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Magnesium in PDB 3uld: High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant

Enzymatic activity of High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant

All present enzymatic activity of High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant:
3.1.26.4;

Protein crystallography data

The structure of High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant, PDB code: 3uld was solved by J.H.Gan, R.Abdur, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.301, 37.672, 62.378, 90.00, 96.76, 90.00
R / Rfree (%) 19.4 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant (pdb code 3uld). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant, PDB code: 3uld:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3uld

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Magnesium binding site 1 out of 4 in the High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:30.3
occ:0.40
 O A:HOH301 1.6 17.1 0.6
OD1 A:ASN132 2.1 16.6 1.0
OE2 A:GLU109 2.1 25.5 1.0
OD1 A:ASP71 2.2 19.6 0.4
ND2 A:ASN132 2.5 18.5 1.0
CG A:ASN132 2.6 15.0 1.0
O3' B:A6 2.7 18.9 1.0
O A:HOH302 3.0 18.3 1.0
CD A:GLU109 3.0 21.6 1.0
O A:HOH383 3.2 49.2 1.0
CG A:ASP71 3.2 18.5 0.4
OE1 A:GLU109 3.3 17.6 1.0
OD2 A:ASP71 3.7 20.4 0.4
C3' B:A6 3.9 18.3 1.0
O2' B:A6 3.9 18.0 1.0
MG A:MG202 3.9 31.2 0.4
CB A:ASN132 4.1 14.3 1.0
C4' B:A6 4.1 17.5 1.0
CG1 A:VAL72 4.3 22.1 1.0
CB A:ASP71 4.4 17.4 0.4
CG A:GLU109 4.4 15.9 1.0
N A:VAL72 4.5 18.9 1.0
C2' B:A6 4.5 17.4 1.0
CB A:ASP71 4.7 18.3 0.6
CA A:ASP71 4.7 17.1 0.4
CA A:ASP71 4.7 17.5 0.6
N A:ASN132 4.7 12.5 1.0
CA A:ASN132 4.7 13.7 1.0
C A:ASN132 4.8 14.7 1.0
C5' B:A6 4.8 18.7 1.0
CG2 A:ILE189 4.9 20.0 1.0
N A:SER133 4.9 13.8 1.0
CB A:SER133 5.0 15.4 1.0

Magnesium binding site 2 out of 4 in 3uld

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Magnesium binding site 2 out of 4 in the High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:31.2
occ:0.40
 O A:HOH383 1.8 49.2 1.0
OD2 A:ASP71 2.0 20.4 0.4
O A:HOH366 2.0 27.7 1.0
OD2 A:ASP192 2.5 44.2 1.0
CG A:ASP71 2.9 18.5 0.4
O A:HOH301 3.1 17.1 0.6
OD1 A:ASP71 3.2 19.6 0.4
O A:VAL72 3.6 18.7 1.0
CG A:ASP192 3.6 42.7 1.0
OD2 A:ASP71 3.7 26.2 0.6
MG A:MG201 3.9 30.3 0.4
CA A:ASP192 4.0 40.5 1.0
O3' B:A6 4.1 18.9 1.0
CB A:ASP71 4.2 17.4 0.4
ND2 A:ASN132 4.3 18.5 1.0
CB A:ASP192 4.3 40.9 1.0
CB A:ASP71 4.3 18.3 0.6
N A:TYR193 4.4 42.1 1.0
CG A:ASP71 4.4 20.6 0.6
OD1 A:ASP192 4.7 43.9 1.0
C A:ASP192 4.8 41.3 1.0
C A:VAL72 4.8 19.6 1.0
CG2 A:ILE189 4.8 20.0 1.0
N A:VAL72 4.9 18.9 1.0
N A:ASP192 5.0 38.6 1.0

Magnesium binding site 3 out of 4 in 3uld

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Magnesium binding site 3 out of 4 in the High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:48.7
occ:1.00
 O A:HOH338 1.9 37.4 1.0
O A:HOH356 1.9 33.9 1.0
NH2 A:ARG118 3.6 25.0 1.0
NE1 A:TRP168 3.6 18.8 1.0
O A:HOH319 3.7 27.1 1.0
O A:HOH379 3.9 36.0 1.0
NE A:ARG118 4.1 24.0 1.0
CD1 A:TRP168 4.2 18.0 1.0
CZ A:ARG118 4.3 25.7 1.0
OE1 A:GLU122 4.4 37.7 1.0
NE2 A:HIS172 4.7 21.4 1.0
CE2 A:TRP168 4.7 18.7 1.0
O A:HOH367 4.8 42.0 1.0
O A:HOH359 4.8 45.6 1.0
CG A:GLU122 5.0 24.9 1.0

Magnesium binding site 4 out of 4 in 3uld

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Magnesium binding site 4 out of 4 in the High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High Resolution Structure of Dna/Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:42.2
occ:1.00
 O A:HOH303 1.7 33.7 1.0
OH A:TYR83 3.0 19.7 1.0
NH1 A:ARG97 3.7 30.0 1.0
CD A:ARG97 3.8 25.2 1.0
O A:HOH325 3.8 24.5 1.0
CZ A:TYR83 4.0 16.9 1.0
CE2 A:TYR83 4.1 16.1 1.0
CD2 A:LEU161 4.2 18.5 1.0
O A:HOH310 4.2 16.6 1.0
CD1 A:LEU161 4.3 17.9 1.0
O A:HOH309 4.3 32.8 1.0
CZ A:ARG97 4.4 29.7 1.0
NE A:ARG97 4.4 28.4 1.0
CG A:ARG97 4.6 21.6 1.0
CD1 A:LEU111 4.6 12.4 1.0
CG A:LEU161 4.6 14.7 1.0
CB A:LEU111 4.7 10.5 1.0
CB A:LEU161 4.7 14.3 1.0
CD2 A:LEU111 4.9 12.2 1.0
CG A:LEU111 5.0 10.0 1.0

Reference:

J.H.Gan, R.Abdur, Z.Huang. Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N To Be Published.
Page generated: Mon Dec 14 08:56:55 2020

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