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Sodium in PDB 8e9a: Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg

Enzymatic activity of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg

All present enzymatic activity of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg, PDB code: 8e9a was solved by E.R.Cramer, A.R.Robart, A.I.Kaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.92 / 2.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.829, 48.419, 139.845, 90, 90, 90
R / Rfree (%) 25.5 / 28.9

Other elements in 8e9a:

The structure of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg (pdb code 8e9a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg, PDB code: 8e9a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 8e9a

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Sodium binding site 1 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:97.8
occ:1.00
 H A:GLN146 2.1 92.1 1.0
H A:ASN145 2.1 84.1 1.0
N A:ASN145 2.1 70.0 1.0
C A:LYS144 2.1 63.5 1.0
N A:LYS144 2.2 78.3 1.0
HA A:LYS144 2.2 70.7 1.0
CA A:LYS144 2.2 58.9 1.0
H A:LYS144 2.3 94.1 1.0
N A:GLN146 2.7 76.7 1.0
O A:HOH310 2.7 46.7 1.0
C A:PHE143 2.8 64.7 1.0
H A:THR147 3.0 75.3 1.0
HB3 A:PHE143 3.0 75.8 1.0
O A:LYS144 3.0 58.0 1.0
CA A:ASN145 3.2 64.0 1.0
C A:ASN145 3.3 62.3 1.0
O A:PHE143 3.3 55.0 1.0
HA A:ASN145 3.5 76.9 1.0
HA A:GLN146 3.6 88.2 1.0
CB A:PHE143 3.7 63.1 1.0
CA A:GLN146 3.7 73.5 1.0
CB A:LYS144 3.7 51.3 1.0
HB2 A:PHE143 3.7 75.8 1.0
N A:THR147 3.8 62.7 1.0
CA A:PHE143 3.8 56.5 1.0
HA A:PHE143 4.1 67.9 1.0
HB3 A:LYS144 4.1 61.6 1.0
O A:THR147 4.2 57.9 1.0
HB2 A:LYS144 4.2 61.6 1.0
C A:GLN146 4.3 74.6 1.0
HB2 A:LYS136 4.3 69.8 1.0
HA A:TYR135 4.3 66.1 1.0
H A:LYS136 4.3 71.3 1.0
O A:ASN145 4.4 72.4 1.0
HB2 A:ASN145 4.4 75.0 1.0
CB A:ASN145 4.4 62.4 1.0
HG3 A:LYS144 4.5 68.5 1.0
CG A:LYS144 4.6 57.0 1.0
HG2 A:LYS144 4.6 68.5 1.0
HB3 A:LYS136 4.7 69.8 1.0
N A:LYS136 4.8 59.3 1.0
HB A:THR147 4.8 102.5 1.0
CA A:THR147 4.9 68.4 1.0
C A:THR147 4.9 65.5 1.0
CB A:LYS136 4.9 58.1 1.0
CB A:GLN146 5.0 77.0 1.0

