Atomistry » Magnesium » PDB 3bdh-3bre » 3bo2
Atomistry »
  Magnesium »
    PDB 3bdh-3bre »
      3bo2 »

Magnesium in PDB 3bo2: A Relaxed Active Site Following Exon Ligation By A Group I Intron

Protein crystallography data

The structure of A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo2 was solved by S.V.Lipchock, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.31
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.960, 108.960, 249.495, 90.00, 90.00, 90.00
R / Rfree (%) 29.1 / 32.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A Relaxed Active Site Following Exon Ligation By A Group I Intron (pdb code 3bo2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 1 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:0.7
occ:1.00
 OP1 B:A172 1.9 0.9 1.0
OP1 B:G170 2.3 0.8 1.0
OP1 B:C88 2.3 0.4 1.0
O C:HOH26 2.4 93.6 1.0
O3' E:U3 2.8 0.9 1.0
P B:A172 2.9 0.0 1.0
OP2 B:A172 3.3 0.4 1.0
O5' B:A172 3.5 0.0 1.0
P B:C88 3.5 0.7 1.0
P B:G170 3.6 0.3 1.0
O5' B:G170 3.9 0.8 1.0
OP2 B:C88 3.9 0.4 1.0
C3' E:U3 3.9 0.4 1.0
C4' E:U3 4.0 0.7 1.0
C5' B:G170 4.2 0.6 1.0
O3' B:C171 4.3 0.5 1.0
MG B:MG2 4.4 0.0 1.0
O2' E:U3 4.4 0.6 1.0
O3' B:A87 4.4 0.3 1.0
OP1 B:U173 4.5 0.4 1.0
OP2 B:G170 4.5 0.2 1.0
O3' B:G169 4.6 0.7 1.0
O5' B:C88 4.6 0.7 1.0
C5' E:U3 4.7 0.7 1.0
C3' B:C171 4.8 1.0 1.0
C2' E:U3 4.8 0.3 1.0
C5' B:A172 4.9 0.8 1.0
O3' C:G206 5.0 0.4 1.0

Magnesium binding site 2 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 2 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2

b:0.0
occ:1.00
 OP1 B:G128 1.8 0.5 1.0
OP2 B:A172 2.1 0.4 1.0
O2' C:G206 2.2 0.7 1.0
O3' C:G206 2.5 0.4 1.0
O C:HOH26 2.6 93.6 1.0
P B:G128 2.9 0.7 1.0
O3' B:A127 3.2 0.2 1.0
C2' C:G206 3.3 0.0 1.0
P B:A172 3.4 0.0 1.0
O5' B:G128 3.4 0.2 1.0
C3' C:G206 3.5 0.8 1.0
OP1 B:A87 3.8 0.7 1.0
OP2 B:C88 3.9 0.4 1.0
O2' B:C171 3.9 0.6 1.0
O3' B:C171 4.1 0.5 1.0
OP1 B:A172 4.1 0.9 1.0
C3' B:A127 4.2 0.7 1.0
OP2 B:G128 4.3 0.1 1.0
C4' B:A127 4.3 0.8 1.0
MG B:MG1 4.4 0.7 1.0
C1' C:G206 4.5 0.2 1.0
C5' B:G128 4.5 0.5 1.0
C4' C:G206 4.5 0.3 1.0
C5' B:A87 4.5 0.1 1.0
O5' B:A172 4.6 0.0 1.0
O B:HOH1022 4.8 67.5 1.0
P B:C88 4.9 0.7 1.0
C5' B:A127 5.0 0.6 1.0

Magnesium binding site 3 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 3 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3

b:97.5
occ:1.00
 OP2 B:A174 1.9 0.7 1.0
OP2 B:U173 2.1 0.8 1.0
P B:A174 3.0 0.6 1.0
OP1 B:A174 3.3 0.1 1.0
P B:U173 3.5 0.8 1.0
N7 C:G206 3.8 0.7 1.0
O3' B:A172 4.0 1.0 1.0
O3' B:U173 4.1 0.4 1.0
O5' B:A174 4.2 0.0 1.0
C3' B:U173 4.3 0.6 1.0
N7 B:A174 4.3 0.7 1.0
OP1 B:U173 4.3 0.4 1.0
C8 C:G206 4.4 0.3 1.0
O5' B:U173 4.5 0.6 1.0
C8 B:A174 4.6 0.8 1.0
C5 C:G206 4.8 0.5 1.0
N7 B:G175 4.8 0.9 1.0
O2' B:A172 4.9 0.4 1.0
C5' B:U173 5.0 0.8 1.0
O6 C:G206 5.0 0.4 1.0

Magnesium binding site 4 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 4 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1015

b:0.2
occ:1.00
 OP2 B:U80 4.7 0.4 1.0
OP2 B:C61 4.9 0.4 1.0
O4 B:U62 5.0 0.9 1.0

Magnesium binding site 5 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 5 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1016

b:0.0
occ:1.00
 OP1 B:U124 2.2 0.5 1.0
OP2 B:C171 2.2 0.7 1.0
OP2 B:A127 3.3 0.8 1.0
P B:C171 3.5 0.2 1.0
P B:U124 3.6 0.0 1.0
C5' B:U124 3.8 0.6 1.0
O5' B:C171 3.9 0.6 1.0
OP2 B:G125 4.1 0.7 1.0
O5' B:U124 4.1 0.8 1.0
O3' B:G170 4.1 0.3 1.0
O3' B:G123 4.4 0.2 1.0
O2' B:U126 4.5 0.1 1.0
OP2 B:U124 4.6 0.0 1.0
P B:A127 4.7 0.5 1.0
OP1 B:C171 4.8 1.0 1.0
O2' B:G170 4.9 0.1 1.0

