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Magnesium in PDB 3nh1: Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site

Protein crystallography data

The structure of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site, PDB code: 3nh1 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.38 / 2.11
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 46.482, 46.482, 315.877, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site (pdb code 3nh1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site, PDB code: 3nh1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3nh1

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Magnesium binding site 1 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg216

b:37.0
occ:1.00
 OP1 E:DG7 2.3 22.8 1.0
OD2 A:ASP186 2.3 35.0 1.0
OE1 A:GLU25 2.4 40.8 1.0
OD2 A:ASP23 3.1 27.2 1.0
OD1 A:ASP23 3.2 22.9 1.0
CG A:ASP186 3.3 32.4 1.0
CD A:GLU25 3.4 32.6 1.0
MG E:MG8 3.4 34.3 1.0
CG A:ASP23 3.5 25.4 1.0
OE2 A:GLU25 3.6 30.5 1.0
O E:HOH131 3.6 31.2 1.0
CB A:ASP186 3.6 26.8 1.0
P E:DG7 3.7 26.2 1.0
CA A:HIS181 3.9 43.4 1.0
C A:HIS181 4.1 43.5 1.0
O A:HIS181 4.4 49.4 1.0
OP2 E:DG7 4.4 27.1 1.0
OD1 A:ASP186 4.4 34.5 1.0
O A:SER182 4.5 30.7 1.0
N A:HIS181 4.5 40.4 1.0
O5' E:DG7 4.5 26.0 1.0
O A:VAL24 4.5 22.6 1.0
O3' E:DG6 4.6 27.2 1.0
ND1 A:HIS181 4.6 43.0 1.0
O A:HOH225 4.7 24.1 1.0
N A:SER182 4.7 41.0 1.0
C A:SER182 4.7 32.2 1.0
O E:HOH68 4.7 28.1 1.0
CG A:GLU25 4.7 29.0 1.0
C5' E:DG7 4.8 21.5 1.0
CB A:HIS181 4.9 44.8 1.0
N A:ALA183 4.9 31.5 1.0
CA A:ALA183 5.0 31.2 1.0
CB A:ASP23 5.0 21.8 1.0

Magnesium binding site 2 out of 8 in 3nh1

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Magnesium binding site 2 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg216

b:33.9
occ:1.00
 OD2 B:ASP186 2.2 31.2 1.0
OP1 F:DG7 2.3 23.8 1.0
OE1 B:GLU25 2.3 35.9 1.0
CD B:GLU25 3.2 32.4 1.0
OD1 B:ASP23 3.2 26.5 1.0
CG B:ASP186 3.3 32.9 1.0
OD2 B:ASP23 3.3 29.2 1.0
MG F:MG8 3.4 32.5 1.0
OE2 B:GLU25 3.4 29.2 1.0
CG B:ASP23 3.6 29.5 1.0
P F:DG7 3.7 26.1 1.0
CB B:ASP186 3.7 29.2 1.0
CA B:HIS181 3.7 40.2 1.0
C B:HIS181 3.9 38.1 1.0
O F:HOH308 4.0 29.6 1.0
O B:HIS181 4.1 45.4 1.0
OD1 B:ASP186 4.4 39.0 1.0
O B:SER182 4.4 30.3 1.0
OP2 F:DG7 4.5 27.1 1.0
N B:SER182 4.5 35.9 1.0
O5' F:DG7 4.5 24.6 1.0
O B:VAL24 4.5 22.9 1.0
O B:HOH230 4.5 23.7 1.0
CG B:GLU25 4.5 27.4 1.0
ND1 B:HIS181 4.5 41.9 1.0
N B:HIS181 4.6 37.6 1.0
C5' F:DG7 4.6 21.4 1.0
O3' F:DG6 4.6 24.2 1.0
C B:SER182 4.6 32.2 1.0
CB B:HIS181 4.6 42.9 1.0
O F:HOH173 4.7 27.6 1.0
N B:ALA183 5.0 32.5 1.0

Magnesium binding site 3 out of 8 in 3nh1

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Magnesium binding site 3 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg216

