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Magnesium in PDB 6bda: Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex)

Protein crystallography data

The structure of Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex), PDB code: 6bda was solved by C.Brown, K.Zhang, M.Laforet, T.Mcmurrough, G.B.Gloor, D.R.Edgell, M.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.28 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.690, 68.980, 161.720, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) (pdb code 6bda). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex), PDB code: 6bda:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6bda

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Magnesium binding site 1 out of 6 in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:24.6
occ:1.00
 OP3 C:DG15 2.0 21.2 1.0
OE2 A:GLU22 2.1 25.1 1.0
OP1 D:DT15 2.1 24.6 1.0
O C:HOH207 2.1 20.4 1.0
O A:HOH541 2.2 19.2 1.0
O A:GLY177 2.3 18.6 1.0
CD A:GLU22 3.1 19.7 1.0
P C:DG15 3.1 26.9 1.0
OP2 C:DG15 3.2 27.5 1.0
C A:GLY177 3.3 15.2 1.0
OE1 A:GLU22 3.4 21.9 1.0
P D:DT15 3.6 23.6 1.0
CA A:GLY177 3.6 16.1 1.0
MG C:MG101 3.7 21.0 1.0
O5' C:DG15 3.9 24.9 1.0
O A:HOH557 4.0 24.5 1.0
O3' D:DA14 4.1 24.0 1.0
OP1 C:DG15 4.2 26.1 1.0
C5' D:DT15 4.3 23.3 1.0
O C:HOH202 4.3 34.0 1.0
CG A:GLU22 4.4 16.4 1.0
O5' D:DT15 4.4 19.6 1.0
C4' D:DT15 4.4 22.9 1.0
N A:GLU178 4.5 13.2 1.0
OE2 A:GLU178 4.5 19.1 1.0
OP2 D:DT15 4.5 21.2 1.0
O3' B:DC14 4.6 15.8 1.0
O A:SER176 4.6 17.8 1.0
C5' C:DG15 4.6 20.6 1.0
N A:GLY177 4.9 14.5 1.0

Magnesium binding site 2 out of 6 in 6bda

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Magnesium binding site 2 out of 6 in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.7
occ:1.00
 OP2 E:DA16 2.0 23.8 1.0
OP1 B:DC14 2.1 18.7 1.0
OE1 A:GLU178 2.1 16.5 1.0
O A:HOH544 2.1 19.0 1.0
O D:HOH109 2.2 16.9 1.0
O A:ALA21 2.2 16.2 1.0
CD A:GLU178 3.1 18.3 1.0
P E:DA16 3.2 33.9 1.0
C A:ALA21 3.3 14.6 1.0
OE2 A:GLU178 3.4 19.1 1.0
P B:DC14 3.5 26.5 1.0
MG B:MG102 3.6 17.0 1.0
OP1 E:DA16 3.7 31.2 1.0
CA A:ALA21 3.8 16.7 1.0
OE1 A:GLN204 4.1 18.5 1.0
O5' E:DA16 4.1 33.2 1.0
O3' B:DT13 4.2 22.2 1.0
O3' D:DT15 4.2 26.3 1.0
NE2 A:GLN204 4.2 11.2 1.0
OP3 E:DA16 4.2 30.0 1.0
OP2 B:DC14 4.3 18.6 1.0
OE1 A:GLU22 4.3 21.9 1.0
C5' B:DC14 4.4 15.7 1.0
CG A:GLU178 4.4 16.0 1.0
N A:GLU22 4.4 14.4 1.0
O5' B:DC14 4.5 18.2 1.0
O A:ASP20 4.5 16.9 1.0
CB A:ALA21 4.5 14.6 1.0
CD A:GLN204 4.5 18.6 1.0
C4' B:DC14 4.6 19.5 1.0
C5' E:DA16 4.8 27.1 1.0
CA A:GLU22 4.8 17.6 1.0
NZ A:LYS103 4.9 27.3 1.0
N A:ALA21 5.0 14.9 1.0
O A:HOH541 5.0 19.2 1.0
O B:HOH212 5.0 26.1 1.0

