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Magnesium in PDB 3td0: Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site

Protein crystallography data

The structure of Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site, PDB code: 3td0 was solved by J.Kondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.70 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.520, 46.730, 55.290, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.6

Other elements in 3td0:

The structure of Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site (pdb code 3td0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site, PDB code: 3td0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3td0

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Magnesium binding site 1 out of 7 in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding 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 the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:24.2
occ:1.00
 O A:HOH1002 2.0 25.3 1.0
O A:HOH1004 2.1 24.4 1.0
O B:HOH1001 2.1 24.7 1.0
O B:HOH1003 2.1 25.0 1.0
O B:HOH1006 2.1 24.9 1.0
O A:HOH1005 2.1 23.1 1.0
O B:HOH145 4.0 37.2 1.0
O A:HOH143 4.2 24.5 1.0
O A:HOH189 4.3 24.4 1.0
OP2 B:G31 4.3 21.5 1.0
O A:HOH2002 4.3 23.5 1.0
O B:HOH204 4.3 26.2 1.0
OP2 A:C12 4.3 14.2 1.0
OP1 A:C12 4.4 15.7 1.0
OP1 B:C30 4.5 20.9 1.0
O B:HOH128 4.6 25.1 1.0
O5' B:C30 4.9 17.2 1.0
O A:HOH2005 4.9 19.9 1.0
P A:C12 4.9 14.5 1.0
O A:HOH2004 5.0 20.8 1.0

Magnesium binding site 2 out of 7 in 3td0

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Magnesium binding site 2 out of 7 in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding 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 the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2000

b:23.5
occ:1.00
 O A:HOH2002 2.0 23.5 1.0
O A:HOH2004 2.1 20.8 1.0
O A:HOH2001 2.1 19.2 1.0
O A:HOH2003 2.1 22.9 1.0
O B:HOH2006 2.1 24.5 1.0
O A:HOH2005 2.1 19.9 1.0
OP2 A:G13 3.9 15.0 1.0
O A:HOH106 4.1 17.9 1.0
O B:HOH129 4.2 26.2 1.0
O B:HOH232 4.2 37.0 1.0
O A:HOH104 4.3 15.0 1.0
O A:HOH168 4.3 26.2 1.0
O A:HOH1004 4.4 24.4 1.0
N7 A:G13 4.5 13.3 1.0
O A:HOH1002 4.6 25.3 1.0
O A:HOH172 4.6 37.2 1.0
OP2 A:C12 4.6 14.2 1.0
O B:HOH204 4.7 26.2 1.0
O A:HOH167 4.8 27.8 1.0
C5 A:C12 5.0 11.7 1.0
C8 A:G13 5.0 12.6 1.0

Magnesium binding site 3 out of 7 in 3td0

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Magnesium binding site 3 out of 7 in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding 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 the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3000

b:25.4
occ:1.00
 O B:HOH3002 2.0 26.4 1.0
O A:HOH3004 2.1 26.8 1.0
O B:HOH3001 2.1 23.5 1.0
O B:HOH3003 2.1 20.5 1.0
O B:HOH3006 2.1 23.3 1.0
O B:HOH3005 2.1 24.8 1.0
O A:HOH109 3.9 22.0 1.0
O B:HOH116 4.1 19.2 1.0
N6 B:A37 4.2 12.8 1.0
O B:HOH105 4.2 21.3 1.0
N4 B:C35 4.4 15.0 1.0
O6 B:G36 4.4 12.5 1.0
O B:HOH179 4.4 36.1 1.0
O B:HOH110 4.5 23.1 1.0
N7 B:G36 4.5 13.1 1.0
O6 A:G10 4.6 14.7 1.0
O A:HOH122 4.6 24.3 1.0
O A:HOH170 4.7 26.6 1.0
C5 B:C35 4.8 15.2 1.0
C4 B:C35 4.9 15.8 1.0

