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Manganese in PDB 5eaq: Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+

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-MN2+, PDB code: 5eaq 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) 27.43 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.251, 87.419, 105.539, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 27.8

Other elements in 5eaq:

The structure of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ also contains other interesting chemical elements:

Vanadium (V) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ (pdb code 5eaq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+, PDB code: 5eaq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5eaq

Go back to Manganese Binding Sites List in 5eaq
Manganese binding site 1 out of 6 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn101

b:0.1
occ:1.00
OP2 A:A22 2.2 85.4 1.0
N7 A:G23 2.7 86.0 1.0
P A:A22 3.6 92.8 1.0
O6 A:G23 3.6 74.2 1.0
C5 A:G23 3.7 84.3 1.0
C8 A:G23 3.7 91.8 1.0
O1V B:CVC7 4.0 86.0 1.0
C6 A:G23 4.0 81.7 1.0
O5' A:A22 4.1 93.9 1.0
O3' A:G21 4.3 95.7 1.0
O5' B:U8 4.6 76.8 1.0
OP1 A:A22 4.8 97.1 1.0
C8 A:A22 4.9 84.1 1.0
C4 A:G23 4.9 86.1 1.0
N9 A:G23 4.9 95.3 1.0

Manganese binding site 2 out of 6 in 5eaq

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Manganese binding site 2 out of 6 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn102

b:0.5
occ:1.00
O6 A:G39 2.6 87.0 1.0
C6 A:G39 3.7 83.5 1.0
O02 B:CVC7 4.0 70.4 1.0
C8 B:CVC7 4.2 76.5 1.0
C01 B:CVC7 4.2 80.6 1.0
N7 A:G39 4.3 91.6 1.0
C5 A:G39 4.4 86.0 1.0
OP2 A:C38 4.6 97.6 1.0
N1 A:G39 4.9 78.0 1.0
OP2 A:A37 5.0 92.3 1.0

Manganese binding site 3 out of 6 in 5eaq

Go back to Manganese Binding Sites List in 5eaq
Manganese binding site 3 out of 6 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn103

b:0.4
occ:1.00
N7 A:G18 2.7 89.8 1.0
C8 A:G18 3.5 85.9 1.0
C5 A:G18 3.9 86.9 1.0
O6 A:G18 4.3 86.3 1.0
O2' A:U17 4.4 90.2 1.0
C6 A:G18 4.5 85.8 1.0
OP1 A:G18 4.6 90.7 1.0
O3' A:U17 4.6 97.9 1.0
N6 A:A19 4.7 94.0 1.0
N9 A:G18 4.8 84.0 1.0
C4 A:G18 5.0 83.7 1.0

Manganese binding site 4 out of 6 in 5eaq

Go back to Manganese Binding Sites List in 5eaq
Manganese binding site 4 out of 6 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn104

b:96.6
occ:0.50
N7 A:G1 2.4 97.6 1.0
OP2 A:G1 3.1 85.0 1.0
C8 A:G1 3.2 96.3 1.0
C5 A:G1 3.6 92.3 1.0
O6 A:G1 3.9 90.1 1.0
C6 A:G1 4.1 93.3 1.0
P A:G1 4.4 0.8 1.0
N9 A:G1 4.5 90.8 1.0
C4 A:G1 4.7 89.1 1.0
O5' A:G1 4.9 0.5 1.0

Manganese binding site 5 out of 6 in 5eaq

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Manganese binding site 5 out of 6 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn105

b:0.3
occ:1.00
OP2 A:A41 2.3 96.7 1.0
P A:A41 3.5 99.7 1.0
O5' A:A41 3.8 92.5 1.0
OP1 A:A41 4.2 0.3 1.0
OP2 A:A40 4.4 84.6 1.0
N7 A:A42 4.6 73.5 1.0
O5' A:A40 4.7 88.0 1.0
O3' A:A40 4.8 91.7 1.0
OP2 A:A42 4.8 74.9 1.0
C8 A:A41 4.8 80.0 1.0
N6 A:A42 4.9 64.2 1.0
N7 A:A41 5.0 78.9 1.0
C3' A:A40 5.0 91.7 1.0

Manganese binding site 6 out of 6 in 5eaq

Go back to Manganese Binding Sites List in 5eaq
Manganese binding site 6 out of 6 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn106

b:0.8
occ:1.00
N7 A:G29 2.6 91.5 1.0
C8 A:G29 3.5 88.7 1.0
C5 A:G29 3.7 81.5 1.0
O6 A:G29 3.8 97.4 1.0
OP2 A:U28 3.9 91.3 1.0
C6 A:G29 4.1 86.4 1.0
OP2 A:G29 4.3 98.3 1.0
C5 A:U28 4.6 83.6 1.0
N9 A:G29 4.7 85.5 1.0
C4 A:G29 4.8 80.4 1.0
C6 A:U28 4.9 83.0 1.0
P A:U28 5.0 0.7 1.0
O5' A:U28 5.0 93.8 1.0
OP2 A:G31 5.0 79.6 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: Tue Dec 15 04:37:53 2020

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