b:41.6
occ:1.00
 OP1 G:DG7 2.3 22.3 1.0
OE1 C:GLU25 2.4 40.8 1.0
OD2 C:ASP186 2.5 35.3 1.0
OD2 C:ASP23 2.7 30.9 1.0
MG G:MG8 3.1 30.3 1.0
OD1 C:ASP23 3.2 26.3 1.0
CG C:ASP23 3.3 27.5 1.0
CD C:GLU25 3.3 37.0 1.0
CG C:ASP186 3.4 33.8 1.0
OE2 C:GLU25 3.6 31.4 1.0
CB C:ASP186 3.7 24.8 1.0
P G:DG7 3.8 27.5 1.0
O C:HOH279 4.0 29.8 1.0
CA C:HIS181 4.0 44.1 1.0
O C:VAL24 4.2 21.1 1.0
C C:HIS181 4.3 43.2 1.0
O C:HOH232 4.4 30.5 1.0
O3' G:DG6 4.4 23.6 1.0
O C:SER182 4.4 36.4 1.0
O5' G:DG7 4.5 27.1 1.0
C C:SER182 4.6 34.5 1.0
N C:SER182 4.6 44.8 1.0
OD1 C:ASP186 4.6 42.5 1.0
CG C:GLU25 4.6 34.9 1.0
C5' G:DG7 4.6 23.8 1.0
N C:HIS181 4.6 44.8 1.0
O C:HIS181 4.7 43.6 1.0
OP2 G:DG7 4.7 31.4 1.0
CB C:ASP23 4.8 23.7 1.0
N C:ALA183 4.8 31.4 1.0
CA C:ALA183 4.8 34.7 1.0
O G:HOH126 5.0 32.4 1.0

Magnesium binding site 4 out of 8 in 3nh1

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Magnesium binding site 4 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg216

b:39.2
occ:1.00
 OP1 H:DG7 2.3 21.8 1.0
OE1 D:GLU25 2.4 39.6 1.0
OD2 D:ASP186 2.5 33.1 1.0
OD2 D:ASP23 2.9 28.7 1.0
MG H:MG8 3.3 30.1 1.0
OD1 D:ASP23 3.4 26.2 1.0
CD D:GLU25 3.4 35.6 1.0
CG D:ASP186 3.5 32.3 1.0
CG D:ASP23 3.5 29.6 1.0
OE2 D:GLU25 3.6 30.6 1.0
P H:DG7 3.7 28.1 1.0
CB D:ASP186 3.7 22.8 1.0
O D:HOH276 3.9 30.1 1.0
CA D:HIS181 4.0 45.9 1.0
C D:HIS181 4.2 43.8 1.0
O D:VAL24 4.3 21.8 1.0
N D:SER182 4.4 42.6 1.0
O D:HOH224 4.4 26.8 1.0
O3' H:DG6 4.4 23.4 1.0
N D:HIS181 4.6 47.0 1.0
O D:SER182 4.6 33.9 1.0
C5' H:DG7 4.6 24.0 1.0
O5' H:DG7 4.6 28.3 1.0
OD1 D:ASP186 4.6 41.4 1.0
OP2 H:DG7 4.6 31.1 1.0
C D:SER182 4.6 32.9 1.0
CG D:GLU25 4.7 29.5 1.0
O H:HOH250 4.8 30.1 1.0
O D:HIS181 4.8 40.6 1.0
N D:ALA183 4.9 29.4 1.0
ND1 D:HIS181 4.9 55.2 1.0
CB D:ASP23 5.0 20.6 1.0

Magnesium binding site 5 out of 8 in 3nh1

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Magnesium binding site 5 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg8

b:34.3
occ:1.00
 OD1 A:ASP23 2.3 22.9 1.0
O A:HOH225 2.4 24.1 1.0
O E:HOH131 2.4 31.2 1.0
OP1 E:DG7 2.5 22.8 1.0
O A:HOH336 2.5 23.2 1.0
O3' E:DG6 2.7 27.2 1.0
P E:DG7 3.2 26.2 1.0
MG A:MG216 3.4 37.0 1.0
CG A:ASP23 3.5 25.4 1.0
O A:HOH246 3.7 25.1 1.0
C3' E:DG6 3.9 23.9 1.0
O A:HOH226 4.0 26.2 1.0
OD1 A:ASP125 4.1 27.4 1.0
OD2 A:ASP23 4.1 27.2 1.0
C5' E:DG7 4.2 21.5 1.0
O5' E:DG7 4.2 26.0 1.0
C2' E:DG6 4.3 21.2 1.0
C4' E:DG6 4.3 21.6 1.0
O A:VAL24 4.3 22.6 1.0
OP2 E:DG7 4.4 27.1 1.0
O E:HOH68 4.5 28.1 1.0
CB A:ASP23 4.6 21.8 1.0
OD2 A:ASP125 4.7 21.8 1.0
CG A:ASP125 4.8 22.5 1.0
O A:HIS120 4.8 22.1 1.0
OD2 A:ASP186 4.9 35.0 1.0
OE1 A:GLU25 4.9 40.8 1.0
N A:VAL24 5.0 23.8 1.0

