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Bromine in PDB 4x4t: Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca

Enzymatic activity of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca

All present enzymatic activity of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca:
2.7.7.72;

Protein crystallography data

The structure of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca, PDB code: 4x4t was solved by C.-D.Kuhn, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.34 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 115.422, 83.959, 135.320, 90.00, 103.51, 90.00
R / Rfree (%) 18.6 / 22.9

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca (pdb code 4x4t). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca, PDB code: 4x4t:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 4x4t

Go back to Bromine Binding Sites List in 4x4t
Bromine binding site 1 out of 6 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br13

b:0.0
occ:1.00
 BR B:5BU13 0.0 0.0 1.0
C5 B:5BU13 1.9 0.8 1.0
C4 B:5BU13 2.9 0.6 1.0
C6 B:5BU13 2.9 0.9 1.0
H6 B:5BU13 3.1 0.1 1.0
O4 B:5BU13 3.1 0.4 1.0
O4 B:U14 3.2 0.8 1.0
H5 B:U14 3.6 0.5 1.0
C4 B:U14 3.6 0.3 1.0
N7 B:G12 3.7 0.8 1.0
H3' B:G12 3.8 0.9 1.0
C5 B:U14 3.8 0.6 1.0
C8 B:G12 3.9 0.2 1.0
C5 B:G12 4.0 0.1 1.0
H8 B:G12 4.1 0.9 1.0
N3 B:5BU13 4.1 0.2 1.0
OP2 B:G12 4.3 1.0 1.0
N1 B:5BU13 4.4 0.6 1.0
N9 B:G12 4.4 0.8 1.0
C4 B:G12 4.5 1.0 1.0
O5' B:G12 4.5 0.6 1.0
N3 B:U14 4.6 0.0 1.0
C6 B:G12 4.6 0.8 1.0
H2' B:G12 4.7 0.5 1.0
C3' B:G12 4.7 0.1 1.0
C2 B:5BU13 4.7 0.6 1.0
H3 B:U14 4.8 0.6 1.0
H3 B:5BU13 4.8 0.3 1.0
C6 B:U14 4.8 1.0 1.0
O5' B:5BU13 4.8 0.6 1.0
O6 B:G12 4.9 0.0 1.0

Bromine binding site 2 out of 6 in 4x4t

Go back to Bromine Binding Sites List in 4x4t
Bromine binding site 2 out of 6 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br22

b:0.7
occ:1.00
 BR B:5BU22 0.0 0.7 1.0
C5 B:5BU22 1.9 0.2 1.0
C4 B:5BU22 2.9 0.9 1.0
C6 B:5BU22 2.9 0.8 1.0
H6 B:5BU22 3.1 0.2 1.0
O4 B:5BU22 3.1 0.6 1.0
C5 B:C21 3.5 0.6 1.0
C4 B:C21 3.6 0.1 1.0
H5 B:C21 3.7 0.8 1.0
H3' B:C21 3.8 0.2 1.0
C6 B:C21 3.8 0.6 1.0
OP2 B:5BU22 3.9 0.9 1.0
N3 B:C21 4.0 0.1 1.0
N4 B:C21 4.0 0.4 1.0
N3 B:5BU22 4.1 0.0 1.0
H6 B:C21 4.2 0.7 1.0
N1 B:C21 4.2 0.5 1.0
H41 B:C21 4.2 0.6 1.0
C2 B:C21 4.3 0.7 1.0
H2' B:C21 4.3 0.4 1.0
N1 B:5BU22 4.4 0.8 1.0
H42 B:C21 4.5 0.6 1.0
C3' B:C21 4.6 0.0 1.0
C2 B:5BU22 4.7 0.7 1.0
O5' B:5BU22 4.7 0.7 1.0
H3 B:5BU22 4.8 0.2 1.0
C2' B:C21 4.9 0.5 1.0
H1 B:G11 4.9 0.9 1.0
P B:5BU22 4.9 0.7 1.0

