Atomistry » Magnesium » PDB 5e79-5eg3 » 5eao
Atomistry »
  Magnesium »
    PDB 5e79-5eg3 »
      5eao »

Magnesium in PDB 5eao: Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+

Protein crystallography data

The structure of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+, PDB code: 5eao was solved by A.Mir, B.L.Golden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.36 / 2.99
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.974, 87.016, 105.370, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27

Other elements in 5eao:

The structure of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ also contains other interesting chemical elements:

Vanadium (V) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ (pdb code 5eao). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+, PDB code: 5eao:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 1 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:33.1
occ:1.00
 OP2 A:A22 2.2 40.8 1.0
N7 A:G23 2.7 36.0 1.0
O6 A:G23 3.3 29.5 1.0
C5 A:G23 3.5 34.2 1.0
P A:A22 3.6 49.3 1.0
C6 A:G23 3.7 32.8 1.0
C8 A:G23 3.8 40.0 1.0
O2V B:CVC7 4.1 36.4 1.0
O3' A:G21 4.1 38.0 1.0
O5' A:A22 4.2 42.9 1.0
O5' B:U8 4.5 25.6 1.0
O2' A:G21 4.7 38.2 1.0
C4 A:G23 4.8 38.0 1.0
OP1 A:A22 4.8 42.9 1.0
C8 A:A22 4.8 35.8 1.0
N9 A:G23 4.9 46.5 1.0
O1V B:CVC7 5.0 39.6 1.0

Magnesium binding site 2 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 2 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:34.4
occ:1.00
 OP2 A:A41 2.4 47.0 1.0
P A:A41 3.5 46.6 1.0
O5' A:A41 3.6 37.5 1.0
N7 A:A42 4.2 31.1 1.0
OP1 A:A41 4.3 45.0 1.0
OP2 A:A42 4.4 31.9 1.0
C8 A:A41 4.6 35.0 1.0
OP2 A:A40 4.7 34.5 1.0
O3' A:A40 4.7 49.5 1.0
N7 A:A41 4.7 34.4 1.0
N6 A:A42 4.8 24.6 1.0
O5' A:A40 4.9 38.8 1.0
C5' A:A41 5.0 33.3 1.0
C3' A:A40 5.0 41.1 1.0

Magnesium binding site 3 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 3 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:53.7
occ:1.00
 OP2 A:G30 3.3 36.5 1.0
C8 A:G29 3.4 36.6 1.0
N7 A:G29 3.5 36.1 1.0
OP2 A:G29 3.7 47.8 1.0
O5' A:G29 3.8 41.6 1.0
OP2 A:G31 3.9 34.4 1.0
C3' A:G29 4.3 38.0 1.0
N9 A:G29 4.4 34.2 1.0
P A:G30 4.4 45.7 1.0
P A:G29 4.4 50.5 1.0
O5' A:G30 4.5 39.2 1.0
C5 A:G29 4.5 30.7 1.0
C5' A:G30 4.7 34.7 1.0
O3' A:G29 4.9 45.2 1.0
P A:G31 4.9 31.3 1.0
C2' A:G29 5.0 34.8 1.0
C5' A:G29 5.0 37.8 1.0

Magnesium binding site 4 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 4 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:33.7
occ:1.00
 O4 A:U17 3.0 41.0 1.0
OP2 A:U20 3.6 37.7 1.0
OP1 A:U20 4.0 42.4 1.0
C4 A:U17 4.0 42.0 1.0
OP1 A:A19 4.1 41.3 1.0
P A:U20 4.2 45.3 1.0
N3 A:U17 4.3 42.1 1.0
P A:A19 5.0 36.3 1.0

Magnesium binding site 5 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 5 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:52.7
occ:1.00
 O6 A:G39 2.7 32.2 1.0
O02 B:CVC7 3.5 42.2 1.0
C6 A:G39 3.8 30.1 1.0
C8 B:CVC7 4.1 32.1 1.0
C01 B:CVC7 4.2 27.8 1.0
N7 A:G39 4.5 32.6 1.0
C5 A:G39 4.5 29.6 1.0
OP2 A:C38 4.8 36.9 1.0
P B:CVC7 4.9 34.2 1.0
C2' B:CVC7 4.9 34.4 1.0
N1 A:G39 4.9 25.4 1.0

Magnesium binding site 6 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 6 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:30.7
occ:0.50
 OP2 B:G14 2.6 32.5 1.0
O2' B:A13 2.9 31.6 1.0
O3' B:A13 3.4 29.7 1.0
P B:G14 3.6 32.8 1.0
C2' B:A13 4.0 27.4 1.0
C3' B:A13 4.3 29.4 1.0
C1' B:A13 4.6 25.6 1.0
OP1 B:G14 4.6 31.6 1.0
O5' B:G14 4.7 29.2 1.0
N7 B:G14 4.9 27.9 1.0

Magnesium binding site 7 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 7 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:55.0
occ:1.00
 OP1 B:C19 3.8 51.8 1.0
OP2 B:C19 4.7 43.2 1.0
P B:C19 4.8 49.5 1.0

Magnesium binding site 8 out of 8 in 5eao

Go back to Magnesium Binding Sites List in 5eao
Magnesium binding site 8 out of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:42.9
occ:1.00
 OP2 B:A16 3.1 33.5 1.0
OP2 B:U15 3.9 31.8 1.0
OP1 A:G1 4.3 65.8 1.0
P B:A16 4.5 33.2 1.0
O5' B:U15 4.6 31.5 1.0
N7 B:A16 4.7 30.7 1.0
C5' A:G1 4.7 59.3 1.0
P B:U15 4.7 33.3 1.0
C5 B:U15 4.9 28.8 1.0
C8 B:A16 4.9 31.4 1.0
P A:G1 5.0 80.9 1.0
C6 B:U15 5.0 28.7 1.0
O5' A:G1 5.0 66.3 1.0
O5' B:A16 5.0 33.2 1.0

Reference:

A.Mir, B.L.Golden. Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analogue. Biochemistry V. 55 633 2016.
ISSN: ISSN 0006-2960
PubMed: 26551631
DOI: 10.1021/ACS.BIOCHEM.5B01139
Page generated: Sun Sep 29 03:33:41 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