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Magnesium in PDB 1zbh: 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease

Protein crystallography data

The structure of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease, PDB code: 1zbh was solved by Y.Cheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.386, 195.148, 87.966, 90.00, 92.13, 90.00
R / Rfree (%) 20.9 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease (pdb code 1zbh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease, PDB code: 1zbh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1zbh

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Magnesium binding site 1 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:21.4
occ:1.00
 O1P A:AMP1002 1.8 47.1 1.0
OD1 A:ASP134 2.2 50.1 1.0
P A:AMP1002 2.7 47.0 1.0
O3P A:AMP1002 2.8 47.1 1.0
CG A:ASP134 3.0 49.0 1.0
OD2 A:ASP134 3.1 49.0 1.0
OD2 A:ASP234 3.6 53.5 1.0
MG A:MG1001 3.6 28.7 1.0
O A:ASP230 3.8 50.4 1.0
O2P A:AMP1002 3.8 47.0 1.0
O5' A:AMP1002 3.9 46.7 1.0
OD2 A:ASP230 4.2 51.2 1.0
CB A:ASP230 4.3 50.6 1.0
CB A:ASP134 4.5 48.4 1.0
CG A:ASP234 4.5 52.6 1.0
OD1 A:ASP234 4.6 53.8 1.0
C5' A:AMP1002 4.6 46.7 1.0
CG A:ASP230 4.7 50.7 1.0
C A:ASP230 4.8 50.5 1.0
O A:PHE135 4.8 48.3 1.0
CA A:ASP230 5.0 50.5 1.0

Magnesium binding site 2 out of 8 in 1zbh

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Magnesium binding site 2 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:28.7
occ:1.00
 OD2 A:ASP134 2.1 49.0 1.0
OE2 A:GLU136 2.2 48.4 1.0
O2P A:AMP1002 2.3 47.0 1.0
OD1 A:ASP298 2.5 50.8 1.0
O1P A:AMP1002 2.6 47.1 1.0
P A:AMP1002 2.9 47.0 1.0
CG A:ASP298 3.1 50.6 1.0
CG A:ASP134 3.2 49.0 1.0
CD A:GLU136 3.3 48.7 1.0
CB A:ASP298 3.5 50.5 1.0
MG A:MG1000 3.6 21.4 1.0
OD1 A:ASP134 3.8 50.1 1.0
OE1 A:GLU136 3.9 48.4 1.0
OD2 A:ASP298 4.0 50.5 1.0
O5' A:AMP1002 4.1 46.7 1.0
O3P A:AMP1002 4.1 47.1 1.0
C5' A:AMP1002 4.2 46.7 1.0
O A:PHE135 4.2 48.3 1.0
CB A:ASP134 4.3 48.4 1.0
CA A:GLY295 4.3 51.5 1.0
O A:ASN293 4.4 52.4 1.0
CG A:GLU136 4.5 48.4 1.0
O A:ASP134 4.5 48.3 1.0
C A:ASN293 4.6 52.3 1.0
CA A:ASN293 4.6 52.4 1.0
N A:GLY295 4.7 51.9 1.0
C A:ASP134 5.0 48.3 1.0
C A:CYS294 5.0 52.1 1.0
O A:GLY295 5.0 51.4 1.0

Magnesium binding site 3 out of 8 in 1zbh

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Magnesium binding site 3 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2000

b:20.8
occ:1.00
 O1P B:AMP2002 1.7 30.5 1.0
OD1 B:ASP134 2.1 51.5 1.0
P B:AMP2002 2.9 30.6 1.0
CG B:ASP134 3.2 50.2 1.0
O3P B:AMP2002 3.3 30.3 1.0
OD2 B:ASP234 3.6 53.4 1.0
O B:ASP230 3.7 51.4 1.0
O5' B:AMP2002 3.8 30.9 1.0
OD2 B:ASP134 3.8 49.8 1.0
MG B:MG2001 3.8 17.8 1.0
OD1 B:ASP234 4.0 52.9 1.0
OD2 B:ASP230 4.1 53.0 1.0
O2P B:AMP2002 4.1 30.4 1.0
CG B:ASP234 4.2 52.4 1.0
C5' B:AMP2002 4.4 31.7 1.0
CB B:ASP230 4.4 51.6 1.0
CB B:ASP134 4.4 49.7 1.0
O B:PHE135 4.7 49.0 1.0
CG B:ASP230 4.7 52.3 1.0
C B:ASP230 4.7 51.3 1.0
CA B:ASP134 4.9 49.7 1.0

Magnesium binding site 4 out of 8 in 1zbh

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Magnesium binding site 4 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:17.8
occ:1.00
 OD2 B:ASP298 2.2 49.6 1.0
OE2 B:GLU136 2.2 48.8 1.0
OD2 B:ASP134 2.2 49.8 1.0
O1P B:AMP2002 2.6 30.5 1.0
O2P B:AMP2002 2.6 30.4 1.0
P B:AMP2002 3.1 30.6 1.0
CD B:GLU136 3.2 49.4 1.0
CG B:ASP134 3.2 50.2 1.0
CG B:ASP298 3.2 49.9 1.0
OD1 B:ASP134 3.4 51.5 1.0
OE1 B:GLU136 3.4 50.1 1.0
C5' B:AMP2002 3.8 31.7 1.0
MG B:MG2000 3.8 20.8 1.0
CB B:ASP298 3.8 50.2 1.0
O5' B:AMP2002 3.9 30.9 1.0
O B:PHE135 4.1 49.0 1.0
OD1 B:ASP298 4.2 50.0 1.0
CA B:ASN293 4.2 52.4 1.0
ND2 B:ASN293 4.3 52.8 1.0
O3P B:AMP2002 4.4 30.3 1.0
C B:ASN293 4.5 52.3 1.0
O B:ASN293 4.6 52.3 1.0
CG B:GLU136 4.6 48.9 1.0
CB B:ASP134 4.6 49.7 1.0
O B:ASP134 4.7 49.5 1.0
CA B:GLY295 4.8 51.4 1.0
N B:ASN293 4.9 52.5 1.0
CB B:ASN293 5.0 52.5 1.0

Magnesium binding site 5 out of 8 in 1zbh

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Magnesium binding site 5 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3000

b:14.4
occ:1.00
 O1P C:AMP3002 1.9 34.8 1.0
OD1 C:ASP134 2.1 51.1 1.0
P C:AMP3002 2.9 34.6 1.0
O3P C:AMP3002 2.9 34.5 1.0
CG C:ASP134 3.2 49.9 1.0
OD1 C:ASP234 3.3 52.6 1.0
OD2 C:ASP234 3.7 53.1 1.0
OD2 C:ASP134 3.7 49.8 1.0
CG C:ASP234 3.9 52.3 1.0
O2P C:AMP3002 3.9 34.7 1.0
NE1 C:TRP233 3.9 55.6 1.0
MG C:MG3001 4.0 10.6 1.0
O C:ASP230 4.0 51.5 1.0
O5' C:AMP3002 4.1 34.7 1.0
C5' C:AMP3002 4.2 35.1 1.0
CB C:ASP134 4.4 49.5 1.0
CB C:ASP230 4.5 51.6 1.0
CD1 C:TRP233 4.5 55.2 1.0
O C:PHE135 4.5 49.0 1.0
OD2 C:ASP230 4.6 53.1 1.0
CA C:ASP134 4.8 49.5 1.0
C C:ASP230 4.9 51.4 1.0
CG C:ASP230 5.0 52.2 1.0

