Atomistry » Magnesium » PDB 2zws-3a0t » 357d
Atomistry »
  Magnesium »
    PDB 2zws-3a0t »
      357d »

Magnesium in PDB 357d: 3.5 A Structure of Fragment I From E. Coli 5S Rrna

Protein crystallography data

The structure of 3.5 A Structure of Fragment I From E. Coli 5S Rrna, PDB code: 357d was solved by C.C.Correll, B.Freeborn, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.670, 58.670, 248.840, 90.00, 90.00, 120.00
R / Rfree (%) 31.2 / 26.5

Other elements in 357d:

The structure of 3.5 A Structure of Fragment I From E. Coli 5S Rrna also contains other interesting chemical elements:

Mercury (Hg) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna (pdb code 357d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna, PDB code: 357d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 1 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg62

b:25.1
occ:1.00
 OP2 B:G75 2.2 57.8 1.0
OP2 C:A99 2.6 65.1 1.0
P B:G75 3.5 58.2 1.0
O5' C:A99 3.5 64.6 1.0
P C:A99 3.6 64.2 1.0
O5' B:G75 3.8 59.3 1.0
N7 B:G76 4.1 73.2 1.0
C3' C:G98 4.2 62.2 1.0
N7 B:G75 4.2 52.6 1.0
C8 B:G75 4.2 52.9 1.0
O3' C:G98 4.3 63.4 1.0
O4 B:U77 4.4 67.5 1.0
O6 B:G76 4.5 76.1 1.0
OP1 B:G75 4.5 57.2 1.0
O3' B:U74 4.5 55.7 1.0
O5' B:U74 4.7 55.5 1.0
C3' B:U74 4.7 53.4 1.0
C5' C:A99 4.8 64.1 1.0
OP2 B:U74 4.8 56.5 1.0
OP1 C:A99 4.9 63.6 1.0
C2' C:G98 4.9 61.3 1.0
OP2 B:G76 4.9 65.4 1.0
C5 B:G76 4.9 73.0 1.0
C8 B:G76 5.0 71.6 1.0

Magnesium binding site 2 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 2 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg63

b:25.4
occ:1.00
 OP1 B:U74 2.2 55.5 1.0
OP1 C:A99 2.9 63.6 1.0
OP2 C:A99 3.3 65.1 1.0
P C:A99 3.6 64.2 1.0
P B:U74 3.7 55.5 1.0
C5' C:G98 3.8 63.4 1.0
C5' B:U74 4.1 55.0 1.0
O5' B:U74 4.2 55.5 1.0
O3' B:A73 4.5 53.4 1.0
OP1 C:G98 4.5 67.0 1.0
O5' C:G98 4.6 65.1 1.0
O3' C:G98 4.6 63.4 1.0
OP2 B:U74 4.7 56.5 1.0
O5' C:A99 4.8 64.6 1.0
OP2 B:G75 4.9 57.8 1.0
C4' C:G98 4.9 62.6 1.0

Magnesium binding site 3 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 3 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg64

b:23.5
occ:1.00
 OP2 C:G100 2.4 63.7 1.0
P C:G100 3.7 62.9 1.0
OP2 B:A73 4.0 60.0 1.0
OP1 C:G100 4.1 63.6 1.0
C5' B:A73 4.3 53.9 1.0
O6 C:G102 4.4 83.9 1.0
OP2 B:U74 4.5 56.5 1.0
N7 C:G102 4.6 80.6 1.0
O5' C:G100 4.6 64.5 1.0
O3' C:A99 4.8 61.5 1.0
C5' C:A99 4.8 64.1 1.0
O5' B:A73 4.9 58.3 1.0
P B:A73 5.0 60.6 1.0

Magnesium binding site 4 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 4 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg65

b:31.9
occ:1.00
 O6 C:G98 2.8 62.5 1.0
C6 C:G98 3.6 61.1 1.0
N7 C:G98 3.9 61.7 1.0
C5 C:G98 4.1 61.5 1.0
OP2 B:G76 4.1 65.4 1.0
OP1 B:G76 4.4 64.4 1.0
OP2 C:C97 4.5 68.9 1.0
P B:G76 4.8 64.5 1.0
N1 C:G98 4.8 60.4 1.0

Magnesium binding site 5 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 5 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg66

b:59.9
occ:1.00
 OP2 B:A78 2.3 70.9 1.0
P B:A78 3.2 70.7 1.0
OP1 B:A78 3.3 71.2 1.0
OP2 B:G79 3.6 80.7 1.0
O5' B:A78 3.9 71.3 1.0
N7 B:G79 4.5 81.5 1.0
O3' B:U77 4.6 69.1 1.0
O4 B:U80 4.8 83.0 1.0

Magnesium binding site 6 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 6 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg67

b:80.9
occ:1.00
 N2 C:G100 4.3 73.6 1.0
N1 C:G100 4.5 67.3 1.0
O2 B:U77 4.8 65.3 1.0
N2 B:G76 4.9 73.7 1.0
C2 C:G100 5.0 69.2 1.0

Magnesium binding site 7 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 7 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg68

b:69.4
occ:1.00
 OP2 C:A119 2.4 0.4 1.0
P C:A119 3.7 0.6 1.0
OP1 C:A119 4.3 0.9 1.0
C5' C:C118 4.3 95.0 1.0
O3' C:C118 4.4 99.9 1.0
C3' C:C118 4.7 97.5 1.0
O5' C:A119 4.9 0.7 1.0

Magnesium binding site 8 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 8 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg69

b:61.1
occ:1.00
 O6 A:G6 3.7 98.5 1.0
O6 A:G7 4.1 88.7 1.0
N7 A:G6 4.4 99.5 1.0
O4 A:SSU5 4.6 98.9 1.0
C6 A:G6 4.6 98.4 1.0
C5 A:SSU5 4.7 99.5 1.0
C5 A:G6 4.9 98.6 1.0
C4 A:SSU5 4.9 99.5 1.0
N4 A:C8 5.0 93.4 1.0

Reference:

C.C.Correll, B.Freeborn, P.B.Moore, T.A.Steitz. Metals, Motifs, and Recognition in the Crystal Structure of A 5S Rrna Domain. Cell(Cambridge,Mass.) V. 91 705 1997.
ISSN: ISSN 0092-8674
PubMed: 9393863
DOI: 10.1016/S0092-8674(00)80457-2
Page generated: Wed Aug 14 08:11:07 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