Sodium binding site 2 out of 12 in 8e9a

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Sodium binding site 2 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:64.2
occ:1.00
 O A:THR103 2.4 50.6 1.0
HE2 A:PHE116 2.9 63.6 1.0
HG3 A:GLN139 3.0 89.7 1.0
HZ A:PHE116 3.1 50.6 1.0
HB2 A:ALA104 3.4 68.7 1.0
HE1 A:TYR140 3.4 85.1 1.0
HD2 A:ARG84 3.5 70.1 1.0
HB2 A:GLN139 3.5 73.2 1.0
HH11 A:ARG84 3.5 87.4 1.0
HA A:ALA104 3.6 69.6 1.0
C A:THR103 3.6 56.5 1.0
CE2 A:PHE116 3.6 52.9 1.0
CZ A:PHE116 3.7 42.1 1.0
HB1 A:ALA112 3.8 76.2 1.0
CG A:GLN139 3.9 74.7 1.0
HB2 A:ALA112 3.9 76.2 1.0
HE21 A:GLN139 3.9 98.1 1.0
CE1 A:TYR140 4.0 70.8 1.0
NH1 A:ARG84 4.1 72.8 1.0
HB3 A:PHE102 4.1 64.6 1.0
CB A:GLN139 4.2 60.9 1.0
CA A:ALA104 4.2 57.9 1.0
CB A:ALA104 4.2 57.2 1.0
OE2 A:GLU108 4.2 81.7 1.0
H A:THR103 4.2 62.1 1.0
N A:ALA104 4.3 53.9 1.0
CB A:ALA112 4.3 63.4 1.0
HD11 A:LEU53 4.3 64.8 1.0
HH12 A:ARG84 4.4 87.4 1.0
CD A:ARG84 4.4 58.4 1.0
OH A:TYR140 4.4 66.9 1.0
HG2 A:GLN139 4.4 89.7 1.0
HB3 A:ARG84 4.5 76.7 1.0
N A:THR103 4.5 51.6 1.0
HB3 A:GLN139 4.5 73.2 1.0
NE2 A:GLN139 4.6 81.7 1.0
HD3 A:ARG84 4.6 70.1 1.0
HB1 A:ALA104 4.6 68.7 1.0
CZ A:TYR140 4.6 81.5 1.0
CA A:THR103 4.7 59.3 1.0
HD13 A:LEU53 4.7 64.8 1.0
CD A:GLN139 4.8 73.9 1.0
CD1 A:TYR140 4.8 69.4 1.0
CZ A:ARG84 4.8 65.0 1.0
HD1 A:TYR140 4.9 83.3 1.0
HB3 A:ALA104 4.9 68.7 1.0
CD2 A:PHE116 4.9 60.2 1.0
O A:GLN139 4.9 78.2 1.0
CD1 A:LEU53 4.9 53.9 1.0
HB2 A:PHE102 5.0 64.6 1.0
CB A:PHE102 5.0 53.8 1.0
NE A:ARG84 5.0 56.1 1.0
HA A:ALA112 5.0 62.7 1.0
HB3 A:ALA112 5.0 76.2 1.0

Sodium binding site 3 out of 12 in 8e9a

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Sodium binding site 3 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:80.1
occ:1.00
 O A:LEU62 2.2 89.5 1.0
O A:GLU83 2.4 57.9 1.0
HG21 A:THR103 2.6 51.9 1.0
H A:LEU66 2.7 79.9 1.0
HB A:VAL65 2.8 92.9 1.0
HG A:LEU66 3.0 66.2 1.0
HD12 A:LEU62 3.1 86.3 1.0
HG1 A:THR103 3.1 76.8 1.0
C A:LEU62 3.3 77.0 1.0
HA A:LEU62 3.4 100.6 1.0
HB2 A:LEU66 3.4 68.2 1.0
H A:VAL65 3.4 88.5 1.0
HG A:LEU62 3.4 92.1 1.0
HA A:GLU83 3.4 88.2 1.0
HD3 A:PRO67 3.5 90.5 1.0
C A:GLU83 3.5 71.6 1.0
N A:LEU66 3.5 66.5 1.0
HG2 A:GLU83 3.5 97.6 1.0
CG2 A:THR103 3.5 43.2 1.0
CB A:VAL65 3.8 77.3 1.0
CD1 A:LEU62 3.8 71.8 1.0
HG23 A:THR103 3.8 51.9 1.0
OG1 A:THR103 3.8 63.9 1.0
CA A:LEU62 3.8 83.8 1.0
CG A:LEU66 3.9 55.1 1.0
HD11 A:LEU62 3.9 86.3 1.0
CB A:LEU66 4.0 56.8 1.0
CA A:GLU83 4.0 73.5 1.0
CG A:LEU62 4.0 76.7 1.0
N A:VAL65 4.0 73.7 1.0
HD2 A:PRO67 4.1 90.5 1.0
HG3 A:GLU83 4.1 97.6 1.0
CB A:THR103 4.2 57.1 1.0
HG22 A:THR103 4.2 51.9 1.0
HG23 A:VAL65 4.2 87.1 1.0
CD A:PRO67 4.2 75.4 1.0
CG A:GLU83 4.2 81.3 1.0
HB A:THR103 4.2 68.6 1.0
CA A:VAL65 4.3 64.6 1.0
CA A:LEU66 4.4 66.3 1.0
C A:VAL65 4.4 64.1 1.0
HA A:ARG84 4.4 76.9 1.0
HA A:LYS63 4.4 105.8 1.0
N A:LYS63 4.4 75.8 1.0
HD12 A:LEU66 4.4 73.8 1.0
CG2 A:VAL65 4.5 72.5 1.0
CB A:LEU62 4.5 86.8 1.0
HG12 A:VAL65 4.5 77.2 1.0
C A:LYS63 4.6 89.5 1.0
HG21 A:VAL65 4.6 87.1 1.0
HD13 A:LEU62 4.6 86.3 1.0
CD1 A:LEU66 4.6 61.5 1.0
N A:ARG84 4.7 67.0 1.0
O A:GLY82 4.7 67.8 1.0
CB A:GLU83 4.7 76.5 1.0
CG1 A:VAL65 4.7 64.3 1.0
CA A:LYS63 4.7 88.0 1.0
HD23 A:LEU66 4.7 74.3 1.0
HD11 A:LEU66 4.8 73.8 1.0
HG21 A:VAL56 4.8 82.6 1.0
O A:LEU61 4.8 84.5 1.0
H A:HIS64 4.8 107.2 1.0
O A:LYS63 4.8 76.9 1.0
N A:HIS64 4.8 89.2 1.0
HB3 A:LEU66 4.8 68.2 1.0
CD2 A:LEU66 4.9 61.9 1.0
HG11 A:VAL65 4.9 77.2 1.0

