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Sodium in PDB 6q8u: Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein

Protein crystallography data

The structure of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein, PDB code: 6q8u was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.42 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.360, 60.800, 119.990, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein (pdb code 6q8u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein, PDB code: 6q8u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 6q8u

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Sodium binding site 1 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:78.8
occ:1.00
 OP2 A:A6 2.6 55.5 1.0
NA A:NA103 2.9 0.5 1.0
O D:PRO91 2.9 55.9 1.0
P A:A6 3.6 54.1 1.0
O5' A:A6 3.6 51.0 1.0
CG2 D:VAL90 3.6 53.7 1.0
CD D:PRO91 3.6 60.3 1.0
N D:PRO91 3.6 67.6 1.0
C D:PRO91 3.7 48.6 1.0
CB D:VAL90 3.7 58.8 1.0
C3' A:A6 3.8 47.4 1.0
CB D:PRO91 3.9 59.8 1.0
CA D:PRO91 4.0 62.2 1.0
C5' A:A6 4.0 52.0 1.0
OP1 A:A6 4.1 54.4 1.0
C2' A:A6 4.2 49.9 1.0
C D:VAL90 4.3 75.0 1.0
OP1 A:A7 4.3 54.1 1.0
CG D:PRO91 4.4 62.6 1.0
C4' A:A6 4.5 52.4 1.0
CA D:VAL90 4.6 65.7 1.0
O2' A:A6 4.7 62.9 1.0
N D:CYS92 4.8 53.0 1.0
CG1 D:VAL90 4.8 63.2 1.0
O3' A:A6 4.9 50.0 1.0
C8 A:A7 4.9 73.9 1.0
O3' A:G5 5.0 58.1 1.0
O D:VAL90 5.0 63.8 1.0

Sodium binding site 2 out of 10 in 6q8u

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Sodium binding site 2 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:70.9
occ:1.00
 N7 A:G15 2.6 54.8 1.0
NZ C:LYS37 2.7 73.8 1.0
OP2 A:G14 3.2 62.4 1.0
N7 A:G14 3.6 55.6 1.0
C8 A:G15 3.6 51.8 1.0
O6 A:G16 3.6 64.4 1.0
C5 A:G15 3.6 60.7 1.0
O6 A:G15 3.6 59.6 1.0
NA C:NA202 3.7 97.4 1.0
C8 A:G14 3.7 51.9 1.0
CE C:LYS37 3.8 84.7 1.0
C6 A:G15 4.0 53.1 1.0
O5' A:G14 4.2 55.1 1.0
P A:G14 4.3 59.7 1.0
ND2 C:ASN33 4.3 71.1 1.0
C6 A:G16 4.5 63.9 1.0
C5 A:G14 4.6 55.9 1.0
OP2 A:G15 4.7 51.6 1.0
N9 A:G14 4.8 52.1 1.0
N9 A:G15 4.8 53.4 1.0
C4 A:G15 4.9 55.6 1.0

Sodium binding site 3 out of 10 in 6q8u

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Sodium binding site 3 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na103

b:0.5
occ:1.00
 OP1 A:A7 2.8 54.1 1.0
NA A:NA101 2.9 78.8 1.0
C8 A:A7 3.0 73.9 1.0
NZ D:LYS79 3.0 66.1 1.0
CE D:LYS79 3.3 76.5 1.0
N7 A:A7 3.5 78.3 1.0
O5' A:A7 3.7 49.8 1.0
O D:PRO91 3.8 55.9 1.0
P A:A7 3.8 54.1 1.0
C D:PRO91 4.0 48.6 1.0
CB D:PRO91 4.0 59.8 1.0
N9 A:A7 4.1 66.7 1.0
C3' A:A6 4.3 47.4 1.0
N D:ALA93 4.3 53.9 1.0
C2' A:A7 4.5 57.1 1.0
N D:CYS92 4.5 53.0 1.0
O3' A:A6 4.6 50.0 1.0
CA D:PRO91 4.6 62.2 1.0
CA D:CYS92 4.7 53.2 1.0
C1' A:A7 4.7 61.8 1.0
CB D:ALA93 4.8 44.7 1.0
C D:CYS92 4.8 57.2 1.0
O4' A:A7 4.8 57.1 1.0
CD D:LYS79 4.8 74.4 1.0
C5 A:A7 4.8 77.8 1.0
C5' A:A7 4.9 45.6 1.0

Sodium binding site 4 out of 10 in 6q8u

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Sodium binding site 4 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:77.8
occ:1.00
 O D:HOH302 2.0 66.8 1.0
O6 B:G15 2.6 52.2 1.0
NA B:NA102 2.9 81.3 1.0
N7 B:G14 3.1 58.7 1.0
C6 B:G15 3.3 58.2 1.0
N7 B:G13 3.9 63.9 1.0
C5 B:G15 3.9 53.6 1.0
N7 B:G15 3.9 61.2 1.0
C8 B:G14 4.0 58.5 1.0
O6 B:G14 4.1 60.2 1.0
C5 B:G14 4.1 57.1 1.0
C5 B:G13 4.4 60.9 1.0
N1 B:G15 4.4 48.1 1.0
O6 B:G13 4.5 61.4 1.0
C6 B:G14 4.5 52.6 1.0
C8 B:G13 4.6 62.8 1.0
C6 B:G13 4.6 57.5 1.0
ND2 D:ASN33 4.7 63.0 1.0
O6 B:G16 4.9 63.5 1.0

Sodium binding site 5 out of 10 in 6q8u

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Sodium binding site 5 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:81.3
occ:1.00
 N7 B:G15 2.8 61.2 1.0
NA B:NA101 2.9 77.8 1.0
O D:HOH302 3.0 66.8 1.0
O6 B:G16 3.1 63.5 1.0
O6 B:G15 3.3 52.2 1.0
C5 B:G15 3.6 53.6 1.0
OP2 B:G14 3.7 59.4 1.0
ND2 D:ASN33 3.8 63.0 1.0
C6 B:G15 3.8 58.2 1.0
C8 B:G15 3.9 50.7 1.0
N7 B:G14 3.9 58.7 1.0
C6 B:G16 4.0 58.3 1.0
NZ D:LYS37 4.1 85.4 1.0
C8 B:G14 4.2 58.5 1.0
CG D:ASN33 4.6 69.1 1.0
O5' B:G14 4.7 61.2 1.0
OP2 B:G15 4.7 60.9 1.0
CB D:ASN33 4.7 57.7 1.0
N1 B:G16 4.8 56.1 1.0
C5 B:G16 4.8 49.0 1.0
P B:G14 4.9 62.9 1.0
C4 B:G15 4.9 51.1 1.0
CD D:LYS37 4.9 98.7 1.0
CE D:LYS37 4.9 0.9 1.0
C5 B:G14 5.0 57.1 1.0

Sodium binding site 6 out of 10 in 6q8u

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Sodium binding site 6 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:75.8
occ:1.00
 N C:LYS105 3.1 64.1 1.0
CB C:LYS105 3.2 94.7 1.0
OE1 C:GLU106 3.2 64.2 1.0
O C:GLU102 3.2 55.9 1.0
N C:ARG104 3.5 68.0 1.0
CA C:LYS105 3.8 69.2 1.0
C C:LEU103 3.9 57.5 1.0
C C:GLU102 4.1 61.0 1.0
C C:ARG104 4.1 63.4 1.0
CA C:LEU103 4.2 53.4 1.0
CA C:ARG104 4.2 67.5 1.0
CD C:GLU106 4.2 69.2 1.0
N C:LEU103 4.4 51.7 1.0
OE2 C:GLU106 4.4 68.3 1.0
CB C:ARG104 4.4 71.4 1.0
N C:GLU106 4.5 55.8 1.0
CG C:LYS105 4.5 0.9 1.0
O C:LEU103 4.6 52.5 1.0
C C:LYS105 4.6 57.7 1.0
CE C:LYS105 4.7 0.7 1.0
CG C:ARG104 4.8 75.6 1.0
CD C:LYS105 4.8 0.2 1.0

Sodium binding site 7 out of 10 in 6q8u

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Sodium binding site 7 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:97.4
occ:1.00
 NZ C:LYS37 2.8 73.8 1.0
N7 A:G16 2.9 62.1 1.0
O6 A:G16 3.0 64.4 1.0
CE C:LYS37 3.1 84.7 1.0
CD C:LYS37 3.1 68.1 1.0
C5 A:G16 3.6 63.5 1.0
C6 A:G16 3.6 63.9 1.0
NA A:NA102 3.7 70.9 1.0
CB C:ASN33 3.7 58.2 1.0
CG C:GLU34 3.8 77.5 1.0
OP2 A:G15 3.9 51.6 1.0
N C:GLU34 4.0 51.2 1.0
N7 A:G15 4.0 54.8 1.0
C C:ASN33 4.0 59.7 1.0
C8 A:G16 4.1 64.4 1.0
CA C:GLU34 4.2 58.5 1.0
O C:ASN33 4.3 56.5 1.0
C8 A:G15 4.3 51.8 1.0
CG C:LYS37 4.5 61.8 1.0
CA C:ASN33 4.5 60.0 1.0
CB C:GLU34 4.6 58.5 1.0
CG C:ASN33 4.7 71.7 1.0
ND2 C:ASN33 4.7 71.1 1.0
C4 A:G16 4.9 60.6 1.0
CD C:GLU34 5.0 72.3 1.0

