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Sodium in PDB 3knt: Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine

Enzymatic activity of Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine

All present enzymatic activity of Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine:
4.2.99.18;

Protein crystallography data

The structure of Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine, PDB code: 3knt was solved by F.Faucher, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.800, 150.030, 90.270, 90.00, 107.53, 90.00
R / Rfree (%) 18.8 / 22.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine (pdb code 3knt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine, PDB code: 3knt:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3knt

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Sodium binding site 1 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine


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 Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:58.4
occ:1.00
 O A:ILE123 2.2 47.2 1.0
O A:VAL120 2.3 46.8 1.0
O A:ILE126 2.3 44.9 1.0
OP1 E:DC26 2.9 44.4 1.0
C A:ILE123 3.3 46.2 1.0
C A:ILE126 3.3 40.4 1.0
O A:HOH215 3.4 53.9 1.0
C A:VAL120 3.4 49.3 1.0
OP2 E:DC26 3.5 43.3 1.0
P E:DC26 3.6 48.7 1.0
N A:ILE126 3.8 44.5 1.0
CA A:ILE126 4.0 39.9 1.0
CA A:LYS124 4.0 47.6 1.0
N A:LYS124 4.0 44.8 1.0
CA A:VAL120 4.1 46.5 1.0
N A:GLY125 4.2 47.5 1.0
C A:LYS124 4.2 46.8 1.0
N A:GLY127 4.3 41.7 1.0
O3' E:DT25 4.3 50.0 1.0
CB A:ILE126 4.3 42.9 1.0
N A:ILE123 4.4 50.8 1.0
CA A:ILE123 4.4 46.5 1.0
CG1 A:VAL120 4.5 46.7 1.0
N A:ARG121 4.5 50.9 1.0
O A:LEU119 4.5 48.4 1.0
CA A:GLY127 4.6 42.7 1.0
CA A:ARG121 4.8 56.2 1.0
C A:GLY125 4.8 47.6 1.0
O A:LYS124 4.9 47.1 1.0
CB A:VAL120 5.0 46.6 1.0
CB A:ILE123 5.0 44.8 1.0
O5' E:DC26 5.0 52.9 1.0

Sodium binding site 2 out of 4 in 3knt

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Sodium binding site 2 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine


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 Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na208

b:51.5
occ:1.00
 O B:ILE126 2.4 55.7 1.0
O B:ILE123 2.5 50.5 1.0
O B:VAL120 2.6 57.2 1.0
OP1 G:DC26 2.9 56.4 1.0
C B:ILE123 3.4 54.2 1.0
C B:VAL120 3.5 59.0 1.0
C B:ILE126 3.5 51.5 1.0
N B:ILE126 3.9 50.6 1.0
P G:DC26 3.9 55.5 1.0
CA B:LYS124 4.0 53.9 1.0
N B:LYS124 4.0 56.7 1.0
CA B:ILE126 4.2 47.2 1.0
N B:GLY125 4.2 54.3 1.0
OP2 G:DC26 4.2 59.6 1.0
N B:ILE123 4.3 52.3 1.0
CA B:VAL120 4.3 57.8 1.0
N B:ARG121 4.3 56.7 1.0
CA B:ILE123 4.4 51.4 1.0
O3' G:DT25 4.4 57.3 1.0
O B:LEU119 4.4 55.4 1.0
CA B:ARG121 4.5 57.6 1.0
O B:HOH214 4.5 56.4 1.0
C B:LYS124 4.5 53.3 1.0
CB B:ILE126 4.6 49.3 1.0
N B:GLY127 4.6 48.4 1.0
C B:ARG121 4.8 59.0 1.0
C B:GLY125 4.9 52.8 1.0
N B:ASN122 4.9 57.9 1.0
CA B:GLY127 5.0 47.3 1.0
CG1 B:VAL120 5.0 54.5 1.0

Sodium binding site 3 out of 4 in 3knt

Go back to Sodium Binding Sites List in 3knt
Sodium binding site 3 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine


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 Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na208

b:57.8
occ:1.00
 O C:VAL120 2.3 50.6 1.0
O C:ILE123 2.3 52.7 1.0
O C:ILE126 2.3 45.6 1.0
OP1 I:DC26 2.3 52.0 1.0
P I:DC26 3.3 47.0 1.0
C C:ILE123 3.3 50.7 1.0
OP2 I:DC26 3.4 50.5 1.0
O C:HOH215 3.4 53.0 1.0
C C:ILE126 3.4 44.0 1.0
C C:VAL120 3.5 52.2 1.0
N C:ILE126 3.9 45.9 1.0
N C:LYS124 4.0 49.3 1.0
CA C:LYS124 4.1 52.8 1.0
O3' I:DT25 4.1 51.3 1.0
CA C:ILE126 4.1 42.0 1.0
CA C:VAL120 4.2 48.0 1.0
N C:GLY125 4.3 48.3 1.0
N C:ILE123 4.3 50.6 1.0
CA C:ILE123 4.4 48.3 1.0
N C:GLY127 4.5 42.2 1.0
C C:LYS124 4.5 51.7 1.0
N C:ARG121 4.5 51.8 1.0
CB C:ILE126 4.6 44.6 1.0
O5' I:DC26 4.6 52.5 1.0
O C:LEU119 4.6 49.4 1.0
O C:ARG121 4.6 55.3 1.0
CG1 C:VAL120 4.7 49.1 1.0
C C:ARG121 4.7 53.1 1.0
CA C:ARG121 4.8 48.6 1.0
CA C:GLY127 4.8 45.1 1.0
C C:GLY125 5.0 47.4 1.0

Sodium binding site 4 out of 4 in 3knt

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Sodium binding site 4 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine


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 Methanocaldococcus Jannaschii 8-Oxoguanine Glycosylase/Lyase in Complex with 15MER Dna Containing 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na208

b:47.9
occ:1.00
 O D:VAL120 2.2 44.4 1.0
OP1 K:DC26 2.2 44.7 1.0
O D:ILE123 2.3 47.5 1.0
O D:ILE126 2.3 49.5 1.0
P K:DC26 3.3 46.8 1.0
C D:VAL120 3.3 47.6 1.0
C D:ILE126 3.3 43.4 1.0
C D:ILE123 3.3 48.0 1.0
O K:HOH1 3.5 46.2 1.0
OP2 K:DC26 3.5 50.8 1.0
N D:ILE126 3.7 46.3 1.0
CA D:ILE126 4.0 45.1 1.0
CA D:VAL120 4.0 45.7 1.0
N D:LYS124 4.1 47.6 1.0
CA D:LYS124 4.1 54.2 1.0
N D:GLY125 4.1 48.5 1.0
O3' K:DT25 4.3 48.8 1.0
O D:LEU119 4.3 52.2 1.0
N D:ILE123 4.3 53.0 1.0
N D:ARG121 4.4 51.9 1.0
N D:GLY127 4.4 44.6 1.0
CA D:ILE123 4.4 48.5 1.0
C D:LYS124 4.4 53.0 1.0
CB D:ILE126 4.4 44.3 1.0
O5' K:DC26 4.4 46.2 1.0
CG1 D:VAL120 4.5 44.1 1.0
CA D:ARG121 4.6 57.0 1.0
CA D:GLY127 4.7 43.8 1.0
C D:ARG121 4.7 57.9 1.0
C D:GLY125 4.8 48.8 1.0
CB D:VAL120 4.9 45.5 1.0

Reference:

F.Faucher, S.S.Wallace, S.Doublie. The C-Terminal Lysine of OGG2 Dna Glycosylases Is A Major Molecular Determinant For Guanine/8-Oxoguanine Distinction. J.Mol.Biol. V. 397 46 2010.
ISSN: ISSN 0022-2836
PubMed: 20083120
DOI: 10.1016/J.JMB.2010.01.024
Page generated: Tue Dec 15 06:16:20 2020

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