Magnesium binding site 6 out of 8 in 3nh1

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Magnesium binding site 6 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg8

b:32.5
occ:1.00
 OD1 B:ASP23 2.3 26.5 1.0
O F:HOH308 2.4 29.6 1.0
O B:HOH230 2.4 23.7 1.0
OP1 F:DG7 2.6 23.8 1.0
O B:HOH271 2.6 24.3 1.0
O3' F:DG6 2.7 24.2 1.0
P F:DG7 3.3 26.1 1.0
MG B:MG216 3.4 33.9 1.0
O B:HOH243 3.5 29.7 1.0
CG B:ASP23 3.5 29.5 1.0
O B:HOH220 4.0 18.7 1.0
C3' F:DG6 4.0 21.5 1.0
OD1 B:ASP125 4.2 25.2 1.0
OD2 B:ASP23 4.2 29.2 1.0
O5' F:DG7 4.3 24.6 1.0
C5' F:DG7 4.3 21.4 1.0
C2' F:DG6 4.4 24.0 1.0
O B:VAL24 4.4 22.9 1.0
C4' F:DG6 4.4 22.4 1.0
OP2 F:DG7 4.5 27.1 1.0
CB B:ASP23 4.6 21.6 1.0
O F:HOH173 4.6 27.6 1.0
OD2 B:ASP125 4.6 24.1 1.0
OD2 B:ASP186 4.7 31.2 1.0
CG B:ASP125 4.8 22.1 1.0
O B:HIS120 4.9 19.4 1.0

Magnesium binding site 7 out of 8 in 3nh1

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Magnesium binding site 7 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg8

b:30.3
occ:1.00
 OD1 C:ASP23 2.3 26.3 1.0
O C:HOH279 2.3 29.8 1.0
O C:HOH232 2.5 30.5 1.0
O3' G:DG6 2.6 23.6 1.0
O C:HOH235 2.6 26.0 1.0
OP1 G:DG7 2.7 22.3 1.0
MG C:MG216 3.1 41.6 1.0
P G:DG7 3.3 27.5 1.0
CG C:ASP23 3.4 27.5 1.0
C3' G:DG6 3.7 26.6 1.0
O C:HOH227 3.8 29.8 1.0
OD2 C:ASP23 3.9 30.9 1.0
C4' G:DG6 4.1 25.8 1.0
C2' G:DG6 4.1 28.0 1.0
O C:HOH247 4.2 22.9 1.0
O5' G:DG7 4.3 27.1 1.0
C5' G:DG7 4.3 23.8 1.0
OD1 C:ASP125 4.3 22.4 1.0
O C:VAL24 4.3 21.1 1.0
O G:HOH126 4.4 32.4 1.0
OP2 G:DG7 4.4 31.4 1.0
OD2 C:ASP125 4.5 22.7 1.0
OD2 C:ASP186 4.6 35.3 1.0
CB C:ASP23 4.7 23.7 1.0
CG C:ASP125 4.9 23.6 1.0
O C:HIS120 4.9 21.9 1.0
C5' G:DG6 4.9 28.0 1.0
N C:VAL24 5.0 20.5 1.0

Magnesium binding site 8 out of 8 in 3nh1

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Magnesium binding site 8 out of 8 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Tagg) with Two Mg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg8

b:30.1
occ:1.00
 O D:HOH276 2.4 30.1 1.0
O3' H:DG6 2.5 23.4 1.0
O D:HOH224 2.5 26.8 1.0
O D:HOH226 2.5 25.5 1.0
OD1 D:ASP23 2.5 26.2 1.0
OP1 H:DG7 2.6 21.8 1.0
P H:DG7 3.2 28.1 1.0
MG D:MG216 3.3 39.2 1.0
CG D:ASP23 3.6 29.6 1.0
C3' H:DG6 3.6 23.8 1.0
O D:HOH284 3.9 26.7 1.0
C2' H:DG6 4.0 24.3 1.0
C4' H:DG6 4.0 24.1 1.0
OD2 D:ASP23 4.0 28.7 1.0
C5' H:DG7 4.2 24.0 1.0
O5' H:DG7 4.2 28.3 1.0
O D:HOH229 4.3 23.9 1.0
O H:HOH250 4.3 30.1 1.0
OD1 D:ASP125 4.3 23.1 1.0
OP2 H:DG7 4.4 31.1 1.0
O D:VAL24 4.4 21.8 1.0
OD2 D:ASP125 4.6 19.6 1.0
O D:HIS120 4.8 23.9 1.0
C5' H:DG6 4.8 25.4 1.0
OD2 D:ASP186 4.8 33.1 1.0
CB D:ASP23 4.9 20.6 1.0
CG D:ASP125 4.9 22.9 1.0

Reference:

Y.-Y.Hsiao, C.-C.Yang, C.L.Lin, J.L.J.Lin, Y.Duh, H.S.Yuan. Structural Basis For Rna Trimming By Rnase T in Stable Rna 3'-End Maturation Nat.Chem.Biol. V. 7 236 2011.
ISSN: ISSN 1552-4450
PubMed: 21317904
DOI: 10.1038/NCHEMBIO.524
Page generated: Thu Aug 15 07:59:43 2024

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