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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 20:14:42 2020

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