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Magnesium in PDB 1drz: U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex

Protein crystallography data

The structure of U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex, PDB code: 1drz was solved by A.R.Ferre-D'amare, K.Zhou, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 109.350, 109.350, 190.680, 90.00, 90.00, 120.00
R / Rfree (%) 28.1 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex (pdb code 1drz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex, PDB code: 1drz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1drz

Go back to Magnesium Binding Sites List in 1drz
Magnesium binding site 1 out of 3 in the U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:71.6
occ:1.00
O6 B:G110 4.4 0.1 1.0
N4 B:C172 4.7 87.0 1.0

Magnesium binding site 2 out of 3 in 1drz

Go back to Magnesium Binding Sites List in 1drz
Magnesium binding site 2 out of 3 in the U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:76.0
occ:1.00
N7 B:G170 2.6 92.1 1.0
O6 B:G170 3.0 91.8 1.0
N7 B:G169 3.2 94.0 1.0
C5 B:G170 3.3 92.1 1.0
O6 B:G169 3.3 94.0 1.0
C6 B:G170 3.5 92.0 1.0
C5 B:G169 3.5 94.0 1.0
C6 B:G169 3.5 94.1 1.0
C8 B:G170 3.7 92.1 1.0
C8 B:G169 4.1 94.0 1.0
C4 B:G169 4.5 94.0 1.0
C4 B:G170 4.6 92.1 1.0
N1 B:G169 4.6 94.1 1.0
N9 B:G170 4.8 92.2 1.0
N9 B:G169 4.8 93.9 1.0
N1 B:G170 4.9 92.0 1.0

Magnesium binding site 3 out of 3 in 1drz

Go back to Magnesium Binding Sites List in 1drz
Magnesium binding site 3 out of 3 in the U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of U1A Spliceosomal Protein/Hepatitis Delta Virus Genomic Ribozyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:87.0
occ:1.00
OP2 B:G106 2.7 0.8 1.0
OP2 B:C107 2.9 0.0 1.0
O5' B:G106 2.9 0.5 1.0
P B:G106 3.2 0.7 1.0
OP1 B:G106 3.8 0.7 1.0
C3' B:G106 3.9 0.7 1.0
C8 B:G106 3.9 0.7 1.0
C5' B:G106 4.1 0.1 1.0
C5 B:C107 4.2 0.7 1.0
P B:C107 4.2 0.1 1.0
N7 B:G106 4.4 0.6 1.0
O3' B:G106 4.4 0.3 1.0
C4' B:G106 4.5 0.8 1.0
O3' B:G105 4.6 0.8 1.0
N9 B:G106 4.7 0.7 1.0
C6 B:C107 4.8 0.7 1.0
C2' B:G106 4.9 0.7 1.0
O4' B:G106 4.9 0.8 1.0
O5' B:C107 4.9 0.8 1.0

Reference:

A.R.Ferre-D'amare, K.Zhou, J.A.Doudna. Crystal Structure of A Hepatitis Delta Virus Ribozyme. Nature V. 395 567 1998.
ISSN: ISSN 0028-0836
PubMed: 9783582
DOI: 10.1038/26912
Page generated: Mon Dec 14 05:50:45 2020

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