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Magnesium in PDB 6r5k: Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase

Enzymatic activity of Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase

All present enzymatic activity of Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase:
3.1.13.4;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase (pdb code 6r5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase, PDB code: 6r5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6r5k

Go back to Magnesium Binding Sites List in 6r5k
Magnesium binding site 1 out of 2 in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:0.4
occ:1.00
MG E:MG102 1.3 1.0 1.0
N3 E:A65 2.2 0.7 1.0
C5' E:A66 2.5 0.1 1.0
C1' E:A65 2.5 0.7 1.0
O3' E:A65 2.7 0.7 1.0
O2' E:A65 3.0 0.7 1.0
C4 E:A65 3.0 0.7 1.0
C2' E:A65 3.2 0.7 1.0
N9 E:A65 3.2 0.7 1.0
C2 E:A65 3.3 0.7 1.0
O5' E:A66 3.4 0.1 1.0
O A:LEU1047 3.4 0.4 1.0
O4' E:A65 3.5 0.7 1.0
C3' E:A65 3.5 0.7 1.0
C4' E:A66 3.5 0.1 1.0
P E:A66 3.5 0.1 1.0
C3' E:A66 3.6 0.1 1.0
NE2 A:HIS1015 3.6 0.3 1.0
OP2 E:A66 3.7 0.1 1.0
CA A:SER1048 3.9 0.1 1.0
C2' E:A66 3.9 0.1 1.0
CD2 A:HIS1015 4.0 0.3 1.0
C4' E:A65 4.0 0.7 1.0
O4' E:A66 4.2 0.1 1.0
C A:LEU1047 4.3 0.4 1.0
C5 E:A65 4.4 0.7 1.0
N A:LEU1049 4.4 0.5 1.0
N A:SER1048 4.5 0.1 1.0
CB A:SER1048 4.5 0.1 1.0
N1 E:A65 4.6 0.7 1.0
C8 E:A65 4.6 0.7 1.0
CD2 A:LEU1049 4.6 0.5 1.0
C1' E:A66 4.7 0.1 1.0
OP2 E:A67 4.7 0.0 1.0
C A:SER1048 4.7 0.1 1.0
O A:TYR1046 4.8 0.6 1.0
CE1 A:HIS1015 4.9 0.3 1.0
OP1 E:A66 4.9 0.1 1.0
O3' E:A66 4.9 0.1 1.0

Magnesium binding site 2 out of 2 in 6r5k

Go back to Magnesium Binding Sites List in 6r5k
Magnesium binding site 2 out of 2 in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg102

b:1.0
occ:1.00
MG E:MG101 1.3 0.4 1.0
O2' E:A65 2.1 0.7 1.0
N3 E:A65 2.2 0.7 1.0
O A:LEU1047 2.6 0.4 1.0
CA A:SER1048 2.6 0.1 1.0
C1' E:A65 2.7 0.7 1.0
C2' E:A65 2.8 0.7 1.0
C4 E:A65 2.9 0.7 1.0
O3' E:A65 3.0 0.7 1.0
N9 E:A65 3.1 0.7 1.0
C A:LEU1047 3.2 0.4 1.0
C2 E:A65 3.2 0.7 1.0
N A:SER1048 3.2 0.1 1.0
CB A:SER1048 3.3 0.1 1.0
C3' E:A65 3.5 0.7 1.0
NE2 A:HIS1015 3.7 0.3 1.0
C A:SER1048 3.7 0.1 1.0
N A:LEU1049 3.7 0.5 1.0
C5' E:A66 3.8 0.1 1.0
O4' E:A65 3.9 0.7 1.0
O A:TYR1046 4.1 0.6 1.0
C5 E:A65 4.1 0.7 1.0
P E:A66 4.2 0.1 1.0
OP2 E:A66 4.2 0.1 1.0
N1 E:A65 4.3 0.7 1.0
C8 E:A65 4.4 0.7 1.0
C4' E:A65 4.4 0.7 1.0
CD2 A:HIS1015 4.4 0.3 1.0
O5' E:A66 4.4 0.1 1.0
CA A:LEU1047 4.6 0.4 1.0
OG A:SER1048 4.7 0.1 1.0
CE1 A:HIS1015 4.7 0.3 1.0
C6 E:A65 4.7 0.7 1.0
C4' E:A66 4.8 0.1 1.0
C3' E:A66 4.8 0.1 1.0
CD2 A:LEU1049 4.8 0.5 1.0
O A:SER1048 4.9 0.1 1.0
C A:TYR1046 4.9 0.6 1.0
N7 E:A65 4.9 0.7 1.0
N A:LEU1047 5.0 0.4 1.0
C2' E:A66 5.0 0.1 1.0

Reference:

I.B.Schafer, M.Yamashita, J.M.Schuller, S.Schussler, P.Reichelt, M.Strauss, E.Conti. Molecular Basis For Poly(A) Rnp Architecture and Recognition By the PAN2-PAN3 Deadenylase. Cell V. 177 1619 2019.
ISSN: ISSN 1097-4172
PubMed: 31104843
DOI: 10.1016/J.CELL.2019.04.013
Page generated: Tue Oct 1 16:37:30 2024

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