Atomistry » Sodium » PDB 3k9g-3la1 » 3knt
Atomistry »
  Sodium »
    PDB 3k9g-3la1 »
      3knt »

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

Go back to Sodium Binding Sites List in 3knt
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

Go back to Sodium Binding Sites List in 3knt
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

Go back to Sodium Binding Sites List in 3knt
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: Mon Oct 7 11:13:52 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy