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Sodium in PDB 3n0u: Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima

Enzymatic activity of Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima

All present enzymatic activity of Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima:
4.2.99.18;

Protein crystallography data

The structure of Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima, PDB code: 3n0u was solved by D.R.Cooper, A.Roy, Z.S.Derewenda, Integrated Center For Structure Andfunction Innovation (Isfi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.85 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.871, 93.635, 135.895, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 19

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima (pdb code 3n0u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima, PDB code: 3n0u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3n0u

Go back to Sodium Binding Sites List in 3n0u
Sodium binding site 1 out of 3 in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima


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 TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:22.1
occ:1.00
 O A:ALA123 2.3 21.4 1.0
O A:VAL120 2.3 20.7 1.0
O A:ILE126 2.4 18.8 1.0
O A:HOH277 2.5 34.0 1.0
O A:HOH399 2.7 42.7 1.0
O A:LEU119 3.1 19.4 1.0
HA A:VAL120 3.2 23.2 1.0
C A:VAL120 3.2 23.7 1.0
H A:ILE126 3.3 20.1 1.0
C A:ALA123 3.4 19.7 1.0
H A:ALA123 3.4 21.4 1.0
HB A:ILE126 3.5 22.3 1.0
C A:ILE126 3.5 16.4 1.0
CA A:VAL120 3.7 19.3 1.0
N A:ALA123 3.8 17.9 1.0
N A:ILE126 4.0 16.8 1.0
HA A:LYS124 4.0 22.9 1.0
HB3 A:ALA123 4.1 24.2 1.0
CA A:ILE126 4.1 16.9 1.0
CA A:ALA123 4.1 18.3 1.0
O A:HOH303 4.1 53.6 1.0
C A:LEU119 4.1 18.8 1.0
HA2 A:GLY127 4.2 25.7 1.0
CB A:ILE126 4.2 18.6 1.0
N A:ARG121 4.2 21.8 1.0
H A:ASN122 4.3 25.7 1.0
C A:ARG121 4.3 20.9 1.0
N A:ASN122 4.3 21.4 1.0
N A:LYS124 4.4 18.6 1.0
HG22 A:ILE126 4.4 24.9 1.0
N A:VAL120 4.4 18.1 1.0
O A:HOH586 4.4 57.5 1.0
HG13 A:VAL120 4.5 31.6 1.0
N A:GLY127 4.5 17.8 1.0
HA A:ARG121 4.5 25.1 1.0
CA A:LYS124 4.6 19.1 1.0
CB A:ALA123 4.6 20.2 1.0
CA A:ARG121 4.6 20.9 1.0
O A:ARG121 4.6 25.6 1.0
H A:GLY125 4.6 21.8 1.0
C A:ASN122 4.7 21.0 1.0
HG12 A:VAL120 4.7 31.6 1.0
N A:GLY125 4.8 18.1 1.0
CG2 A:ILE126 4.8 20.7 1.0
C A:LYS124 4.8 17.4 1.0
CA A:GLY127 4.9 21.4 1.0
H A:ARG121 4.9 26.1 1.0
CG1 A:VAL120 4.9 26.3 1.0
CB A:VAL120 4.9 22.4 1.0
O A:HOH213 5.0 20.7 1.0
HD3 A:LYS124 5.0 44.6 1.0
HA A:ALA123 5.0 22.0 1.0

Sodium binding site 2 out of 3 in 3n0u

Go back to Sodium Binding Sites List in 3n0u
Sodium binding site 2 out of 3 in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima


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 TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na208