Magnesium binding site 6 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 6 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1017

b:0.0
occ:1.00
 OP1 B:G125 2.3 1.0 1.0
P B:G125 3.7 0.8 1.0
OP1 B:A127 3.7 0.5 1.0
N6 B:A172 3.8 0.4 1.0
N7 B:A127 4.1 0.9 1.0
N7 B:A172 4.2 0.5 1.0
OP2 B:G125 4.5 0.7 1.0
O2' B:U50 4.5 0.1 1.0
OP2 B:A131 4.5 0.2 1.0
C8 B:A127 4.5 0.1 1.0
O3' B:U124 4.6 1.0 1.0
O5' B:G125 4.6 0.4 1.0
C5' B:G125 4.7 0.9 1.0
C6 B:A172 4.7 0.3 1.0
OP2 B:U51 4.8 0.3 1.0
C5 B:A172 4.8 0.5 1.0
C5 B:A127 4.9 0.2 1.0

Magnesium binding site 7 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 7 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1018

b:0.7
occ:1.00
 OP2 B:A39 2.2 0.8 1.0
OP2 B:G38 2.3 0.3 1.0
O5' E:C1 2.5 0.8 1.0
O2' B:G37 2.9 0.1 1.0
OP1 B:G38 3.1 0.4 1.0
P B:G38 3.1 0.4 1.0
P B:A39 3.6 0.9 1.0
C5' E:C1 3.7 0.8 1.0
O3' B:G37 4.0 0.8 1.0
C4' E:C1 4.2 0.6 1.0
O4' E:C1 4.2 0.1 1.0
C2' B:G37 4.2 0.9 1.0
OP1 B:A39 4.3 1.0 1.0
O3' B:G38 4.5 0.3 1.0
O5' B:G38 4.5 0.2 1.0
C3' B:G38 4.5 0.0 1.0
O5' B:A39 4.6 0.2 1.0
C3' B:G37 4.6 0.1 1.0
N7 B:A39 4.7 0.4 1.0

Magnesium binding site 8 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 8 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1019

b:0.4
occ:1.00
 OP2 B:A48 2.2 0.4 1.0
OP2 B:U133 2.9 0.3 1.0
OP1 B:U133 3.2 1.0 1.0
P B:U133 3.4 0.4 1.0
OP2 B:A134 3.4 0.8 1.0
P B:A48 3.6 0.1 1.0
O5' B:U133 3.9 0.3 1.0
O2' B:A47 4.0 0.4 1.0
OP1 B:A48 4.1 0.9 1.0
O3' B:A47 4.5 0.3 1.0
O5' B:A48 4.6 0.2 1.0
O B:HOH1037 4.7 0.6 1.0
C5' B:U133 4.8 0.7 1.0
O3' B:C132 4.9 0.5 1.0
P B:A134 4.9 0.9 1.0

Magnesium binding site 9 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 9 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1020

b:0.6
occ:1.00
 OP1 B:U126 2.2 0.7 1.0
N7 B:G53 3.1 0.8 1.0
P B:U126 3.4 0.1 1.0
O2' B:G125 3.5 0.2 1.0
O3' B:G125 3.9 0.9 1.0
C8 B:G53 4.0 0.0 1.0
C5 B:G53 4.1 0.8 1.0
O6 B:G53 4.1 0.7 1.0
OP2 B:U126 4.1 0.2 1.0
C2' B:G125 4.2 0.9 1.0
N7 B:G54 4.2 0.9 1.0
C6 B:G53 4.5 0.7 1.0
O6 B:G54 4.5 0.9 1.0
C3' B:G125 4.7 1.0 1.0
O5' B:U126 4.7 0.2 1.0
N4 B:C52 4.8 0.4 1.0

Magnesium binding site 10 out of 10 in 3bo2

Go back to Magnesium Binding Sites List in 3bo2
Magnesium binding site 10 out of 10 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1021

b:0.2
occ:1.00
 N4 B:C66 3.9 0.1 1.0
O6 B:G67 4.5 0.2 1.0
C5 B:C66 4.6 0.7 1.0
C4 B:C66 4.7 0.7 1.0
O6 B:G77 4.7 0.8 1.0
OP2 B:G65 4.9 0.6 1.0
N4 B:C68 5.0 0.7 1.0

Reference:

S.V.Lipchock, S.A.Strobel. A Relaxed Active Site After Exon Ligation By the Group I Intron Proc.Natl.Acad.Sci.Usa V. 105 5699 2008.
ISSN: ISSN 0027-8424
PubMed: 18408159
DOI: 10.1073/PNAS.0712016105
Page generated: Wed Aug 14 09:13:04 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy