Atomistry » Magnesium » PDB 6u1j-6uey » 6uey
Atomistry »
  Magnesium »
    PDB 6u1j-6uey »
      6uey »

Magnesium in PDB 6uey: Pistol Ribozyme Transition-State Analog Vanadate

Protein crystallography data

The structure of Pistol Ribozyme Transition-State Analog Vanadate, PDB code: 6uey was solved by M.Teplova, C.Falschlunger, O.Krasheninina, D.J.Patel, R.Micura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 2.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.829, 91.829, 123.444, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.2

Other elements in 6uey:

The structure of Pistol Ribozyme Transition-State Analog Vanadate also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pistol Ribozyme Transition-State Analog Vanadate (pdb code 6uey). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Pistol Ribozyme Transition-State Analog Vanadate, PDB code: 6uey:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 1 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:88.2
occ:1.00
 N7 A:G33 2.6 0.6 1.0
O2V B:Q6110 3.3 0.1 1.0
C8 A:G33 3.5 0.6 1.0
O1V B:Q6110 3.6 0.3 1.0
C5 A:G33 3.6 0.3 1.0
O6 A:G33 3.8 0.4 1.0
O5' B:U11 4.0 0.9 1.0
V B:Q6110 4.1 0.0 1.0
C5' B:U11 4.1 0.4 1.0
C6 A:G33 4.1 1.0 1.0
OP2 A:G33 4.2 0.1 1.0
O4 A:U6 4.3 0.8 1.0
N9 A:G33 4.7 0.9 1.0
OP2 A:U35 4.7 0.2 1.0
O2' A:G32 4.8 0.5 1.0
C4 A:G33 4.8 0.8 1.0

Magnesium binding site 2 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 2 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:0.1
occ:1.00
 N7 A:A38 3.2 0.6 1.0
OP2 A:A37 3.4 0.9 1.0
OP2 A:A38 3.8 0.6 1.0
C8 A:A38 3.8 0.4 1.0
C5 A:A38 4.4 0.1 1.0
P A:A37 4.5 0.3 1.0
O5' A:A37 4.6 0.5 1.0
N7 A:A37 4.7 0.3 1.0
N6 A:A38 4.8 0.6 1.0
C8 A:A37 4.8 0.9 1.0
O1V B:Q6110 4.8 0.3 1.0

Magnesium binding site 3 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 3 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:80.5
occ:1.00
 N6 A:A10 3.7 0.6 1.0
O6 A:G5 4.0 96.4 1.0
O6 A:G11 4.1 93.6 1.0
N7 A:G11 4.4 96.6 1.0
N7 A:A10 4.6 0.9 1.0
N4 A:C12 4.6 0.4 1.0
C6 A:A10 4.7 0.2 1.0
C6 A:G5 4.9 92.6 1.0
C6 A:G11 5.0 95.4 1.0
C5 A:A10 5.0 1.0 1.0

Magnesium binding site 4 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 4 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:70.3
occ:1.00
 OP1 A:U7 2.0 0.7 1.0
P A:U7 3.4 0.8 1.0
C5' A:U7 3.8 0.7 1.0
O3' A:U6 4.0 0.9 1.0
O5' A:U7 4.0 0.9 1.0
OP1 A:C4 4.0 0.3 1.0
OP2 A:G5 4.3 92.4 1.0
OP2 A:U8 4.4 0.6 1.0
OP2 A:U7 4.6 0.7 1.0

Magnesium binding site 5 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 5 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:79.6
occ:1.00
 N7 C:G33 2.7 88.0 1.0
C8 C:G33 3.2 82.1 1.0
O2V D:Q6110 3.7 0.1 0.9
C5 C:G33 4.0 82.4 1.0
O1V D:Q6110 4.0 0.8 1.0
OP2 C:G33 4.1 0.6 1.0
O4 C:U6 4.2 83.2 1.0
C5' D:U11 4.4 0.9 1.0
OP2 C:U35 4.4 83.6 1.0
O5' D:U11 4.5 0.3 1.0
N9 C:G33 4.5 81.6 1.0
O2' C:G32 4.6 97.9 1.0
V D:Q6110 4.6 0.5 1.0
O6 C:G33 4.6 84.1 1.0
C6 C:G33 4.7 83.2 1.0
C4 C:G33 4.9 81.7 1.0

Magnesium binding site 6 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 6 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:0.2
occ:1.00
 N7 C:A38 2.9 92.0 1.0
C8 C:A38 3.6 94.2 1.0
OP2 C:A37 3.8 98.2 1.0
OP2 C:A38 4.0 0.5 1.0
N7 C:A37 4.1 98.9 1.0
C5 C:A38 4.1 91.3 1.0
C8 C:A37 4.4 98.5 1.0
N6 C:A38 4.5 87.8 1.0
C6 C:A38 4.8 89.4 1.0
N7 C:A39 4.8 96.7 1.0
O1V D:Q6110 4.8 0.8 1.0
N9 C:A38 4.9 95.0 1.0
C5 C:A37 4.9 97.9 1.0
O5' C:A37 4.9 99.4 1.0

Magnesium binding site 7 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 7 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:0.2
occ:1.00
 OP2 C:G42 2.3 94.6 1.0
OP2 C:C41 3.1 0.7 1.0
P C:G42 3.6 93.9 1.0
OP1 C:G42 4.1 96.1 1.0
N7 C:G43 4.1 92.7 1.0
O5' C:G42 4.3 91.6 1.0
P C:C41 4.4 0.1 1.0
O5' C:C41 4.4 0.1 1.0
O6 C:G43 4.5 96.3 1.0
O3' C:C41 4.8 99.0 1.0

Magnesium binding site 8 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 8 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:81.0
occ:1.00
 OP1 C:U7 2.1 0.9 1.0
P C:U7 3.6 0.1 1.0
OP2 C:G5 4.1 94.5 1.0
C5' C:U7 4.2 0.2 1.0
O5' C:U7 4.2 0.9 1.0
OP2 C:U8 4.3 0.8 1.0
O3' C:U6 4.4 0.0 1.0
OP2 C:U7 4.5 0.2 1.0
OP1 C:C4 4.6 99.9 1.0
OP1 C:U8 4.8 0.6 1.0
P C:U8 4.9 1.0 1.0

Magnesium binding site 9 out of 9 in 6uey

Go back to Magnesium Binding Sites List in 6uey
Magnesium binding site 9 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg105

b:80.5
occ:1.00
 O6 C:G11 4.2 85.5 1.0
N6 C:A10 4.3 92.5 1.0
O6 C:G5 4.3 90.2 1.0
N7 C:A10 4.3 97.6 1.0
N7 C:G11 4.4 89.5 1.0
N4 C:C12 4.6 90.8 1.0
C5 C:A10 5.0 96.4 1.0
C6 C:G11 5.0 86.6 1.0

Reference:

M.Teplova, C.Falschlunger, O.Krasheninina, M.Egger, A.Ren, D.J.Patel, R.Micura. On Crucial Roles of Two Hydrated MG2+ Ions in Reaction Catalysis of the Pistol Ribozyme. Angew.Chem.Int.Ed.Engl. 2019.
ISSN: ESSN 1521-3773
PubMed: 31804735
DOI: 10.1002/ANIE.201912522
Page generated: Tue Oct 1 20:59:19 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