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Sodium in PDB 1rzt: Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule

Enzymatic activity of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule

All present enzymatic activity of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule, PDB code: 1rzt was solved by L.C.Pedersen, M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.Blanco, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 191.321, 99.034, 104.838, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 26

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule (pdb code 1rzt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule, PDB code: 1rzt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 1rzt

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Sodium binding site 1 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2009

b:48.3
occ:1.00
 O B:HOH1016 1.9 56.5 1.0
O B:HOH1015 2.0 39.2 1.0
O B:HOH1013 2.0 42.9 1.0
O B:HOH1014 2.2 35.1 1.0
N7 B:DG2 4.1 33.7 1.0
O6 B:DG3 4.3 25.3 1.0
O6 B:DG2 4.4 28.6 1.0
O B:HOH588 4.4 38.6 1.0
N4 D:DC2 4.4 22.2 1.0
O D:HOH743 4.5 53.8 1.0
O6 D:DG1 4.6 27.4 1.0
C5 B:DG2 4.9 30.4 1.0
C6 B:DG2 5.0 29.8 1.0

Sodium binding site 2 out of 10 in 1rzt

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Sodium binding site 2 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na2007

b:64.0
occ:1.00
 O F:HOH1008 1.9 62.8 1.0
O F:HOH1009 1.9 48.7 1.0
O F:HOH1010 1.9 67.0 1.0
O F:HOH1011 2.0 53.4 1.0
O F:HOH1012 2.0 60.4 1.0
N7 F:DG2 4.0 47.4 1.0
O6 F:DG3 4.2 39.5 1.0
O F:HOH232 4.3 36.3 1.0
N4 H:DC2 4.4 38.1 1.0
O6 F:DG2 4.5 46.6 1.0
O6 H:DG1 4.9 38.1 1.0
C5 F:DG2 4.9 46.6 1.0
C8 F:DG2 4.9 48.1 1.0

Sodium binding site 3 out of 10 in 1rzt

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Sodium binding site 3 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na2010

b:74.9
occ:1.00
 O J:HOH1018 2.0 50.5 1.0
O J:HOH1017 2.1 53.2 1.0
O6 J:DG3 4.1 38.4 1.0
N7 J:DG2 4.1 48.9 1.0
O J:HOH720 4.4 45.8 1.0
O6 J:DG2 4.4 46.2 1.0
N4 L:DC2 4.4 40.5 1.0
O6 L:DG1 4.6 44.0 1.0
C5 J:DG2 4.8 48.9 1.0
C6 J:DG2 4.9 48.5 1.0
C8 J:DG2 5.0 50.5 1.0

Sodium binding site 4 out of 10 in 1rzt

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Sodium binding site 4 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na2011

b:57.4
occ:1.00
 O J:HOH1019 2.0 60.7 1.0
O J:HOH1021 2.0 52.4 1.0
O J:HOH1020 2.0 53.1 1.0
C7 K:DT2 4.6 50.9 1.0
O6 J:DG8 4.6 28.9 1.0
O6 K:DG3 4.7 36.8 1.0
N4 J:DC9 4.7 33.3 1.0
C5 J:DC7 4.9 39.3 1.0
N7 J:DG8 5.0 29.8 1.0

Sodium binding site 5 out of 10 in 1rzt

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Sodium binding site 5 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2001

b:26.5
occ:1.00
 O A:HOH2092 2.1 29.8 1.0
O A:SER339 2.3 28.2 1.0
O A:ALA344 2.4 23.9 1.0
OP1 C:DG5 2.5 20.6 1.0
O C:HOH52 2.6 31.0 1.0
O A:ILE341 2.7 21.5 1.0
C A:SER339 3.4 26.5 1.0
C A:ALA344 3.4 22.9 1.0
P C:DG5 3.6 21.9 1.0
C A:ILE341 3.6 22.9 1.0
O A:HOH2093 3.6 39.4 1.0
OP2 C:DG5 3.7 24.4 1.0
N A:ALA344 3.8 21.1 1.0
CA A:SER339 4.0 27.4 1.0
N A:ILE341 4.1 24.3 1.0
CA A:ALA344 4.1 23.1 1.0
N A:GLY343 4.1 19.2 1.0
O C:HOH751 4.2 44.9 1.0
CA A:TRP342 4.2 22.3 1.0
N A:TRP342 4.3 22.8 1.0
N A:GLY345 4.3 23.7 1.0
C A:ASN340 4.3 26.3 1.0
N A:ASN340 4.4 25.3 1.0
CA A:ILE341 4.5 24.9 1.0
CA A:GLY345 4.5 24.5 1.0
C A:TRP342 4.6 21.2 1.0
CA A:ASN340 4.6 25.5 1.0
CB A:SER339 4.6 25.3 1.0
CB A:ALA344 4.6 21.9 1.0
O5' C:DG5 4.7 24.6 1.0
O3' C:DC4 4.7 22.4 1.0
C A:GLY343 4.7 21.4 1.0
O A:ASN340 4.9 25.4 1.0
O A:PHE338 4.9 28.4 1.0
O C:HOH576 5.0 31.9 1.0