Sodium binding site 4 out of 12 in 8e9a

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Sodium binding site 4 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:84.2
occ:1.00
 HZ3 A:LYS144 1.8 84.8 1.0
HZ1 A:LYS144 1.8 84.8 1.0
NZ A:LYS144 2.1 70.6 1.0
HZ2 A:LYS144 2.7 84.8 1.0
HG13 A:VAL149 3.3 74.5 1.0
CE A:LYS144 3.3 61.2 1.0
HE2 A:LYS144 3.4 73.6 1.0
HE3 A:LYS144 3.6 73.6 1.0
HG11 A:VAL149 3.7 74.5 1.0
CG1 A:VAL149 3.9 62.0 1.0
OH A:TYR135 4.3 76.3 1.0
HG22 A:VAL149 4.4 76.5 1.0
HG12 A:VAL149 4.5 74.5 1.0
HG21 A:VAL149 4.6 76.5 1.0
CD A:LYS144 4.6 64.7 1.0
HD3 A:LYS144 4.6 77.7 1.0
HH A:TYR135 4.6 91.7 1.0
CG2 A:VAL149 4.8 63.7 1.0
HD2 A:LYS144 4.9 77.7 1.0
CB A:VAL149 5.0 70.6 1.0

Sodium binding site 5 out of 12 in 8e9a

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Sodium binding site 5 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:76.8
occ:1.00
 O A:THR166 2.4 61.4 1.0
HD2 A:ARG168 2.9 93.7 1.0
OH A:TYR122 3.2 58.9 1.0
HB3 A:PHE165 3.2 81.5 1.0
HB A:THR166 3.3 90.7 1.0
HD3 A:ARG168 3.3 93.7 1.0
HE1 A:TYR122 3.4 79.0 1.0
C A:THR166 3.4 66.5 1.0
H A:THR166 3.5 97.5 1.0
HH11 A:ARG168 3.5 119.0 1.0
CD A:ARG168 3.5 78.0 1.0
N A:THR166 3.7 81.2 1.0
HH A:TYR122 3.7 70.8 1.0
HG3 A:ARG168 3.9 94.3 1.0
CA A:THR166 3.9 79.4 1.0
CB A:THR166 4.0 75.5 1.0
CB A:PHE165 4.1 67.8 1.0
HB2 A:PHE165 4.1 81.5 1.0
CZ A:TYR122 4.1 68.2 1.0
CE1 A:TYR122 4.1 65.8 1.0
HD11 A:ILE126 4.2 73.9 1.0
CG A:ARG168 4.2 78.5 1.0
HB2 A:ARG168 4.3 83.0 1.0
NH1 A:ARG168 4.3 99.1 1.0
C A:PHE165 4.4 77.1 1.0
N A:TYR167 4.6 62.0 1.0
NE A:ARG168 4.7 98.5 1.0
HA A:TYR167 4.7 90.3 1.0
OG1 A:THR166 4.8 67.4 1.0
CA A:PHE165 4.8 78.4 1.0
CB A:ARG168 4.8 69.1 1.0
HA A:THR166 4.9 95.4 1.0
HD12 A:ILE160 4.9 80.5 1.0
HD2 A:PHE165 4.9 86.1 1.0
HH12 A:ARG168 4.9 119.0 1.0
C A:TYR167 4.9 79.2 1.0
HA A:PHE165 4.9 94.1 1.0
N A:ARG168 5.0 73.7 1.0
CZ A:ARG168 5.0 96.9 1.0
CA A:TYR167 5.0 75.2 1.0