Magnesium binding site 4 out of 7 in 3td0

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Magnesium binding site 4 out of 7 in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding 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 the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4000

b:27.3
occ:1.00
 O A:HOH4002 2.0 26.0 1.0
O B:HOH4004 2.1 24.9 1.0
O B:HOH4001 2.1 22.7 1.0
O B:HOH4003 2.1 26.3 1.0
O A:HOH4006 2.1 27.4 1.0
O B:HOH4005 2.1 26.4 1.0
O A:HOH157 3.7 25.6 1.0
OP2 B:G33 3.9 21.3 1.0
O A:HOH106 4.1 17.9 1.0
O B:HOH135 4.2 29.7 1.0
O A:HOH109 4.3 22.0 1.0
O B:HOH129 4.5 26.2 1.0
N7 B:G33 4.5 14.6 1.0
O B:HOH235 4.6 32.1 1.0
OP2 B:C32 4.6 20.6 1.0
BR B:5BU34 4.6 20.8 1.0
O B:HOH160 4.8 33.0 1.0
BR A:5BU11 4.8 18.2 1.0
O B:HOH176 4.9 44.8 1.0

Magnesium binding site 5 out of 7 in 3td0

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Magnesium binding site 5 out of 7 in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding 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 the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5000

b:38.5
occ:1.00
 O B:HOH5002 2.0 38.0 1.0
O B:HOH5004 2.1 37.2 1.0
O A:HOH5001 2.1 39.1 1.0
O B:HOH5003 2.1 39.5 1.0
O A:HOH5006 2.1 38.5 1.0
O B:HOH5005 2.1 37.4 1.0
O A:HOH264 3.8 29.8 1.0
O A:HOH203 3.9 32.5 1.0
O B:HOH134 4.0 24.9 1.0
O B:HOH125 4.1 25.3 1.0
O A:HOH262 4.4 34.7 1.0
O A:HOH197 4.4 28.6 1.0
O B:HOH174 4.4 30.0 1.0
N7 B:A40 4.4 14.5 1.0
N6 B:A40 4.5 15.7 1.0

Magnesium binding site 6 out of 7 in 3td0

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Magnesium binding site 6 out of 7 in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding 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 the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6000

b:30.5
occ:1.00
 O A:HOH6002 2.0 30.5 1.0
O B:HOH6004 2.1 29.8 1.0
O B:HOH6001 2.1 27.8 1.0
O B:HOH6003 2.1 30.3 1.0
O A:HOH6005 2.1 30.0 1.0
OP1 B:U25 2.3 21.1 1.0
P B:U25 3.6 19.2 1.0
OP1 A:A18 4.0 20.8 1.0
O A:HOH259 4.1 32.9 1.0
O5' B:U25 4.2 19.6 1.0
OP2 B:U25 4.2 22.2 1.0
C5' B:U25 4.5 21.6 1.0
O B:HOH199 4.7 36.0 1.0
O3' B:U24 4.7 19.2 1.0
OP2 A:A18 4.8 21.0 1.0
O A:HOH137 4.9 28.4 1.0
P A:A18 5.0 18.5 1.0

Magnesium binding site 7 out of 7 in 3td0

Go back to Magnesium Binding Sites List in 3td0
Magnesium binding site 7 out of 7 in the Crystal Structure of the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding 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 the Bacterial A1408G-Mutant and the Protozoa Cytoplasmic Ribosomal Decoding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7000

b:34.1
occ:1.00
 O B:HOH7002 2.0 34.8 1.0
O B:HOH7004 2.1 34.3 1.0
O B:HOH7001 2.1 34.2 1.0
O B:HOH7003 2.1 34.2 1.0
O B:HOH7006 2.1 34.8 1.0
O B:HOH7005 2.1 34.3 1.0
O B:HOH118 4.3 22.2 1.0
OP2 B:C44 4.5 23.7 1.0
O B:HOH215 4.6 32.3 1.0

Reference:

J.Kondo, J.Kondo. N/A N/A.
ISSN: ISSN 1433-7851
PubMed: 22110016
DOI: 10.1002/ANIE.201106084
Page generated: Thu Aug 15 12:03:21 2024

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