Sodium binding site 6 out of 10 in 1rzt

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Sodium binding site 6 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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 Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2008

b:72.5
occ:1.00
 CE1 A:TYR267 3.6 37.3 1.0
NE2 A:GLN270 3.7 46.4 1.0
CZ A:TYR267 3.9 38.8 1.0
OH A:TYR267 4.0 41.2 1.0
CE A:LYS324 4.1 56.4 1.0
CD1 A:TYR267 4.2 35.4 1.0
NZ A:LYS324 4.3 57.5 1.0
CD1 A:LEU263 4.4 33.7 1.0
CD A:GLN270 4.5 45.9 1.0
CG1 A:ILE328 4.7 45.3 1.0
CB A:ALA266 4.7 31.2 1.0
CE2 A:TYR267 4.7 37.9 1.0
OE1 A:GLN270 4.7 44.2 1.0
CG A:TYR267 5.0 36.0 1.0

Sodium binding site 7 out of 10 in 1rzt

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Sodium binding site 7 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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 Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na2002

b:47.4
occ:1.00
 O E:SER339 2.2 47.0 1.0
O E:ALA344 2.3 38.3 1.0
O G:HOH359 2.6 39.7 1.0
OP1 G:DG5 2.6 42.0 1.0
O E:ILE341 2.6 42.1 1.0
O G:HOH360 2.8 36.5 1.0
C E:SER339 3.2 47.9 1.0
C E:ALA344 3.4 37.5 1.0
C E:ILE341 3.4 43.1 1.0
N E:ALA344 3.5 37.0 1.0
P G:DG5 3.7 42.0 1.0
N E:GLY343 3.8 38.5 1.0
OP2 G:DG5 3.9 42.0 1.0
N E:ILE341 3.9 43.9 1.0
CA E:SER339 3.9 48.1 1.0
CA E:ALA344 3.9 37.8 1.0
CA E:TRP342 4.0 41.7 1.0
N E:TRP342 4.0 43.2 1.0
C E:ASN340 4.2 45.2 1.0
N E:ASN340 4.2 47.6 1.0
CA E:ILE341 4.3 44.3 1.0
C E:TRP342 4.3 40.7 1.0
N E:GLY345 4.4 37.6 1.0
CB E:ALA344 4.4 36.8 1.0
CA E:ASN340 4.5 46.8 1.0
C E:GLY343 4.5 36.8 1.0
CB E:SER339 4.5 46.1 1.0
CA E:GLY343 4.7 37.3 1.0
CA E:GLY345 4.7 39.0 1.0
O3' G:DC4 4.7 42.3 1.0
O5' G:DG5 4.8 42.8 1.0
O E:ASN340 4.8 45.1 1.0
O E:PHE338 4.9 46.8 1.0

Sodium binding site 8 out of 10 in 1rzt

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Sodium binding site 8 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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 Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na2003

b:29.8
occ:1.00
 O K:HOH578 2.2 34.6 1.0
O K:HOH407 2.3 42.6 1.0
O I:SER339 2.3 36.7 1.0
O I:ALA344 2.3 32.3 1.0
OP1 K:DG5 2.5 34.4 1.0
O I:ILE341 2.6 33.0 1.0
C I:SER339 3.3 37.2 1.0
C I:ALA344 3.4 32.4 1.0
C I:ILE341 3.5 34.1 1.0
P K:DG5 3.6 33.3 1.0
N I:ALA344 3.6 30.6 1.0
OP2 K:DG5 3.8 35.6 1.0
CA I:SER339 3.9 37.2 1.0
N I:GLY343 3.9 30.7 1.0
CA I:ALA344 4.0 31.7 1.0
O I:HOH2092 4.0 53.2 1.0
N I:ILE341 4.1 35.8 1.0
CA I:TRP342 4.1 32.9 1.0
N I:TRP342 4.2 34.0 1.0
N I:ASN340 4.3 36.0 1.0
C I:ASN340 4.4 37.2 1.0
N I:GLY345 4.4 33.7 1.0
C I:TRP342 4.4 32.4 1.0
CB I:SER339 4.4 37.8 1.0
CB I:ALA344 4.5 31.4 1.0
CA I:ILE341 4.5 34.6 1.0
O K:HOH408 4.6 36.6 1.0
CA I:ASN340 4.6 37.2 1.0
CA I:GLY345 4.6 34.0 1.0
C I:GLY343 4.6 30.4 1.0
O5' K:DG5 4.6 34.7 1.0
O3' K:DC4 4.7 34.3 1.0
CA I:GLY343 4.8 30.7 1.0
O I:PHE338 4.9 35.3 1.0
O I:HOH2093 4.9 46.8 1.0
O I:ASN340 4.9 39.2 1.0

