Atomistry » Magnesium » PDB 3r11-3ren » 3r4f
Atomistry »
  Magnesium »
    PDB 3r11-3ren »
      3r4f »

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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Go back to Magnesium Binding Sites List in 3r4f
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy