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Sodium in PDB 1xsp: Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate

Enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate, PDB code: 1xsp was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.72 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.845, 62.758, 140.720, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate (pdb code 1xsp). 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 Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate, PDB code: 1xsp:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1xsp

Go back to Sodium Binding Sites List in 1xsp
Sodium binding site 1 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate


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 Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:79.5
occ:1.00
 OP1 D:DG1 2.6 71.0 1.0
NZ A:LYS324 3.3 81.9 1.0
P D:DG1 3.9 73.2 1.0
O A:HOH685 4.1 34.3 1.0
CE A:LYS324 4.2 81.3 1.0
OP2 D:DG1 4.3 72.0 1.0
NH1 A:ARG275 4.6 42.1 1.0
OP3 D:DG1 4.7 71.0 1.0
OH A:TYR267 4.8 40.8 1.0
CZ A:ARG275 4.9 40.1 1.0
O D:HOH138 5.0 56.0 1.0

Sodium binding site 2 out of 4 in 1xsp

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Sodium binding site 2 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate


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 Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na576

b:28.5
occ:1.00
 O12 A:PPV579 2.3 33.0 1.0
OD1 A:ASP427 2.4 35.5 1.0
OD2 A:ASP429 2.4 27.6 1.0
O A:HOH686 2.5 35.7 1.0
O A:HOH608 2.6 36.6 1.0
OP1 P:DG7 2.8 25.6 1.0
O22 A:PPV579 3.0 40.2 1.0
P2 A:PPV579 3.1 34.0 1.0
CG A:ASP429 3.3 28.6 1.0
CG A:ASP427 3.3 32.5 1.0
OD1 A:ASP429 3.5 28.1 1.0
O11 A:PPV579 3.6 41.6 1.0
OD2 A:ASP427 3.6 32.3 1.0
P P:DG7 3.9 27.1 1.0
OPP A:PPV579 4.0 42.7 1.0
O A:ASP427 4.1 29.4 1.0
C5' P:DG7 4.2 24.9 1.0
O5' P:DG7 4.2 26.9 1.0
CA A:GLY416 4.2 29.6 1.0
N A:SER417 4.3 28.8 1.0
P1 A:PPV579 4.3 49.3 1.0
O P:HOH126 4.4 47.8 1.0
N A:ASP427 4.4 29.8 1.0
C A:ASP427 4.4 28.9 1.0
O31 A:PPV579 4.5 48.2 1.0
OG A:SER417 4.5 29.5 1.0
O32 A:PPV579 4.5 36.9 1.0
CB A:ASP427 4.6 29.5 1.0
OP2 P:DG7 4.6 25.8 1.0
CB A:ASP429 4.6 27.2 1.0
O A:HOH590 4.7 28.6 1.0
CA A:ASP427 4.8 29.7 1.0
C A:GLY416 4.9 30.4 1.0
N A:ASP429 4.9 26.1 1.0

Sodium binding site 3 out of 4 in 1xsp

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Sodium binding site 3 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate


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 Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na577

b:29.6
occ:1.00
 OP1 P:DA5 2.4 22.0 1.0
O A:SER339 2.5 21.5 1.0
O A:ALA344 2.6 26.1 1.0
O A:ILE341 2.6 20.6 1.0
O P:HOH172 2.7 38.6 1.0
O P:HOH40 2.9 31.7 1.0
P P:DA5 3.5 22.3 1.0
C A:ILE341 3.5 21.1 1.0
C A:SER339 3.6 23.5 1.0
OP2 P:DA5 3.6 26.5 1.0
C A:ALA344 3.7 24.1 1.0
O A:HOH626 3.7 58.7 1.0
N A:ALA344 3.9 21.2 1.0
N A:GLY343 3.9 23.4 1.0
CA A:TRP342 4.0 21.3 1.0
N A:ILE341 4.0 21.1 1.0
O P:HOH183 4.0 41.7 1.0
N A:TRP342 4.1 22.7 1.0
C A:ASN340 4.2 22.2 1.0
CA A:ALA344 4.3 23.3 1.0
C A:TRP342 4.3 22.1 1.0
CA A:ASN340 4.4 22.0 1.0
N A:ASN340 4.4 22.0 1.0
O3' P:DT4 4.4 22.1 1.0
CA A:ILE341 4.5 20.3 1.0
CA A:SER339 4.5 24.9 1.0
OG A:SER339 4.6 35.9 1.0
O5' P:DA5 4.7 23.4 1.0
N A:GLY345 4.7 24.6 1.0
O A:ASN340 4.7 22.7 1.0
C A:GLY343 4.7 21.6 1.0
CB A:ALA344 4.8 20.0 1.0
CA A:GLY345 4.9 24.4 1.0
O P:HOH191 4.9 50.8 1.0
CA A:GLY343 4.9 21.4 1.0

Sodium binding site 4 out of 4 in 1xsp

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Sodium binding site 4 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate


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 Human Dna Polymerase Lambda in Complex with Nicked Dna and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na578

b:43.9
occ:1.00
 O T:HOH44 2.4 35.8 1.0
O A:SER463 2.4 31.1 1.0
O A:HOH738 2.5 50.5 1.0
O A:HOH613 2.5 34.5 1.0
O A:HOH691 2.7 41.3 1.0
O T:HOH21 2.9 48.6 1.0
C A:SER463 3.5 31.2 1.0
OP1 T:DT10 3.7 30.8 1.0
OE2 A:GLU466 4.1 56.5 1.0
O T:HOH60 4.3 51.6 1.0
CA A:GLN464 4.3 35.2 1.0
N A:GLN464 4.3 32.8 1.0
N A:GLU465 4.3 37.3 1.0
OP2 T:DT10 4.4 30.6 1.0
CA A:SER463 4.5 29.6 1.0
P T:DT10 4.6 30.4 1.0
CB A:SER463 4.6 29.5 1.0
N A:SER463 4.7 28.0 1.0
C A:GLN464 4.9 35.3 1.0
OE2 A:GLU465 5.0 40.9 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen. A Closed Conformation For the Pol Lambda Catalytic Cycle. Nat.Struct.Mol.Biol. V. 12 97 2005.
ISSN: ISSN 1545-9993
PubMed: 15608652
DOI: 10.1038/NSMB876
Page generated: Mon Oct 7 00:34:31 2024

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