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 Dec 15 01:01:37 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy