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Magnesium in PDB 5vaj: Bhrnase H - Amide-Rna/Dna Complex

Enzymatic activity of Bhrnase H - Amide-Rna/Dna Complex

All present enzymatic activity of Bhrnase H - Amide-Rna/Dna Complex:
3.1.26.4;

Protein crystallography data

The structure of Bhrnase H - Amide-Rna/Dna Complex, PDB code: 5vaj was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.90 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.180, 37.513, 93.863, 90.00, 121.65, 90.00
R / Rfree (%) 16.6 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bhrnase H - Amide-Rna/Dna Complex (pdb code 5vaj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bhrnase H - Amide-Rna/Dna Complex, PDB code: 5vaj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5vaj

Go back to Magnesium Binding Sites List in 5vaj
Magnesium binding site 1 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:21.8
occ:1.00
OD1 A:ASN132 2.2 15.6 1.0
OD1 A:ASP71 2.2 19.9 1.0
OE2 A:GLU109 2.3 14.1 1.0
O A:HOH336 2.7 16.0 1.0
OP1 C:URU10 2.8 17.2 1.0
OE1 A:GLU109 2.8 14.9 1.0
CD A:GLU109 2.9 14.2 1.0
CG A:ASN132 3.0 15.6 1.0
O3' C:A9 3.0 14.1 1.0
CG A:ASP71 3.3 21.9 1.0
ND2 A:ASN132 3.3 14.7 1.0
P C:URU10 3.5 16.0 1.0
OD2 A:ASP71 3.9 24.8 1.0
C5' C:URU10 4.0 14.5 1.0
MG A:MG207 4.2 23.6 1.0
O2' C:A9 4.2 14.4 1.0
O5' C:URU10 4.3 16.0 1.0
C3' C:A9 4.3 14.6 1.0
N A:VAL72 4.3 15.9 1.0
CB A:ASP71 4.4 19.2 1.0
CA A:ASP71 4.4 18.5 1.0
CB A:ASN132 4.4 14.4 1.0
CG A:GLU109 4.4 13.8 1.0
C4' C:A9 4.7 14.7 1.0
N A:ASN132 4.7 15.0 1.0
C2' C:A9 4.8 14.2 1.0
OP2 C:URU10 4.8 15.7 1.0
CA A:ASN132 4.9 14.8 1.0
N A:SER133 4.9 14.9 1.0
C A:ASN132 4.9 15.6 1.0
C A:ASP71 4.9 16.7 1.0
CG2 A:VAL72 5.0 14.6 0.5

Magnesium binding site 2 out of 4 in 5vaj

Go back to Magnesium Binding Sites List in 5vaj
Magnesium binding site 2 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:23.6
occ:1.00
OP1 C:URU10 2.1 17.2 1.0
OD2 A:ASP71 2.1 24.8 1.0
O A:HOH334 2.3 27.6 1.0
OD1 A:ASP192 2.4 31.0 1.0
CG A:ASP71 3.0 21.9 1.0
OD1 A:ASP71 3.2 19.9 1.0
CG A:ASP192 3.4 32.8 1.0
P C:URU10 3.4 16.0 1.0
OP2 C:URU10 4.0 15.7 1.0
CA A:ASP192 4.0 26.0 1.0
CB A:ASP192 4.0 29.6 1.0
MG A:MG206 4.2 21.8 1.0
ND2 A:ASN132 4.2 14.7 1.0
O5' C:URU10 4.3 16.0 1.0
O A:VAL72 4.4 16.3 1.0
N A:TYR193 4.4 26.1 1.0
OD2 A:ASP192 4.4 38.2 1.0
CB A:ASP71 4.5 19.2 1.0
CG2 A:ILE189 4.5 21.9 1.0
O A:HOH345 4.6 17.4 0.5
O3' C:A9 4.6 14.1 1.0
C5' C:URU10 4.7 14.5 1.0
O A:TYR193 4.7 40.8 1.0
C A:ASP192 4.8 27.1 1.0

Magnesium binding site 3 out of 4 in 5vaj

Go back to Magnesium Binding Sites List in 5vaj
Magnesium binding site 3 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:32.0
occ:1.00
OD1 B:ASP71 2.0 24.1 1.0
OE2 B:GLU109 2.3 23.2 1.0
OD1 B:ASN132 2.5 15.0 1.0
OP1 C:C5 2.7 18.1 1.0
O B:HOH326 2.8 14.9 1.0
OE1 B:GLU109 3.0 18.9 1.0
CD B:GLU109 3.0 20.5 1.0
CG B:ASP71 3.1 25.1 1.0
CG B:ASN132 3.2 13.7 1.0
O3' C:A4 3.2 16.1 1.0
ND2 B:ASN132 3.2 13.1 1.0
P C:C5 3.5 17.6 1.0
OD2 B:ASP71 3.8 27.0 1.0
C5' C:C5 3.9 17.9 1.0
N B:VAL72 4.1 20.8 1.0
MG B:MG204 4.1 34.5 1.0
CB B:ASP71 4.2 22.4 1.0
CA B:ASP71 4.2 21.5 1.0
O5' C:C5 4.3 18.0 1.0
O2' C:A4 4.3 14.8 1.0
CG1 B:VAL72 4.4 24.9 1.0
C3' C:A4 4.4 14.7 1.0
CG B:GLU109 4.5 18.1 1.0
CB B:ASN132 4.6 13.0 1.0
O B:VAL72 4.8 20.0 1.0
C B:ASP71 4.8 21.2 1.0
C4' C:A4 4.8 14.1 1.0
N B:ASN132 4.8 12.0 1.0
OP2 C:C5 4.8 15.2 1.0
O B:VAL70 4.9 19.6 1.0
CG2 B:ILE189 4.9 21.5 1.0
C2' C:A4 5.0 14.8 1.0

Magnesium binding site 4 out of 4 in 5vaj

Go back to Magnesium Binding Sites List in 5vaj
Magnesium binding site 4 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:34.5
occ:1.00
OD1 B:ASP192 2.2 45.6 1.0
OD2 B:ASP71 2.2 27.0 1.0
OP1 C:C5 2.2 18.1 1.0
O B:HOH310 2.4 31.8 1.0
CG B:ASP71 3.1 25.1 1.0
CG B:ASP192 3.3 50.5 1.0
OD1 B:ASP71 3.3 24.1 1.0
P C:C5 3.4 17.6 1.0
CB B:ASP192 3.8 48.4 1.0
O5' C:C5 3.9 18.0 1.0
CA B:ASP192 3.9 45.2 1.0
OP2 C:C5 3.9 15.2 1.0
O B:VAL72 4.0 20.0 1.0
MG B:MG203 4.1 32.0 1.0
OD2 B:ASP192 4.3 62.3 1.0
OE2 B:GLU188 4.3 49.4 0.5
N B:TYR193 4.3 52.2 1.0
C5' C:C5 4.3 17.9 1.0
OP2 C:C6 4.5 19.2 1.0
CB B:ASP71 4.5 22.4 1.0
ND2 B:ASN132 4.6 13.1 1.0
CG2 B:ILE189 4.6 21.5 1.0
C B:ASP192 4.7 51.0 1.0
O3' C:A4 4.7 16.1 1.0
CG B:GLU188 4.9 35.8 0.5
N B:ASP192 5.0 41.0 1.0

Reference:

D.Mutisya, T.Hardcastle, S.K.Cheruiyot, P.S.Pallan, S.D.Kennedy, M.Egli, M.L.Kelley, A.V.B.Smith, E.Rozners. Amide Linkages Mimic Phosphates in Rna Interactions with Proteins and Are Well Tolerated in the Guide Strand of Short Interfering Rnas. Nucleic Acids Res. V. 45 8142 2017.
ISSN: ESSN 1362-4962
PubMed: 28854734
DOI: 10.1093/NAR/GKX558
Page generated: Mon Sep 30 06:07:40 2024

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