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Magnesium in PDB 3r4f: Prohead Rna

Protein crystallography data

The structure of Prohead Rna, PDB code: 3r4f was solved by F.Ding, C.Lu, W.Zhano, K.R.Rajashankar, D.L.Anderson, P.J.Jardine, S.Grimes, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.50
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.197, 104.197, 208.793, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 27.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Prohead Rna (pdb code 3r4f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Prohead Rna, PDB code: 3r4f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3r4f

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Magnesium binding site 1 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Prohead Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg200

b:0.1
occ:1.00
 MG A:MG205 2.3 0.7 1.0
O5' A:G1 3.3 0.3 1.0
C5' A:G1 4.3 0.4 1.0
O4' A:G1 4.4 0.1 1.0
C8 A:G1 4.5 0.9 1.0

Magnesium binding site 2 out of 9 in 3r4f

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Magnesium binding site 2 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Prohead Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:93.9
occ:1.00
 N2 A:G29 2.8 0.6 1.0
N4 A:C32 3.6 0.5 1.0
N6 A:A33 3.9 0.3 1.0
C2 A:G29 4.0 0.7 1.0
N1 A:G29 4.2 0.4 1.0
O4 A:U22 4.4 0.3 1.0
C5 A:C32 4.5 0.6 1.0
C4 A:C32 4.5 0.6 1.0
N4 A:C21 4.7 0.1 1.0

Magnesium binding site 3 out of 9 in 3r4f

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Magnesium binding site 3 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Prohead Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:0.8
occ:1.00
 OP2 A:G29 2.4 0.9 1.0
O4 A:U26 2.9 0.7 1.0
P A:G29 3.0 0.3 1.0
OP1 A:G29 3.2 0.1 1.0
O3' A:A28 3.5 1.0 1.0
C4 A:U26 3.9 0.2 1.0
N3 A:U26 4.1 0.1 1.0
C3' A:A28 4.4 0.2 1.0
O5' A:G29 4.5 0.0 1.0
C5' A:A28 4.7 0.2 1.0
O5' A:A28 4.8 0.8 1.0
C5 A:U30 4.9 0.1 1.0

Magnesium binding site 4 out of 9 in 3r4f

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Magnesium binding site 4 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Prohead Rna within 5.0Å range:

Magnesium binding site 5 out of 9 in 3r4f

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Magnesium binding site 5 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Prohead Rna within 5.0Å range:

Magnesium binding site 6 out of 9 in 3r4f

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Magnesium binding site 6 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Prohead Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:0.7
occ:1.00
 O5' A:G1 2.3 0.3 1.0
MG A:MG200 2.3 0.1 1.0
C5' A:G1 3.6 0.4 1.0
C4' A:G1 4.7 0.8 1.0
O4' A:G1 4.7 0.1 1.0

Magnesium binding site 7 out of 9 in 3r4f

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Magnesium binding site 7 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Prohead Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:0.5
occ:1.00
 O3' A:A8 2.6 0.6 1.0
OP1 A:U9 2.8 0.1 1.0
P A:U9 3.0 0.2 1.0
OP2 A:U9 3.5 0.9 1.0
C5' A:A8 3.5 0.6 1.0
C3' A:A8 3.5 0.2 1.0
C4' A:A8 3.8 0.6 1.0
O5' A:A8 4.0 0.6 1.0
O5' A:U9 4.5 0.9 1.0
OP1 A:A8 4.6 0.8 1.0
C2' A:A8 4.9 0.5 1.0

Magnesium binding site 8 out of 9 in 3r4f

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Magnesium binding site 8 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Prohead Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:0.7
occ:1.00
 N6 A:A28 2.9 0.0 1.0
C6 A:A28 4.2 0.9 1.0
O6 A:G27 4.5 0.5 1.0
N1 A:A28 4.6 0.4 1.0
O2' A:U30 4.9 0.5 1.0

Magnesium binding site 9 out of 9 in 3r4f

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Magnesium binding site 9 out of 9 in the Prohead Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Prohead Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:0.9
occ:1.00
 N1 A:G27 3.5 0.2 1.0
N2 A:G27 4.1 0.8 1.0
O6 A:G27 4.2 0.5 1.0
C2 A:G27 4.3 0.9 1.0
C6 A:G27 4.4 0.7 1.0
C2 A:A28 4.5 0.5 1.0
N1 A:A28 4.7 0.4 1.0

Reference:

F.Ding, C.Lu, W.Zhao, K.R.Rajashankar, D.L.Anderson, P.J.Jardine, S.Grimes, A.Ke. Structure and Assembly of the Essential Rna Ring Component of A Viral Dna Packaging Motor. Proc.Natl.Acad.Sci.Usa V. 108 7357 2011.
ISSN: ISSN 0027-8424
PubMed: 21471452
DOI: 10.1073/PNAS.1016690108
Page generated: Thu Aug 15 10:17:21 2024

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