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Sodium in PDB 3lwl: Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site

Enzymatic activity of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site

All present enzymatic activity of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site, PDB code: 3lwl was solved by A.Marx, K.Diederichs, S.Obeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.73 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.228, 110.228, 91.265, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 23.4

Other elements in 3lwl:

The structure of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site (pdb code 3lwl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site, PDB code: 3lwl:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3lwl

Go back to Sodium Binding Sites List in 3lwl
Sodium binding site 1 out of 4 in the Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na837

b:39.9
occ:1.00
 OE1 A:GLU445 2.9 30.8 1.0
OD1 A:ASP355 3.0 41.7 1.0
NE A:ARG563 3.0 27.7 1.0
O A:HOH100 3.1 34.6 1.0
NZ A:LYS354 3.4 32.7 1.0
OE2 A:GLU445 3.5 30.8 1.0
CG A:PRO316 3.6 23.8 1.0
CD A:GLU445 3.6 30.7 1.0
CB A:ARG563 3.6 25.3 1.0
NH2 A:ARG563 3.7 32.4 1.0
CG A:ARG563 3.7 28.2 1.0
CD A:PRO316 3.8 25.9 1.0
CZ A:ARG563 3.8 35.2 1.0
CG A:ASP355 3.9 50.0 1.0
CD A:ARG563 3.9 27.0 1.0
C1 A:GOL6 4.2 37.9 1.0
CA A:ARG563 4.2 25.8 1.0
C3 A:GOL836 4.4 62.0 1.0
OD2 A:ASP355 4.4 54.9 1.0
O A:HOH126 4.5 56.5 1.0
O1 A:GOL6 4.6 34.8 1.0
CE A:LYS354 4.8 34.9 1.0
CA A:ASP355 4.8 41.2 1.0
O3 A:GOL836 4.9 63.3 1.0
CB A:PRO316 4.9 24.5 1.0
N A:PHE564 4.9 25.2 1.0
CG2 A:VAL358 4.9 19.7 1.0
C A:ARG563 4.9 27.5 1.0
CB A:ASP355 4.9 46.4 1.0

Sodium binding site 2 out of 4 in 3lwl

Go back to Sodium Binding Sites List in 3lwl
Sodium binding site 2 out of 4 in the Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na838

b:86.4
occ:1.00
 NZ A:LYS314 3.5 51.5 1.0
OD1 A:ASP578 3.5 37.1 1.0
OP2 C:DC209 3.7 25.7 1.0
CE A:LYS314 4.4 48.2 1.0
P C:DC209 4.6 20.3 1.0
OP1 C:DC209 4.6 24.8 1.0
CG A:ASP578 4.7 37.5 1.0

Sodium binding site 3 out of 4 in 3lwl

Go back to Sodium Binding Sites List in 3lwl
Sodium binding site 3 out of 4 in the Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na839

b:71.0
occ:1.00
 OD2 A:ASP381 3.2 43.0 1.0
OG A:SER383 3.5 38.1 1.0
OD1 A:ASP381 4.0 41.5 1.0
CG A:ASP381 4.0 42.2 1.0
CB A:SER383 4.2 36.9 1.0
O A:HOH151 4.4 31.9 1.0
CB A:TYR729 4.5 41.2 1.0
NH1 A:ARG393 4.9 59.6 1.0

Sodium binding site 4 out of 4 in 3lwl

Go back to Sodium Binding Sites List in 3lwl
Sodium binding site 4 out of 4 in the Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Klenow Fragment of Taq Polymerase in Complex with An Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:69.9
occ:1.00
 OP1 C:DC207 3.3 28.2 1.0
O A:ALA568 3.4 27.6 1.0
CG2 A:THR385 3.7 31.7 1.0
N A:ALA570 4.0 26.1 1.0
C A:ALA568 4.1 21.7 1.0
C A:THR569 4.1 25.6 1.0
CA A:THR569 4.2 19.3 1.0
O A:PRO382 4.4 32.8 1.0
N A:THR569 4.4 18.2 1.0
O A:HOH62 4.5 44.2 1.0
CA A:ALA570 4.6 28.1 1.0
CB A:ALA570 4.6 29.2 1.0
P C:DC207 4.6 22.5 1.0
O A:THR569 4.6 25.4 1.0
OXT C:ACT1 4.9 59.7 1.0
CB A:THR385 4.9 36.4 1.0

Reference:

S.Obeid, N.Blatter, R.Kranaster, A.Schnur, K.Diederichs, W.Welte, A.Marx. Replication Through An Abasic Dna Lesion: Structural Basis For Adenine Selectivity Embo J. V. 29 1738 2010.
ISSN: ISSN 0261-4189
PubMed: 20400942
DOI: 10.1038/EMBOJ.2010.64
Page generated: Mon Oct 7 11:24:35 2024

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