Sodium binding site 6 out of 12 in 8e9a

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Sodium binding site 6 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:70.6
occ:1.00
 N B:LYS28 2.1 63.7 1.0
HB2 B:LYS28 2.2 90.3 1.0
OE1 A:GLU21 2.5 82.2 1.0
HA B:ILE27 2.6 79.6 1.0
CB B:LYS28 2.9 75.2 1.0
CA B:LYS28 2.9 67.9 1.0
HG23 B:ILE27 3.0 92.8 1.0
HH22 A:ARG70 3.0 84.1 1.0
C B:ILE27 3.0 60.1 1.0
CD A:GLU21 3.2 91.8 1.0
CA B:ILE27 3.2 66.3 1.0
OE2 A:GLU21 3.3 85.0 1.0
O B:LYS28 3.3 60.3 1.0
HD3 B:LYS28 3.4 111.0 1.0
HH21 A:ARG70 3.4 84.1 1.0
NH2 A:ARG70 3.6 70.0 1.0
C B:LYS28 3.6 64.4 1.0
HG22 B:ILE27 3.6 92.8 1.0
O B:HOH302 3.7 66.0 1.0
CG2 B:ILE27 3.7 77.2 1.0
HB3 B:LYS28 3.7 90.3 1.0
HG3 B:LYS28 3.7 97.9 1.0
CG B:LYS28 3.8 81.5 1.0
HA B:LYS28 3.8 81.6 1.0
OD1 A:ASN68 3.8 80.1 1.0
CD B:LYS28 4.0 92.4 1.0
CB B:ILE27 4.1 70.7 1.0
O B:LEU26 4.1 75.9 1.0
O B:ILE27 4.2 61.4 1.0
HD13 B:ILE27 4.2 84.0 1.0
N B:ILE27 4.4 68.6 1.0
HE3 B:LYS28 4.5 92.7 1.0
HB3 A:ASN68 4.5 82.5 1.0
HG21 B:ILE27 4.5 92.8 1.0
HB3 A:GLU21 4.6 93.0 1.0
HG2 B:LYS28 4.7 97.9 1.0
C B:LEU26 4.7 69.8 1.0
CG A:GLU21 4.7 85.5 1.0
CE B:LYS28 4.8 77.2 1.0
CG A:ASN68 4.8 74.4 1.0
HB B:ILE27 4.8 85.0 1.0
HD2 B:LYS28 4.8 111.0 1.0
HD23 B:LEU26 4.9 86.9 1.0
CZ A:ARG70 4.9 78.3 1.0
N B:ILE29 4.9 77.4 1.0
HE2 B:LYS28 5.0 92.7 1.0

Sodium binding site 7 out of 12 in 8e9a

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Sodium binding site 7 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:72.6
occ:1.00
 O B:HOH304 2.5 56.3 1.0
HB3 B:ARG84 2.6 99.8 1.0
O B:ARG84 2.6 61.8 1.0
H4' D:DG4 2.6 76.8 1.0
HB2 B:LYS85 3.0 100.7 1.0
HZ B:PHE116 3.0 79.4 1.0
HB2 B:ARG84 3.2 99.8 1.0
C B:ARG84 3.2 74.4 1.0
CB B:ARG84 3.3 83.1 1.0
HD1 B:PHE102 3.3 86.1 1.0
H5'' D:DG4 3.4 73.2 1.0
HE21 B:GLN139 3.4 82.7 1.0
C4' D:DG4 3.5 64.0 1.0
HB3 B:PHE102 3.5 89.6 1.0
O D:HOH207 3.8 79.2 1.0
C5' D:DG4 3.8 61.0 1.0
H5' D:DG4 3.8 73.2 1.0
CB B:LYS85 3.9 83.8 1.0
CA B:ARG84 3.9 78.1 1.0
CZ B:PHE116 3.9 66.1 1.0
NE2 B:GLN139 4.0 68.8 1.0
N B:LYS85 4.0 77.3 1.0
CD1 B:PHE102 4.0 71.7 1.0
HE22 B:GLN139 4.0 82.7 1.0
HB3 B:LYS85 4.1 100.7 1.0
HA B:LYS85 4.1 82.7 1.0
CA B:LYS85 4.2 68.9 1.0
HA B:ARG84 4.3 93.8 1.0
HE1 B:PHE116 4.4 83.4 1.0
CB B:PHE102 4.4 74.6 1.0
O4' D:DG4 4.4 62.4 1.0
O3' D:DG4 4.4 61.1 1.0
C3' D:DG4 4.5 73.3 1.0
CG B:ARG84 4.5 91.0 1.0
HD2 B:ARG84 4.6 85.7 1.0
HA B:PHE102 4.6 86.4 1.0
CG B:PHE102 4.6 67.6 1.0
HG3 B:ARG84 4.6 109.2 1.0
H B:THR103 4.6 83.8 1.0
CE1 B:PHE116 4.6 69.4 1.0
H B:LYS85 4.7 92.9 1.0
OH B:TYR140 4.7 63.4 1.0
H3' D:DG4 4.7 88.1 1.0
HG3 B:GLN139 4.8 94.2 1.0
HE2 B:PHE116 4.8 75.3 1.0
CE1 B:PHE102 4.9 59.9 1.0
HE1 B:PHE102 4.9 72.0 1.0
CE2 B:PHE116 4.9 62.7 1.0
HD2 B:LYS85 4.9 100.2 1.0

Sodium binding site 8 out of 12 in 8e9a

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Sodium binding site 8 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:81.4
occ:1.00
 OE2 B:GLU83 2.4 96.1 1.0
OE1 B:GLU83 2.5 95.4 1.0
CD B:GLU83 2.8 98.4 1.0
HD23 B:LEU62 3.9 107.0 1.0
HB3 B:LEU62 4.0 117.6 1.0
CG B:GLU83 4.3 99.1 1.0
HD22 B:LEU62 4.6 107.0 1.0
HB2 B:LEU62 4.6 117.6 1.0
HG3 B:GLU83 4.6 119.0 1.0
CD2 B:LEU62 4.7 89.1 1.0
HE2 B:LYS63 4.7 130.9 1.0
CB B:LEU62 4.7 98.0 1.0
HG2 B:GLU83 4.7 119.0 1.0
HB3 B:GLU83 4.8 106.9 1.0

Sodium binding site 9 out of 12 in 8e9a

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Sodium binding site 9 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:71.3
occ:1.00
 OP1 D:DC52 2.3 71.9 1.0
OG B:SER39 2.4 84.0 1.0
OD2 B:ASP51 2.5 71.2 1.0
H B:SER39 2.5 75.6 1.0
OD1 B:ASP49 2.8 75.9 1.0
NA D:NA104 2.9 69.2 1.0
HB3 B:SER39 3.3 78.8 1.0
OD2 B:ASP49 3.3 67.3 1.0
N B:SER39 3.3 63.0 1.0
CB B:SER39 3.4 65.6 1.0
CG B:ASP49 3.4 73.4 1.0
H5'' D:DC52 3.5 93.3 1.0
P D:DC52 3.6 86.2 1.0
CG B:ASP51 3.6 67.6 1.0
HA3 B:GLY38 3.8 99.3 1.0
O B:HOH303 3.9 60.9 1.0
O5' D:DC52 3.9 74.4 1.0
CA B:SER39 4.0 68.4 1.0
C5' D:DC52 4.2 77.6 1.0
HB2 B:SER39 4.2 78.8 1.0
OD1 B:ASP51 4.2 72.0 1.0
C B:GLY38 4.3 72.7 1.0
CA B:GLY38 4.4 82.7 1.0
NH2 B:ARG42 4.4 81.4 1.0
HA2 B:GLY38 4.4 99.3 1.0
OP2 D:DC52 4.4 75.3 1.0
O B:ASP49 4.4 64.2 1.0
HH21 B:ARG42 4.5 97.8 1.0
HB3 B:ASN48 4.5 100.2 1.0
H B:ASP49 4.5 94.0 1.0
H5' D:DC52 4.6 93.3 1.0
HA B:SER39 4.6 82.1 1.0
HB2 B:ASP51 4.7 80.9 1.0
O D:HOH202 4.7 69.7 1.0
H B:LEU40 4.7 103.8 1.0
O3' D:DG51 4.8 70.5 1.0
CB B:ASP49 4.8 71.5 1.0
CB B:ASP51 4.8 67.4 1.0
C B:ASP49 4.9 68.6 1.0
N B:ASP49 4.9 78.3 1.0
H B:ASN48 5.0 93.0 1.0

Sodium binding site 10 out of 12 in 8e9a

Go back to Sodium Binding Sites List in 8e9a
Sodium binding site 10 out of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na102

b:85.8
occ:1.00
 H5'' C:DT37 1.6 106.0 1.0
H5' C:DT37 2.3 106.0 1.0
C5' C:DT37 2.3 88.3 1.0
O C:HOH205 2.4 87.0 1.0
O3' C:DC36 2.6 103.2 1.0
H3' C:DT37 2.7 107.0 1.0
H4' C:DC36 3.0 127.5 1.0
O5' C:DT37 3.4 103.3 1.0
C4' C:DT37 3.4 86.7 1.0
C3' C:DT37 3.4 89.1 1.0
H2'' C:DC36 3.5 129.5 1.0
C3' C:DC36 3.5 106.5 1.0
OP2 C:DC39 3.6 127.2 1.0
P C:DT37 3.6 104.2 1.0
OP2 C:DA38 3.6 103.1 1.0
C4' C:DC36 3.7 106.2 1.0
H5' C:DC39 3.7 110.0 1.0
H4' C:DA38 3.9 147.6 1.0
H4' C:DT37 3.9 104.2 1.0
H2' C:DT37 3.9 102.2 1.0
H5 C:DC39 4.0 94.5 1.0
H6 C:DC39 4.0 75.8 1.0
C2' C:DC36 4.0 107.9 1.0
H1' C:DA38 4.1 145.5 1.0
H5'' C:DC36 4.1 118.7 1.0
OP1 C:DT37 4.1 95.7 1.0
C2' C:DT37 4.3 85.1 1.0
H3' C:DC36 4.4 127.9 1.0
O4' C:DT37 4.5 80.7 1.0
O3' C:DT37 4.5 94.9 1.0
C5' C:DC36 4.5 98.9 1.0
C5' C:DC39 4.5 91.6 1.0
C5 C:DC39 4.5 78.7 1.0
C6 C:DC39 4.6 63.1 1.0
H5'' C:DC39 4.6 110.0 1.0
O4' C:DA38 4.6 114.7 1.0
P C:DA38 4.6 97.7 1.0
C4' C:DA38 4.7 122.9 1.0
H1' C:DC36 4.7 130.0 1.0
H2' C:DC36 4.8 129.5 1.0
O4' C:DC36 4.8 112.3 1.0
OP2 C:DT37 4.8 91.3 1.0
C1' C:DC36 4.8 108.3 1.0
C1' C:DA38 4.8 121.2 1.0
P C:DC39 4.8 122.4 1.0
O5' C:DC39 4.9 97.6 1.0
H2'' C:DT37 5.0 102.2 1.0

Reference:

E.R.Cramer, S.A.Starcovic, R.M.Avey, A.I.Kaya, A.R.Robart. Structure of A 10-23 Deoxyribozyme Exhibiting A Homodimer Conformation. Commun Chem V. 6 119 2023.
ISSN: ESSN 2399-3669
PubMed: 37301907
DOI: 10.1038/S42004-023-00924-3
Page generated: Wed Oct 9 11:40:23 2024

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