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Sodium in PDB 4khy: Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position

Enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position, PDB code: 4khy 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) 22.34 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.795, 118.240, 127.610, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.1

Other elements in 4khy:

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position (pdb code 4khy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position, PDB code: 4khy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4khy

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Sodium binding site 1 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 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 Ribonucleotide at -3 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:54.3
occ:1.00
 O A:HOH1467 2.4 59.6 1.0
OE1 A:GLU172 2.4 51.4 1.0
OE2 A:GLU177 2.4 50.4 1.0
O A:HOH1441 2.4 61.4 1.0
OE2 A:GLU172 2.5 48.0 1.0
CD A:GLU172 2.8 47.8 1.0
CD A:GLU177 3.2 51.7 1.0
OE1 A:GLU177 3.3 56.5 1.0
CG A:GLU172 4.3 44.9 1.0
CB A:GLN171 4.3 39.4 1.0
N A:GLN171 4.4 28.3 1.0
CG A:GLU177 4.6 46.0 1.0
N A:GLU172 4.6 39.9 1.0
CG A:GLN171 4.6 45.0 1.0
CA A:GLN171 4.9 34.0 1.0

Sodium binding site 2 out of 6 in 4khy

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Sodium binding site 2 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 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 Ribonucleotide at -3 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:0.3
occ:1.00
 ND2 A:ASN505 3.8 98.0 1.0
O A:LYS531 3.9 74.5 1.0
CA A:CA1010 4.0 85.9 1.0
O A:HOH1453 4.4 46.8 1.0
CB A:LYS531 4.5 75.9 1.0
CB A:ASN505 4.6 90.8 1.0
CG A:ASN505 4.6 96.2 1.0
O A:HOH1452 4.7 51.3 1.0
ND2 A:ASN507 4.7 0.1 1.0
C A:LYS531 4.9 75.2 1.0

Sodium binding site 3 out of 6 in 4khy

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Sodium binding site 3 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 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 Ribonucleotide at -3 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1008

b:0.2
occ:1.00
 O A:THR611 4.2 76.9 1.0
O A:GLY610 4.4 93.0 1.0
CA A:GLU607 4.7 84.5 1.0
O A:ASN606 4.9 79.0 1.0

Sodium binding site 4 out of 6 in 4khy

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Sodium binding site 4 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 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 Ribonucleotide at -3 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1011

b:58.1
occ:1.00
 O A:HOH1401 2.4 47.3 1.0
O A:HOH1400 2.4 54.4 1.0
OD1 A:ASN232 2.4 45.8 1.0
O A:HOH1399 2.4 42.0 1.0
CG A:ASN232 3.4 44.7 1.0
ND2 A:ASN232 3.7 46.2 1.0
CB A:ASN232 4.7 45.1 1.0
CA A:ASN232 5.0 46.3 1.0
O A:SER127 5.0 43.8 1.0

Sodium binding site 5 out of 6 in 4khy

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Sodium binding site 5 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1012

b:58.5
occ:1.00
 O A:HOH1439 2.4 33.9 1.0
O A:HOH1437 2.4 69.1 1.0
O A:HOH1471 2.4 44.0 1.0
O A:HOH1438 2.4 42.6 1.0
O A:ILE115 3.2 33.3 1.0
OD2 A:ASP114 3.2 45.0 1.0
OE1 A:GLU116 3.3 42.9 1.0
OE2 A:GLU116 3.4 46.0 1.0
OD1 A:ASP114 3.5 39.8 1.0
CD A:GLU116 3.6 42.5 1.0
CG A:ASP114 3.7 40.7 1.0
O A:HOH1132 4.2 28.0 1.0
C A:ILE115 4.3 32.4 1.0
O A:HOH1444 4.4 66.4 1.0
CG A:GLU116 4.8 38.0 1.0
CA A:GLU116 4.9 29.4 1.0
N A:ILE115 4.9 28.5 1.0

Sodium binding site 6 out of 6 in 4khy

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Sodium binding site 6 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1013

b:61.1
occ:1.00
 O A:HOH1141 2.4 45.6 1.0
O A:HOH1424 2.4 57.8 1.0
OD2 A:ASP411 2.4 45.0 1.0
OD2 A:ASP623 2.5 33.8 1.0
O1A A:TTP1001 2.5 34.9 1.0
CG A:ASP623 3.4 35.8 1.0
CG A:ASP411 3.5 42.9 1.0
CA A:CA1002 3.6 30.0 1.0
OD1 A:ASP623 3.6 34.2 1.0
O2A A:TTP1001 3.7 35.1 1.0
PA A:TTP1001 3.7 32.3 1.0
C3' P:DC115 3.9 28.9 1.0
CB A:SER624 4.1 39.8 1.0
C5' P:DC115 4.3 35.8 1.0
OD1 A:ASP411 4.3 45.0 1.0
C5' A:TTP1001 4.3 28.9 1.0
CB A:ASP411 4.4 39.0 1.0
O5' A:TTP1001 4.5 36.5 1.0
C4' P:DC115 4.5 34.0 1.0
OG A:SER624 4.6 40.7 1.0
O A:ASP621 4.6 30.6 1.0
O A:HOH1166 4.7 37.8 1.0
C A:ASP623 4.7 35.0 1.0
O A:ASP623 4.8 37.8 1.0
N A:SER624 4.8 36.1 1.0
CB A:ASP623 4.8 33.1 1.0
O2G A:TTP1001 4.9 24.4 1.0
O1B A:TTP1001 4.9 25.5 1.0
CA A:SER624 5.0 38.2 1.0
O3A A:TTP1001 5.0 46.3 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 16:31:35 2024

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