Bromine binding site 3 out of 6 in 4x4t

Go back to Bromine Binding Sites List in 4x4t
Bromine binding site 3 out of 6 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br30

b:0.0
occ:0.30
 BR B:5BU30 0.0 0.0 0.3
C5 B:5BU30 1.9 89.8 0.3
C5 B:C33 2.5 89.5 0.7
C4 B:5BU30 2.9 89.8 0.3
C6 B:5BU30 2.9 89.3 0.3
H6 B:5BU30 3.1 0.2 0.3
O4 B:5BU30 3.1 90.1 0.3
N7 B:A29 3.3 96.6 0.3
H3' B:G32 3.3 0.2 0.7
C6 B:C33 3.4 88.1 0.7
C4 B:C33 3.4 89.6 0.7
H3' B:A29 3.4 0.9 0.3
OP2 B:C33 3.5 88.2 0.7
N4 B:C33 3.5 90.1 0.7
C8 B:A29 3.5 96.7 0.3
N7 B:G32 3.6 96.7 0.7
C5 B:A29 3.6 96.8 0.3
OP2 B:5BU30 3.6 89.0 0.3
C8 B:G32 3.7 96.8 0.7
H8 B:A29 3.8 0.0 0.3
H8 B:G32 3.9 0.1 0.7
C5 B:G32 3.9 97.0 0.7
N9 B:A29 3.9 96.9 0.3
C4 B:A29 4.0 96.8 0.3
N9 B:G32 4.1 97.0 0.7
N3 B:5BU30 4.1 88.9 0.3
H2' B:G32 4.2 0.7 0.7
H2' B:A29 4.2 1.0 0.3
C4 B:G32 4.2 96.8 0.7
C6 B:A29 4.2 97.5 0.3
C3' B:G32 4.2 96.0 0.7
O5' B:G32 4.3 0.1 0.7
H41 B:C31 4.3 0.5 0.3
O5' B:A29 4.3 0.1 0.3
H41 B:C34 4.3 0.5 0.7
C3' B:A29 4.4 96.6 0.3
OP2 B:A29 4.4 0.1 0.3
H62 B:A29 4.4 0.7 0.3
OP2 B:G32 4.4 0.1 0.7
N1 B:5BU30 4.4 86.4 0.3
P B:C33 4.6 89.2 0.7
N6 B:A29 4.6 98.1 0.3
C6 B:G32 4.6 97.5 0.7
O5' B:C33 4.6 89.5 0.7
C2' B:G32 4.6 95.6 0.7
C2' B:A29 4.7 95.8 0.3
H5 B:C31 4.7 0.9 0.3
N1 B:C33 4.7 86.5 0.7
N3 B:C33 4.7 88.3 0.7
H5 B:C34 4.7 0.8 0.7
O5' B:5BU30 4.7 89.3 0.3
C2 B:5BU30 4.7 87.2 0.3
P B:5BU30 4.8 90.6 0.3
H3 B:5BU30 4.8 0.7 0.3
C1' B:A29 4.9 97.6 0.3
N3 B:A29 4.9 96.8 0.3
C1' B:G32 4.9 97.4 0.7
O3' B:G32 4.9 93.9 0.7
O6 B:G32 5.0 97.8 0.7

Bromine binding site 4 out of 6 in 4x4t

Go back to Bromine Binding Sites List in 4x4t
Bromine binding site 4 out of 6 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br13

b:0.5
occ:1.00
 BR D:5BU13 0.0 0.5 1.0
C5 D:5BU13 1.9 0.8 1.0
C4 D:5BU13 2.9 0.7 1.0
C6 D:5BU13 2.9 0.6 1.0
H6 D:5BU13 3.1 0.9 1.0
O4 D:5BU13 3.1 0.1 1.0
O4 D:U14 3.2 0.6 1.0
H3' D:G12 3.7 0.7 1.0
N7 D:G12 3.7 0.8 1.0
H5'' D:G12 3.8 0.2 1.0
OP2 D:G12 3.8 0.2 1.0
C8 D:G12 3.8 0.9 1.0
H8 D:G12 3.9 0.1 1.0
C4 D:U14 3.9 0.8 1.0
H5 D:U14 4.0 0.3 1.0
N3 D:5BU13 4.1 0.1 1.0
C5 D:G12 4.2 0.9 1.0
C5 D:U14 4.3 0.3 1.0
N9 D:G12 4.4 0.2 1.0
N1 D:5BU13 4.4 0.8 1.0
C4 D:G12 4.6 0.8 1.0
C3' D:G12 4.6 0.9 1.0
C5' D:G12 4.7 0.0 1.0
C2 D:5BU13 4.7 0.8 1.0
H3 D:5BU13 4.8 1.0 1.0
N3 D:U14 4.9 0.3 1.0
C6 D:G12 4.9 0.6 1.0

