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Sodium in PDB 3mgh: Binary Complex of A Dna Polymerase Lambda Loop Mutant

Enzymatic activity of Binary Complex of A Dna Polymerase Lambda Loop Mutant

All present enzymatic activity of Binary Complex of A Dna Polymerase Lambda Loop Mutant:
2.7.7.7;

Protein crystallography data

The structure of Binary Complex of A Dna Polymerase Lambda Loop Mutant, PDB code: 3mgh was solved by M.Garcia-Diaz, K.Bebenek, R.Z.Zhou, L.F.Povirk, T.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.46 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.998, 190.886, 58.734, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex of A Dna Polymerase Lambda Loop Mutant (pdb code 3mgh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Binary Complex of A Dna Polymerase Lambda Loop Mutant, PDB code: 3mgh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3mgh

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Sodium binding site 1 out of 4 in the Binary Complex of A Dna Polymerase Lambda Loop Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of A Dna Polymerase Lambda Loop Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na800

b:39.7
occ:1.00
 OP1 P:DA5 2.7 29.4 1.0
O A:SER339 2.7 33.2 1.0
O P:HOH75 2.7 23.6 1.0
O A:HOH29 2.8 41.0 1.0
O A:ILE341 2.9 29.4 1.0
O A:ALA344 3.0 32.0 1.0
O A:HOH88 3.1 34.8 1.0
C A:ILE341 3.4 29.6 1.0
O A:HOH153 3.4 29.8 1.0
C A:SER339 3.5 30.4 1.0
P P:DA5 3.7 27.3 1.0
N A:TRP342 3.7 27.2 1.0
CA A:TRP342 3.8 30.7 1.0
N A:ILE341 3.8 29.1 1.0
C A:ASN340 3.9 31.9 1.0
OP2 P:DA5 3.9 28.6 1.0
C A:ALA344 4.1 30.2 1.0
CA A:ASN340 4.2 27.9 1.0
CA A:ILE341 4.3 31.8 1.0
N A:ASN340 4.3 30.0 1.0
N A:GLY343 4.3 32.4 1.0
O A:ASN340 4.3 28.5 1.0
N A:ALA344 4.3 25.9 1.0
CA A:SER339 4.3 31.2 1.0
C A:TRP342 4.4 33.8 1.0
O5' P:DA5 4.7 33.9 1.0
CA A:ALA344 4.8 32.6 1.0
CB A:SER339 4.9 30.0 1.0
O3' P:DT4 4.9 30.1 1.0
O A:HOH54 5.0 33.1 1.0

Sodium binding site 2 out of 4 in 3mgh

Go back to Sodium Binding Sites List in 3mgh
Sodium binding site 2 out of 4 in the Binary Complex of A Dna Polymerase Lambda Loop Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex of A Dna Polymerase Lambda Loop Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na802

b:42.1
occ:1.00
 OP1 F:DA5 2.6 39.2 1.0
O C:SER339 2.6 41.0 1.0
O C:ALA344 2.8 40.8 1.0
O C:HOH50 2.8 39.9 1.0
O C:ILE341 3.1 47.6 1.0
O C:HOH233 3.2 43.3 1.0
OP2 F:DA5 3.3 41.2 1.0
P F:DA5 3.4 40.6 1.0
C C:SER339 3.6 45.8 1.0
C C:ALA344 3.7 42.1 1.0
C C:ILE341 3.8 47.4 1.0
N C:ALA344 4.1 42.5 1.0
O C:HOH106 4.1 40.5 1.0
N C:GLY343 4.2 42.4 1.0
CA C:TRP342 4.2 41.0 1.0
N C:TRP342 4.3 43.8 1.0
CA C:SER339 4.3 51.0 1.0
N C:ILE341 4.4 47.6 1.0
O5' F:DA5 4.4 39.1 1.0
C C:ASN340 4.4 51.6 1.0
CA C:ALA344 4.5 47.0 1.0
N C:ASN340 4.6 47.8 1.0
C C:TRP342 4.6 42.9 1.0
N C:GLY345 4.6 42.0 1.0
O3' F:DT4 4.6 33.8 1.0
CA C:ASN340 4.7 44.0 1.0
CA C:ILE341 4.7 46.2 1.0
CB C:SER339 4.8 47.4 1.0
CA C:GLY345 4.8 45.7 1.0
O C:ASN340 4.9 51.8 1.0

