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Sodium in PDB 4khu: Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position

Enzymatic activity of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position, PDB code: 4khu was solved by A.R.Clausen, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.62 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.977, 119.350, 127.860, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.7

Other elements in 4khu:

The structure of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position (pdb code 4khu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position, PDB code: 4khu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4khu

Go back to Sodium Binding Sites List in 4khu
Sodium binding site 1 out of 4 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:54.8
occ:1.00
 O A:HOH1556 2.4 62.5 1.0
OE1 A:GLU716 3.3 63.3 1.0
OE2 A:GLU686 3.4 60.1 1.0
CD A:GLU716 3.8 60.1 1.0
OD1 A:ASP411 3.9 47.5 1.0
CG A:GLU716 4.0 53.4 1.0
O A:ASP411 4.1 33.9 1.0
CB A:ASP684 4.3 52.2 1.0
NZ A:LYS486 4.5 43.8 1.0
CD A:GLU686 4.6 56.2 1.0
CB A:ASP411 4.6 40.5 1.0
O A:ASP684 4.6 45.3 1.0
OE2 A:GLU716 4.7 61.2 1.0
CG A:ASP411 4.7 42.8 1.0
OD1 A:ASP684 4.7 56.3 1.0
OG1 A:THR413 4.7 38.5 1.0
C A:ASP411 4.9 34.0 1.0
O A:ARG685 4.9 41.6 1.0

Sodium binding site 2 out of 4 in 4khu

Go back to Sodium Binding Sites List in 4khu
Sodium binding site 2 out of 4 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:57.5
occ:1.00
 O A:HOH1554 2.4 61.1 1.0
O A:HOH1237 2.4 46.9 1.0
OD2 A:ASP684 2.4 53.7 1.0
OE1 A:GLU660 3.2 46.8 1.0
CG A:ASP684 3.6 54.9 1.0
CD A:GLU660 4.2 48.4 1.0
OD1 A:ASP684 4.2 56.3 1.0
CB A:GLU660 4.6 46.1 1.0
OD1 A:ASP664 4.6 63.0 1.0
OD2 A:ASP664 4.6 63.1 1.0
CB A:ASP684 4.7 52.2 1.0
O A:MET683 4.7 47.5 1.0
CG A:GLU660 4.8 46.5 1.0
CA A:ASP684 4.9 47.4 1.0

Sodium binding site 3 out of 4 in 4khu

Go back to Sodium Binding Sites List in 4khu
Sodium binding site 3 out of 4 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:57.4
occ:1.00
 OE2 A:GLU177 2.4 49.9 1.0
CD A:GLU177 3.2 52.3 1.0
OE1 A:GLU177 3.2 55.5 1.0
OE1 A:GLU172 3.3 45.5 1.0
OE2 A:GLU172 3.4 43.1 1.0
CD A:GLU172 3.7 43.0 1.0
CG A:GLU177 4.6 48.1 1.0
CB A:GLN171 4.7 36.0 1.0
CG A:GLN171 4.9 47.0 1.0
N A:GLN171 4.9 30.3 1.0

Sodium binding site 4 out of 4 in 4khu

Go back to Sodium Binding Sites List in 4khu
Sodium binding site 4 out of 4 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1008

b:46.2
occ:1.00
 O A:HOH1214 2.4 35.8 1.0
OD2 A:ASP411 2.4 40.5 1.0
OD2 A:ASP623 2.5 31.6 1.0
O1A A:TTP1001 2.5 23.0 1.0
CG A:ASP623 3.3 30.3 1.0
OD1 A:ASP623 3.5 28.3 1.0
CA A:CA1002 3.5 29.6 1.0
CG A:ASP411 3.6 42.8 1.0
PA A:TTP1001 3.8 32.1 1.0
O2A A:TTP1001 3.9 34.6 1.0
CB A:SER624 4.0 34.9 1.0
C3' P:DC115 4.0 24.8 1.0
C5' P:DC115 4.3 31.6 1.0
O5' A:TTP1001 4.4 34.1 1.0
CB A:ASP411 4.5 40.5 1.0
OD1 A:ASP411 4.5 47.5 1.0
C5' A:TTP1001 4.5 26.2 1.0
C A:ASP623 4.6 32.2 1.0
O A:ASP621 4.6 26.9 1.0
C4' P:DC115 4.6 28.3 1.0
N A:SER624 4.6 32.9 1.0
O A:ASP623 4.6 30.2 1.0
OG A:SER624 4.6 32.6 1.0
O A:HOH1311 4.7 41.1 1.0
CA A:SER624 4.7 33.2 1.0
CB A:ASP623 4.7 28.5 1.0
O2G A:TTP1001 4.8 24.4 1.0
O1B A:TTP1001 4.9 25.5 1.0
N A:ASP623 5.0 27.0 1.0

Reference:

A.R.Clausen, M.S.Murray, A.R.Passer, L.C.Pedersen, T.A.Kunkel. Structure-Function Analysis of Ribonucleotide Bypass By B Family Dna Replicases. Proc.Natl.Acad.Sci.Usa V. 110 16802 2013.
ISSN: ISSN 0027-8424
PubMed: 24082122
DOI: 10.1073/PNAS.1309119110
Page generated: Mon Oct 7 16:31:36 2024

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