Sodium binding site 9 out of 10 in 1rzt

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Sodium binding site 9 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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 Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na2005

b:20.5
occ:1.00
 OP1 O:DG5 2.3 19.0 1.0
O O:HOH7 2.4 27.5 1.0
O M:SER339 2.5 18.1 1.0
O M:ALA344 2.5 18.4 1.0
O O:HOH6 2.5 27.3 1.0
O M:ILE341 2.6 16.0 1.0
C M:ALA344 3.4 18.2 1.0
P O:DG5 3.4 19.6 1.0
C M:SER339 3.4 19.2 1.0
O M:HOH2888 3.5 36.5 1.0
C M:ILE341 3.6 16.7 1.0
OP2 O:DG5 3.6 20.2 1.0
N M:ALA344 3.7 16.4 1.0
N M:GLY343 4.0 18.2 1.0
CA M:SER339 4.0 18.3 1.0
CA M:ALA344 4.1 17.6 1.0
CA M:TRP342 4.1 17.0 1.0
N M:ILE341 4.2 16.9 1.0
N M:TRP342 4.3 18.7 1.0
N M:GLY345 4.3 18.5 1.0
C M:TRP342 4.4 17.6 1.0
O3' O:DC4 4.5 20.2 1.0
N M:ASN340 4.5 18.5 1.0
CB M:SER339 4.5 17.9 1.0
C M:ASN340 4.5 17.6 1.0
CA M:GLY345 4.6 17.8 1.0
O5' O:DG5 4.6 21.1 1.0
CA M:ILE341 4.6 16.3 1.0
CB M:ALA344 4.6 13.8 1.0
O O:HOH15 4.6 48.0 1.0
C M:GLY343 4.6 19.4 1.0
CA M:ASN340 4.7 18.8 1.0
O M:HOH2980 4.7 47.1 1.0
CA M:GLY343 4.9 17.6 1.0

Sodium binding site 10 out of 10 in 1rzt

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Sodium binding site 10 out of 10 in the Crystal Structure of Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule


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 Dna Polymerase Lambda Complexed with A Two Nucleotide Gap Dna Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na2006

b:34.2
occ:1.00
 O M:HOH2930 2.2 25.2 1.0
O M:ILE305 2.2 25.9 1.0
O P:HOH468 2.4 41.1 1.0
O M:ILE302 2.6 22.8 1.0
O M:CYS300 2.7 29.9 1.0
OP1 P:DC3 2.7 35.7 1.0
C M:ILE305 3.3 27.6 1.0
C M:ILE302 3.5 25.3 1.0
C M:CYS300 3.6 29.6 1.0
P P:DC3 3.6 36.8 1.0
OP2 P:DC3 3.6 34.6 1.0
N M:ILE305 3.7 27.6 1.0
CA M:ILE305 4.0 27.9 1.0
N M:ILE302 4.1 27.9 1.0
CA M:CYS300 4.1 29.9 1.0
N M:GLY304 4.2 25.9 1.0
N M:PRO303 4.2 26.1 1.0
CA M:PRO303 4.2 27.8 1.0
N M:GLY306 4.3 28.2 1.0
CA M:ILE302 4.4 26.0 1.0
CB M:ILE305 4.4 27.7 1.0
O3' P:DC2 4.5 34.5 1.0
C M:SER301 4.5 29.4 1.0
C M:PRO303 4.5 26.9 1.0
N M:SER301 4.5 29.0 1.0
O M:ALA299 4.6 27.0 1.0
CA M:GLY306 4.6 30.2 1.0
O P:HOH930 4.7 55.4 1.0
C M:GLY304 4.8 27.5 1.0
CA M:SER301 4.8 28.9 1.0
O5' P:DC3 4.9 35.9 1.0
CB M:CYS300 5.0 29.0 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.Blanco, T.A.Kunkel, L.C.Pedersen. A Structural Solution For the Dna Polymerase Lambda-Dependent Repair of Dna Gaps with Minimal Homology. Mol.Cell V. 13 561 2004.
ISSN: ISSN 1097-2765
PubMed: 14992725
DOI: 10.1016/S1097-2765(04)00061-9
Page generated: Sun Aug 17 07:32:44 2025

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