b:20.3
occ:1.00
 O B:ILE126 2.3 18.1 1.0
O B:ALA123 2.3 19.8 1.0
O B:VAL120 2.4 19.1 1.0
O B:HOH267 2.5 35.7 1.0
O B:HOH298 2.6 35.4 1.0
O B:LEU119 2.8 17.9 1.0
HA B:VAL120 2.9 20.9 1.0
C B:VAL120 3.1 19.1 1.0
H B:ALA123 3.3 20.5 1.0
H B:ILE126 3.3 19.0 1.0
C B:ALA123 3.4 17.1 1.0
HB B:ILE126 3.4 18.9 1.0
C B:ILE126 3.4 17.0 1.0
CA B:VAL120 3.5 17.4 1.0
N B:ALA123 3.7 17.1 1.0
C B:LEU119 3.8 16.4 1.0
HB3 B:ALA123 3.9 24.8 1.0
N B:ILE126 4.0 15.8 1.0
CA B:ALA123 4.0 16.8 1.0
CA B:ILE126 4.1 15.9 1.0
HA B:LYS124 4.1 19.4 1.0
HA2 B:GLY127 4.1 19.4 1.0
N B:ARG121 4.1 19.7 1.0
CB B:ILE126 4.1 15.7 1.0
N B:VAL120 4.1 16.0 1.0
H B:ASN122 4.2 23.0 1.0
N B:ASN122 4.2 19.2 1.0
O B:HOH329 4.2 43.4 1.0
C B:ARG121 4.3 18.6 1.0
HG22 B:ILE126 4.3 24.6 1.0
N B:LYS124 4.4 17.5 1.0
HG13 B:VAL120 4.4 29.3 1.0
N B:GLY127 4.5 15.8 1.0
CB B:ALA123 4.5 20.7 1.0
C B:ASN122 4.6 23.3 1.0
CA B:LYS124 4.6 16.1 1.0
CA B:ARG121 4.6 20.1 1.0
O B:ARG121 4.6 22.9 1.0
HA B:ARG121 4.6 24.1 1.0
O B:HOH265 4.7 50.1 1.0
O B:HOH209 4.7 19.9 1.0
H B:GLY125 4.8 21.1 1.0
CG2 B:ILE126 4.8 20.5 1.0
H B:ARG121 4.8 23.6 1.0
CB B:VAL120 4.8 19.8 1.0
HG12 B:VAL120 4.8 29.3 1.0
CA B:GLY127 4.8 16.2 1.0
C B:LYS124 4.9 17.2 1.0
N B:GLY125 4.9 17.6 1.0
CG1 B:VAL120 4.9 24.4 1.0
HA B:ALA123 4.9 20.1 1.0
CA B:ASN122 4.9 20.4 1.0
H B:VAL120 5.0 19.2 1.0
HA B:ILE126 5.0 19.1 1.0

Sodium binding site 3 out of 3 in 3n0u

Go back to Sodium Binding Sites List in 3n0u
Sodium binding site 3 out of 3 in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima


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 TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na208

b:23.0
occ:1.00
 O C:ALA123 2.3 21.3 1.0
O C:VAL120 2.4 22.1 1.0
O C:ILE126 2.4 18.5 1.0
O C:HOH334 2.5 32.9 1.0
O C:HOH415 2.6 34.5 1.0
O C:LEU119 3.0 20.8 1.0
HA C:VAL120 3.1 23.8 1.0
C C:VAL120 3.1 20.5 1.0
H C:ILE126 3.3 19.9 1.0
C C:ALA123 3.4 18.9 1.0
HB C:ILE126 3.4 19.8 1.0
H C:ALA123 3.4 22.5 1.0
C C:ILE126 3.5 20.6 1.0
CA C:VAL120 3.6 19.8 1.0
N C:ALA123 3.8 18.7 1.0
O C:HOH628 3.9 50.7 1.0
HB3 C:ALA123 4.0 23.3 1.0
HA C:LYS124 4.0 20.0 1.0
N C:ILE126 4.0 16.6 1.0
C C:LEU119 4.0 19.6 1.0
CA C:ALA123 4.1 17.7 1.0
CA C:ILE126 4.1 16.6 1.0
HA2 C:GLY127 4.1 23.6 1.0
N C:ARG121 4.2 21.2 1.0
CB C:ILE126 4.2 16.5 1.0
H C:ASN122 4.2 28.2 1.0
N C:ASN122 4.3 23.5 1.0
C C:ARG121 4.3 21.8 1.0
HG22 C:ILE126 4.3 24.1 1.0
N C:VAL120 4.3 18.1 1.0
N C:LYS124 4.3 18.1 1.0
HG13 C:VAL120 4.5 28.6 1.0
N C:GLY127 4.5 17.6 1.0
HA C:ARG121 4.5 29.1 1.0
CA C:LYS124 4.5 16.6 1.0
CB C:ALA123 4.6 19.4 1.0
CA C:ARG121 4.6 24.3 1.0
O C:ARG121 4.6 28.1 1.0
C C:ASN122 4.6 21.3 1.0
HG12 C:VAL120 4.7 28.6 1.0
H C:GLY125 4.7 23.1 1.0
CG2 C:ILE126 4.8 20.1 1.0
CA C:GLY127 4.8 19.6 1.0
H C:ARG121 4.8 25.5 1.0
C C:LYS124 4.8 16.1 1.0
CB C:VAL120 4.8 21.0 1.0
N C:GLY125 4.9 19.3 1.0
CG1 C:VAL120 4.9 23.8 1.0
HA C:ALA123 5.0 21.2 1.0
CA C:ASN122 5.0 21.9 1.0

Reference:

D.R.Cooper, A.Roy, Z.S.Derewenda. Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima To Be Published.
Page generated: Sun Aug 17 16:24:21 2025

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