Bromine binding site 5 out of 6 in 4x4t

Go back to Bromine Binding Sites List in 4x4t
Bromine binding site 5 out of 6 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br22

b:0.5
occ:1.00
 BR D:5BU22 0.0 0.5 1.0
C5 D:5BU22 1.9 0.2 1.0
C4 D:5BU22 2.9 0.1 1.0
C6 D:5BU22 2.9 0.1 1.0
H6 D:5BU22 3.1 0.1 1.0
O4 D:5BU22 3.1 0.8 1.0
H5 D:C21 3.4 0.5 1.0
C5 D:C21 3.4 0.9 1.0
C4 D:C21 3.5 0.5 1.0
H41 D:C21 3.6 0.6 1.0
N4 D:C21 3.7 0.2 1.0
C6 D:C21 4.0 0.9 1.0
N3 D:5BU22 4.1 0.1 1.0
H42 D:C21 4.2 0.6 1.0
N3 D:C21 4.2 0.3 1.0
H6 D:C21 4.3 0.1 1.0
N1 D:5BU22 4.4 0.6 1.0
H5'' D:5BU22 4.5 0.9 1.0
N1 D:C21 4.6 0.4 1.0
H3' D:C21 4.6 0.6 1.0
H5' D:5BU22 4.6 0.9 1.0
C2 D:C21 4.7 0.3 1.0
C2 D:5BU22 4.7 0.5 1.0
H3 D:5BU22 4.8 0.9 1.0
OP2 D:C21 4.9 0.6 1.0

Bromine binding site 6 out of 6 in 4x4t

Go back to Bromine Binding Sites List in 4x4t
Bromine binding site 6 out of 6 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccacca within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br30

b:1.0
occ:0.50
 BR G:C30 0.0 1.0 0.5
C5 G:C30 1.9 41.7 0.5
N7 G:G8 2.5 41.7 0.5
C4 G:C30 2.9 42.1 0.5
C6 G:C30 3.0 41.5 0.5
O4 G:C30 3.1 42.9 0.5
H6 G:C30 3.1 49.8 0.5
H8 G:G8 3.1 49.9 0.5
C8 G:G8 3.2 41.6 0.5
N7 G:G29 3.6 71.3 0.5
H3' G:G7 3.6 82.7 0.5
OP2 G:G8 3.7 48.4 0.5
N7 G:G7 3.7 69.5 0.5
OP2 G:C30 3.7 48.7 0.5
H3' G:G29 3.7 83.7 0.5
C5 G:G8 3.8 41.5 0.5
C8 G:G29 3.8 70.5 0.5
C5 G:G29 3.9 72.0 0.5
C8 G:G7 3.9 69.0 0.5
H41 G:C31 4.0 64.2 0.5
C5 G:G7 4.0 69.2 0.5
H41 G:C9 4.0 64.3 0.5
H8 G:G29 4.1 84.7 0.5
N3 G:C30 4.1 41.5 0.5
H8 G:G7 4.1 82.8 0.5
N9 G:G7 4.3 67.3 0.5
O6 G:G8 4.3 40.0 0.5
N9 G:G29 4.3 70.8 0.5
C4 G:G29 4.3 70.8 0.5
OP2 G:G7 4.4 69.2 0.5
C4 G:G7 4.4 68.1 0.5
H2' G:G7 4.4 79.8 0.5
C6 G:G29 4.4 73.1 0.5
N1 G:C30 4.4 41.6 0.5
OP2 G:G29 4.4 73.9 0.5
C6 G:G8 4.5 40.4 0.5
H2' G:G29 4.5 82.3 0.5
H62 G:G29 4.5 88.6 0.5
N9 G:G8 4.5 41.6 0.5
C6 G:G7 4.5 69.5 0.5
C3' G:G7 4.6 68.9 0.5
N4 G:C31 4.6 53.5 0.5
C3' G:G29 4.7 69.8 0.5
N6 G:G29 4.7 73.8 0.5
N4 G:C9 4.7 53.6 0.5
H5 G:C31 4.7 63.4 0.5
O5' G:G29 4.7 75.1 0.5
C2 G:C30 4.7 41.6 0.5
O5' G:G8 4.8 47.8 0.5
P G:G8 4.8 48.3 0.5
H3 G:C30 4.8 49.7 0.5
H5 G:C9 4.8 63.4 0.5
C4 G:G8 4.8 41.7 0.5
O5' G:G7 4.8 68.6 0.5
O6 G:G7 4.9 67.2 0.5
P G:C30 4.9 50.1 0.5
O5' G:C30 4.9 47.8 0.5
C2' G:G7 4.9 66.5 0.5
C2' G:G29 5.0 68.6 0.5

Reference:

C.-D.Kuhn, J.E.Wilusz, Y.Zheng, P.A.Beal, L.Joshua-Tor. On-Enzyme Refolding Permits Small Rna and Trna Surveillance By the Cca-Adding Enzyme To Be Published.
Page generated: Wed Jul 10 22:52:00 2024

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