Magnesium binding site 6 out of 8 in 1zbh

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Magnesium binding site 6 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:10.6
occ:1.00
 OE2 C:GLU136 2.1 48.7 1.0
OD2 C:ASP134 2.1 49.8 1.0
O1P C:AMP3002 2.5 34.8 1.0
CG C:ASP298 3.0 50.0 1.0
CD C:GLU136 3.1 49.1 1.0
CG C:ASP134 3.2 49.9 1.0
OD1 C:ASP298 3.2 50.0 1.0
O2P C:AMP3002 3.2 34.7 1.0
OD2 C:ASP298 3.2 49.3 1.0
P C:AMP3002 3.3 34.6 1.0
OD1 C:ASP134 3.5 51.1 1.0
OE1 C:GLU136 3.6 49.6 1.0
CB C:ASP298 3.6 50.3 1.0
O5' C:AMP3002 3.8 34.7 1.0
OD1 C:ASN293 3.9 53.5 1.0
MG C:MG3000 4.0 14.4 1.0
CA C:ASN293 4.0 52.8 1.0
C5' C:AMP3002 4.2 35.1 1.0
O C:PHE135 4.4 49.0 1.0
C C:ASN293 4.4 52.8 1.0
CG C:GLU136 4.4 48.7 1.0
O C:ASN293 4.5 53.0 1.0
CA C:GLY295 4.5 51.7 1.0
CB C:ASP134 4.5 49.5 1.0
CG C:ASN293 4.7 53.1 1.0
O3P C:AMP3002 4.7 34.5 1.0
CB C:ASN293 4.8 52.8 1.0
N C:GLY295 4.8 52.2 1.0
N C:ASN293 4.8 52.8 1.0

Magnesium binding site 7 out of 8 in 1zbh

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Magnesium binding site 7 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4000

b:38.6
occ:1.00
 O1P D:AMP4002 2.0 49.1 1.0
OD1 D:ASP134 2.1 49.7 1.0
P D:AMP4002 2.8 49.0 1.0
O3P D:AMP4002 2.8 49.4 1.0
CG D:ASP134 3.1 48.9 1.0
OD2 D:ASP134 3.4 48.8 1.0
MG D:MG4001 3.5 50.3 1.0
OD2 D:ASP234 3.6 52.9 1.0
O2P D:AMP4002 3.7 49.2 1.0
O D:ASP230 3.8 50.6 1.0
OD1 D:ASP230 4.1 51.6 1.0
O5' D:AMP4002 4.1 49.2 1.0
OD1 D:ASP234 4.2 53.3 1.0
CG D:ASP234 4.3 52.4 1.0
C5' D:AMP4002 4.4 50.0 1.0
CB D:ASP134 4.5 48.4 1.0
O D:PHE135 4.6 48.4 1.0
CB D:ASP230 4.7 50.7 1.0
CG D:ASP230 4.8 51.0 1.0
C D:ASP230 4.9 50.6 1.0

Magnesium binding site 8 out of 8 in 1zbh

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Magnesium binding site 8 out of 8 in the 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'- Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4001

b:50.3
occ:1.00
 O1P D:AMP4002 1.9 49.1 1.0
OE1 D:GLU136 2.2 48.1 1.0
OD2 D:ASP134 2.2 48.8 1.0
OD1 D:ASP298 2.3 51.0 1.0
P D:AMP4002 3.0 49.0 1.0
CG D:ASP134 3.3 48.9 1.0
CG D:ASP298 3.3 50.7 1.0
O5' D:AMP4002 3.3 49.2 1.0
CD D:GLU136 3.3 48.5 1.0
O2P D:AMP4002 3.5 49.2 1.0
MG D:MG4000 3.5 38.6 1.0
OD1 D:ASP134 3.6 49.7 1.0
C5' D:AMP4002 3.7 50.0 1.0
OE2 D:GLU136 3.7 48.7 1.0
CB D:ASP298 3.9 50.5 1.0
OD2 D:ASP298 4.1 50.5 1.0
O D:PHE135 4.2 48.4 1.0
O3P D:AMP4002 4.3 49.4 1.0
CA D:ASN293 4.5 52.2 1.0
C D:ASN293 4.5 52.3 1.0
O D:ASN293 4.5 52.3 1.0
CG D:GLU136 4.6 48.4 1.0
CB D:ASP134 4.6 48.4 1.0
O D:ASP134 4.8 48.0 1.0
CA D:GLY295 4.9 51.6 1.0
N D:GLY295 4.9 51.9 1.0

Reference:

Y.Cheng, D.J.Patel. Structural Basis For 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'-Exonuclease, A Human Nuclease That Also Targets Sirna To Be Published.
Page generated: Tue Aug 13 20:05:37 2024

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