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
|