0.4
P D:A34L 4.9 44.2 0.6

Cadmium binding site 4 out of 8 in 488d

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Cadmium binding site 4 out of 8 in the Catalytic Rna Enzyme-Product Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd4

b:25.8
occ:1.00
N7 B:G114 2.0 57.8 0.4
N7 D:G114 2.0 58.7 0.6
C5 B:G114 2.8 59.8 0.4
C5 D:G114 2.8 61.8 0.6
O6 B:G114 2.9 62.5 0.4
O6 D:G114 2.9 65.2 0.6
C8 B:G114 3.1 59.4 0.4
C8 D:G114 3.1 61.5 0.6
C6 B:G114 3.2 60.6 0.4
C6 D:G114 3.2 62.7 0.6
C4 B:G114 4.1 59.9 0.4
C4 D:G114 4.1 61.9 0.6
N9 B:G114 4.2 59.8 0.4
N9 D:G114 4.2 62.3 0.6
N1 B:G114 4.6 59.6 0.4
N1 D:G114 4.6 61.2 0.6
O6 B:G113 4.8 43.2 0.4
O6 D:G113 4.8 41.5 0.6

Cadmium binding site 5 out of 8 in 488d

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Cadmium binding site 5 out of 8 in the Catalytic Rna Enzyme-Product Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd5

b:44.7
occ:1.00
N7 B:G120 2.2 31.0 0.4
N7 D:G120 2.2 27.5 0.6
O6 B:G120 3.1 36.5 0.4
O6 D:G120 3.1 36.6 0.6
C5 B:G120 3.1 32.4 0.4
C5 D:G120 3.1 29.6 0.6
C8 B:G120 3.3 33.9 0.4
C8 D:G120 3.3 31.9 0.6
C6 B:G120 3.4 33.0 0.4
C6 D:G120 3.4 31.1 0.6
OP2 B:C111 4.2 44.8 0.4
OP2 D:C111 4.2 48.2 0.6
C4 B:G120 4.3 32.6 0.4
C4 D:G120 4.3 30.4 0.6
N9 B:G120 4.4 35.6 0.4
N9 D:G120 4.4 34.5 0.6
C5 B:C111 4.6 32.2 0.4
C5 D:C111 4.6 29.6 0.6
O6 A:G80 4.7 31.9 1.0
N1 B:G120 4.8 30.0 0.4
N1 D:G120 4.8 26.4 0.6

Cadmium binding site 6 out of 8 in 488d

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Cadmium binding site 6 out of 8 in the Catalytic Rna Enzyme-Product Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd6

b:46.6
occ:1.00
N7 A:G25 2.0 35.7 1.0
C5 A:G25 2.6 41.9 1.0
C8 A:G25 2.9 45.3 1.0
O6 A:G25 3.0 44.8 1.0
C6 A:G25 3.1 43.3 1.0
C4 A:G25 3.7 48.1 1.0
N9 A:G25 3.9 49.2 1.0
N1 A:G25 4.3 45.8 1.0
N3 A:G25 4.9 47.3 1.0
O4 A:U24 5.0 33.3 1.0

Cadmium binding site 7 out of 8 in 488d

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Cadmium binding site 7 out of 8 in the Catalytic Rna Enzyme-Product Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd7

b:22.6
occ:1.00
N7 B:G162 2.0 24.6 0.4
N7 D:G162 2.0 25.2 0.6
C5 B:G162 2.9 26.2 0.4
C5 D:G162 2.9 27.7 0.6
O6 B:G162 3.0 35.7 0.4
O6 D:G162 3.0 40.6 0.6
C8 B:G162 3.1 25.6 0.4
C8 D:G162 3.1 26.6 0.6
C6 B:G162 3.3 30.0 0.4
C6 D:G162 3.3 32.7 0.6
OP2 B:G162 4.0 28.7 0.4
OP2 D:G162 4.0 30.5 0.6
C4 B:G162 4.2 26.1 0.4
C4 D:G162 4.2 26.9 0.6
N9 B:G162 4.3 27.2 0.4
N9 D:G162 4.3 29.1 0.6
O4 D:U161 4.5 40.4 0.6
N1 B:G162 4.7 29.6 0.4
N1 D:G162 4.7 32.0 0.6
N7 B:A163 4.7 23.0 0.4
N7 D:A163 4.7 21.3 0.6
C5 B:A163 4.9 20.4 0.4
C5 D:A163 4.9 17.4 0.6
C8 B:A163 4.9 23.8 0.4
C8 D:A163 4.9 22.9 0.6

Cadmium binding site 8 out of 8 in 488d

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Cadmium binding site 8 out of 8 in the Catalytic Rna Enzyme-Product Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd8

b:20.3
occ:1.00
N7 A:G101 1.9 42.9 1.0
OP2 A:A90 2.2 59.7 1.0
C5 A:G101 2.8 46.1 1.0
O6 A:G101 3.0 46.1 1.0
C8 A:G101 3.0 49.7 1.0
C6 A:G101 3.2 46.6 1.0
P A:A90 3.6 59.0 1.0
O3' A:G80 4.0 56.2 1.0
C4 A:G101 4.0 47.4 1.0
N9 A:G101 4.1 50.2 1.0
O2' A:G80 4.2 60.5 1.0
OP1 A:A90 4.5 59.0 1.0
N1 A:G101 4.6 45.3 1.0
O3' A:A90 4.7 51.0 1.0
O5' A:A90 4.7 58.5 1.0
N2 B:G120 4.9 29.2 0.4
N2 D:G120 4.9 24.9 0.6
C3' A:G80 4.9 54.3 1.0
N7 A:G102 5.0 33.6 1.0

Reference:

J.B.Murray, H.Szoke, A.Szoke, W.G.Scott. Capture and Visualization of A Catalytic Rna Enzyme-Product Complex Using Crystal Lattice Trapping and X-Ray Holographic Reconstruction. Mol.Cell V. 5 279 2000.
ISSN: ISSN 1097-2765
PubMed: 10882069
DOI: 10.1016/S1097-2765(00)80423-2
Page generated: Fri Aug 28 14:12:42 2020
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