Sodium binding site 8 out of 10 in 6q8u

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Sodium binding site 8 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:76.0
occ:1.00
 N C:GLU100 3.2 63.9 1.0
NH1 C:ARG104 3.6 79.8 1.0
OD1 C:ASN99 3.6 99.4 1.0
O C:HOH301 3.7 67.7 1.0
CE C:LYS45 3.7 67.8 1.0
CB C:GLU100 3.8 74.8 1.0
CA C:ASN99 3.9 56.6 1.0
CG C:GLU100 4.1 81.2 1.0
C C:ASN99 4.1 64.6 1.0
CA C:GLU100 4.1 65.2 1.0
O C:ILE98 4.4 61.3 1.0
CG C:LYS45 4.4 56.4 1.0
NZ C:LYS45 4.4 61.8 1.0
CD C:LYS45 4.5 61.7 1.0
CG C:ASN99 4.5 90.4 1.0
OE1 C:GLU100 4.6 0.1 1.0
CB C:ASN99 4.7 59.0 1.0
CD C:GLU100 4.7 92.5 1.0
CZ C:ARG104 4.8 90.7 1.0
N C:GLY101 4.8 61.5 1.0
N C:ASN99 4.9 55.8 1.0
C C:GLU100 5.0 64.3 1.0

Sodium binding site 9 out of 10 in 6q8u

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Sodium binding site 9 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:81.1
occ:1.00
 OE1 D:GLU34 2.9 68.5 1.0
N D:LYS30 3.0 54.0 1.0
CD D:GLU34 3.3 76.5 1.0
OE2 D:GLU34 3.4 85.6 1.0
CG D:LYS30 3.4 77.3 1.0
CA D:LYS29 3.6 64.6 1.0
O2' B:G16 3.7 59.6 1.0
O D:LYS30 3.7 51.6 1.0
C D:LYS29 3.7 58.3 1.0
CA D:LYS30 3.9 55.7 1.0
CB D:LYS30 3.9 64.2 1.0
O D:VAL28 4.0 71.8 1.0
CD D:LYS29 4.0 71.2 1.0
CD D:LYS30 4.1 82.3 1.0
C D:LYS30 4.3 53.0 1.0
CB D:LYS29 4.3 65.2 1.0
CG D:GLU34 4.5 66.6 1.0
CE D:LYS30 4.6 93.1 1.0
CB D:GLU34 4.6 61.0 1.0
N D:LYS29 4.6 60.7 1.0
C D:VAL28 4.7 72.0 1.0
C2' B:G16 4.7 58.6 1.0
CG D:LYS29 4.8 69.4 1.0
O D:LYS29 4.9 54.5 1.0
N2 A:G8 5.0 57.5 1.0
N1 A:G8 5.0 53.5 1.0

Sodium binding site 10 out of 10 in 6q8u

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Sodium binding site 10 out of 10 in the Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of the Standard Kink Turn Hmkt-7 Variant A2BM6A Bound with AFL7AE Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:77.2
occ:1.00
 N D:VAL28 3.5 76.6 1.0
O D:VAL28 3.8 71.8 1.0
CB D:VAL28 4.1 66.2 1.0
O D:ARG23 4.1 0.3 1.0
CA D:VAL28 4.2 68.0 1.0
CA D:LYS27 4.2 74.0 1.0
CE D:LYS30 4.3 93.1 1.0
C D:LYS27 4.3 72.9 1.0
CG D:ARG23 4.4 94.4 1.0
CA D:ARG23 4.4 0.6 1.0
O D:GLY26 4.4 88.5 1.0
C D:VAL28 4.5 72.0 1.0
NZ D:LYS30 4.5 97.7 1.0
CB D:ARG23 4.5 0.8 1.0
CG2 D:VAL28 4.6 69.5 1.0
C D:ARG23 4.7 0.5 1.0

Reference:

S.Ashraf, L.Huang, D.M.J.Lilley. Effect of Methylation of Adenine N6ON Kink Turn Structure Depends on Location. Rna Biol. V. 16 1377 2019.
ISSN: ESSN 1555-8584
PubMed: 31234702
DOI: 10.1080/15476286.2019.1630797
Page generated: Tue Oct 8 12:48:38 2024

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