Sodium binding site 3 out of 4 in 3mgh

Go back to Sodium Binding Sites List in 3mgh
Sodium binding site 3 out of 4 in the Binary Complex of A Dna Polymerase Lambda Loop Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Binary Complex of A Dna Polymerase Lambda Loop Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na803

b:60.8
occ:1.00
 OD1 C:ASP427 2.8 54.3 1.0
OD2 C:ASP490 2.9 41.9 1.0
OP1 F:DC6 3.1 41.1 1.0
OD1 C:ASP429 3.1 47.4 1.0
CG C:ASP490 3.6 40.6 1.0
CG C:ASP427 3.8 48.8 1.0
O5' F:DC6 3.8 40.1 1.0
O F:HOH215 3.8 46.4 1.0
C5' F:DC6 3.8 39.0 1.0
P F:DC6 4.0 37.6 1.0
OD1 C:ASP490 4.0 37.0 1.0
NH2 C:ARG488 4.2 49.0 1.0
CG C:ASP429 4.2 49.4 1.0
CB C:ASP427 4.3 44.3 1.0
O F:HOH81 4.3 37.4 1.0
OD2 C:ASP429 4.4 53.6 1.0
CZ C:ARG488 4.5 42.4 1.0
C3' F:DC6 4.5 34.7 1.0
CB C:ASP490 4.7 38.5 1.0
OD2 C:ASP427 4.7 52.5 1.0
C4' F:DC6 4.7 41.9 1.0
OP2 F:DC6 4.7 46.0 1.0
NH1 C:ARG488 4.9 39.1 1.0

Sodium binding site 4 out of 4 in 3mgh

Go back to Sodium Binding Sites List in 3mgh
Sodium binding site 4 out of 4 in the Binary Complex of A Dna Polymerase Lambda Loop Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Binary Complex of A Dna Polymerase Lambda Loop Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1

b:44.0
occ:1.00
 O C:ILE305 2.8 33.7 1.0
O C:HOH16 2.8 46.8 1.0
OP1 G:DC3 2.8 40.2 1.0
O C:CYS300 2.9 34.1 1.0
O C:ILE302 3.0 30.8 1.0
OP2 G:DC3 3.5 40.7 1.0
P G:DC3 3.6 36.9 1.0
C C:ILE302 3.6 32.5 1.0
C C:ILE305 3.8 35.2 1.0
C C:CYS300 3.8 34.7 1.0
CA C:PRO303 3.9 35.2 1.0
N C:ILE305 4.1 32.0 1.0
N C:PRO303 4.1 31.4 1.0
N C:GLY304 4.1 33.1 1.0
O C:HOH229 4.2 41.0 1.0
O C:HOH587 4.3 39.7 1.0
N C:ILE302 4.3 23.3 1.0
C C:SER301 4.3 29.9 1.0
CA C:ILE305 4.5 30.4 1.0
C C:PRO303 4.5 33.6 1.0
O3' G:DC2 4.5 36.8 1.0
N C:SER301 4.6 30.0 1.0
CA C:CYS300 4.6 33.4 1.0
CA C:ILE302 4.6 29.0 1.0
O C:SER301 4.6 34.6 1.0
CA C:SER301 4.7 32.9 1.0
N C:GLY306 4.8 38.0 1.0
O5' G:DC3 4.8 41.2 1.0
O C:ALA299 4.9 28.5 1.0
CA C:GLY306 4.9 36.2 1.0

Reference:

K.Bebenek, M.Garcia-Diaz, R.Z.Zhou, L.F.Povirk, T.A.Kunkel. Loop 1 Modulates the Fidelity of Dna Polymerase Lambda Nucleic Acids Res. V. 38 5419 2010.
ISSN: ISSN 0305-1048
PubMed: 20435673
DOI: 10.1093/NAR/GKQ261
Page generated: Mon Oct 7 11:30:03 2024

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