Magnesium binding site 3 out of 6 in 6bda

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Magnesium binding site 3 out of 6 in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:17.7
occ:1.00
 O E:HOH110 2.3 28.7 1.0
O2 B:DT12 2.5 26.2 1.0
O B:HOH217 2.6 27.6 1.0
O B:HOH211 2.6 19.9 1.0
O2 D:DT15 2.8 23.9 1.0
O4' B:DT13 2.9 21.6 1.0
O2 B:DT13 3.4 17.6 1.0
C2 B:DT12 3.7 28.9 1.0
C1' B:DT13 3.7 19.5 1.0
C4' B:DT13 3.8 20.4 1.0
C2 B:DT13 3.9 20.1 1.0
MG B:MG102 3.9 17.0 1.0
C2 D:DT15 4.0 25.6 1.0
N1 B:DT13 4.1 22.9 1.0
C2 D:DA14 4.1 23.6 1.0
C2 B:DA11 4.1 26.5 1.0
C1' B:DT12 4.2 30.3 1.0
N1 B:DT12 4.5 30.2 1.0
O4' B:DT12 4.5 29.1 1.0
C5' B:DT13 4.6 24.2 1.0
C1' D:DT15 4.6 23.5 1.0
N3 D:DA14 4.7 24.1 1.0
N3 B:DT12 4.7 26.6 1.0
N3 B:DA11 4.7 28.2 1.0
O4' E:DA16 4.8 33.2 1.0
N1 D:DT15 4.8 24.4 1.0
N1 D:DA14 4.8 23.5 1.0
N3 B:DT13 4.8 20.8 1.0
N1 B:DA11 4.9 26.6 1.0
N3 D:DT15 4.9 24.5 1.0
O D:HOH122 4.9 22.0 1.0
C3' B:DT13 4.9 21.4 1.0
O3' B:DT13 5.0 22.2 1.0

Magnesium binding site 4 out of 6 in 6bda

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Magnesium binding site 4 out of 6 in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:17.0
occ:1.00
 OP2 E:DA16 2.6 23.8 1.0
O E:HOH110 2.8 28.7 1.0
O D:HOH109 2.8 16.9 1.0
O B:HOH211 2.8 19.9 1.0
O3' B:DT13 2.9 22.2 1.0
O3' D:DT15 3.0 26.3 1.0
OP1 B:DC14 3.3 18.7 1.0
OP3 E:DA16 3.4 30.0 1.0
P E:DA16 3.5 33.9 1.0
MG A:MG402 3.6 18.7 1.0
P B:DC14 3.7 26.5 1.0
C4' B:DT13 3.8 20.4 1.0
O4' B:DT13 3.9 21.6 1.0
MG B:MG101 3.9 17.7 1.0
C3' B:DT13 3.9 21.4 1.0
C5' E:DA16 4.0 27.1 1.0
C4' B:DC14 4.1 19.5 1.0
C1' B:DT13 4.2 19.5 1.0
O5' E:DA16 4.2 33.2 1.0
C3' D:DT15 4.2 24.6 1.0
O4' B:DC14 4.3 20.7 1.0
C4' E:DA16 4.3 34.6 1.0
O4' E:DA16 4.5 33.2 1.0
C1' D:DT15 4.5 23.5 1.0
C2' D:DT15 4.6 24.9 1.0
O5' B:DC14 4.6 18.2 1.0
C2' B:DT13 4.7 19.1 1.0
C5' B:DC14 4.8 15.7 1.0
O A:ALA21 4.8 16.2 1.0
O3' B:DC14 4.8 15.8 1.0
OP1 E:DA16 4.8 31.2 1.0
O D:HOH122 4.9 22.0 1.0
OP2 B:DC14 4.9 18.6 1.0
C4' D:DT15 4.9 22.9 1.0
O2 D:DT15 5.0 23.9 1.0
O2 B:DT13 5.0 17.6 1.0

Magnesium binding site 5 out of 6 in 6bda

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Magnesium binding site 5 out of 6 in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:21.0
occ:1.00
 OP3 C:DG15 2.5 21.2 1.0
O D:HOH122 2.6 22.0 1.0
O C:HOH226 2.7 22.8 1.0
O3' D:DA14 3.0 24.0 1.0
O A:HOH541 3.1 19.2 1.0
O3' B:DC14 3.1 15.8 1.0
OP1 C:DG15 3.5 26.1 1.0
P C:DG15 3.6 26.9 1.0
O4' D:DA14 3.6 24.7 1.0
OP1 D:DT15 3.6 24.6 1.0
MG A:MG401 3.7 24.6 1.0
C4' D:DA14 3.8 26.0 1.0
C5' C:DG15 3.9 20.6 1.0
P D:DT15 4.0 23.6 1.0
C3' D:DA14 4.0 24.5 1.0
C1' D:DA14 4.0 23.2 1.0
O4' D:DT15 4.1 20.3 1.0
C4' D:DT15 4.2 22.9 1.0
O5' C:DG15 4.2 24.9 1.0
O D:HOH116 4.2 25.7 1.0
C3' B:DC14 4.4 19.7 1.0
O C:HOH223 4.4 26.1 1.0
O5' D:DT15 4.5 19.6 1.0
C4' C:DG15 4.5 17.8 1.0
C2' D:DA14 4.7 21.2 1.0
O4' C:DG15 4.7 19.0 1.0
C2' B:DC14 4.7 19.8 1.0
OP2 C:DG15 4.8 27.5 1.0
C5' D:DT15 4.8 23.3 1.0
O A:GLY177 4.8 18.6 1.0
C1' B:DC14 4.9 18.9 1.0
O B:HOH211 5.0 19.9 1.0

Magnesium binding site 6 out of 6 in 6bda

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Magnesium binding site 6 out of 6 in the Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:26.4
occ:1.00
 OP1 C:DG15 2.2 26.1 1.0
OP1 C:DA16 2.2 29.4 1.0
O C:HOH214 2.2 28.4 1.0
O C:HOH233 2.3 33.6 1.0
O A:HOH719 2.3 28.5 1.0
O C:HOH223 2.4 26.1 1.0
P C:DG15 3.4 26.9 1.0
P C:DA16 3.6 19.2 1.0
O C:HOH234 3.7 22.6 1.0
OP2 C:DG15 3.9 27.5 1.0
O3' C:DG15 4.0 29.2 1.0
O C:HOH202 4.1 34.0 1.0
C5' C:DA16 4.1 19.5 1.0
NZ A:LYS52 4.1 40.0 1.0
C4' C:DG15 4.1 17.8 1.0
O5' C:DG15 4.2 24.9 1.0
O5' C:DA16 4.3 20.6 1.0
O A:HOH534 4.4 23.3 1.0
C4' D:DA14 4.5 26.0 1.0
OP3 C:DG15 4.5 21.2 1.0
C5' D:DA14 4.5 23.0 1.0
C3' C:DG15 4.6 20.2 1.0
OP2 C:DA16 4.7 20.1 1.0
C5' C:DG15 4.7 20.6 1.0
O D:HOH118 4.7 28.5 1.0
CE A:LYS52 4.8 29.3 1.0
O D:HOH114 4.8 40.8 1.0
O C:HOH226 5.0 22.8 1.0

Reference:

M.Laforet, T.Mcmurrough, C.Brown, K.Zhang, M.Junop, G.B.Gloor, D.R.Edgell. Wild-Type I-Onui Bound to A3G Substrate (Post-Cleavage Complex) To Be Published.
Page generated: Mon Sep 30 19:43:20 2024

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