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Sodium in PDB 4khq: Ternary Complex of RB69 Mutant L415F Wit Dumpnpp

Enzymatic activity of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp, PDB code: 4khq 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) 46.24 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.659, 119.360, 128.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.2

Other elements in 4khq:

The structure of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp 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 Wit Dumpnpp (pdb code 4khq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp, PDB code: 4khq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4khq

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Sodium binding site 1 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:62.6
occ:1.00
 O A:HOH1465 2.4 69.3 1.0
O A:HOH1463 2.4 52.8 1.0
O A:HOH1251 2.4 53.3 1.0
O A:HOH1464 2.4 67.7 1.0
OE2 A:GLU116 2.5 46.7 1.0
OD2 A:ASP114 2.9 38.2 1.0
O A:ILE115 3.1 33.6 1.0
CD A:GLU116 3.1 41.6 1.0
OE1 A:GLU116 3.3 43.8 1.0
OD1 A:ASP114 3.5 37.4 1.0
CG A:ASP114 3.5 35.3 1.0
O A:HOH1118 4.1 30.2 1.0
C A:ILE115 4.2 32.0 1.0
O A:HOH1238 4.4 44.5 1.0
CG A:GLU116 4.4 38.9 1.0
CA A:GLU116 4.8 34.1 1.0
ND2 A:ASN324 4.9 29.3 1.0
N A:ILE115 4.9 29.2 1.0
N A:GLU116 4.9 31.0 1.0

Sodium binding site 2 out of 8 in 4khq

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Sodium binding site 2 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:71.4
occ:1.00
 OE2 A:GLU177 2.7 62.9 1.0
OE1 A:GLU177 3.2 66.8 1.0
OE1 A:GLU172 3.2 62.8 1.0
CD A:GLU177 3.3 62.4 1.0
OE2 A:GLU172 3.3 62.0 1.0
CD A:GLU172 3.7 61.0 1.0
CB A:GLN171 4.6 52.3 1.0
CG A:GLU177 4.8 57.0 1.0
CG A:GLN171 4.8 61.4 1.0
N A:GLN171 4.9 37.9 1.0

Sodium binding site 3 out of 8 in 4khq

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Sodium binding site 3 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1008

b:68.4
occ:1.00
 O A:HOH1539 2.4 60.1 1.0
O A:HOH1346 2.4 46.4 1.0
O A:HOH1540 2.4 97.9 1.0
O A:HOH1499 2.4 56.8 1.0
OD1 A:ASN232 2.4 55.1 1.0
CG A:ASN232 3.3 50.5 1.0
ND2 A:ASN232 3.5 48.8 1.0
CD A:LYS231 4.5 56.0 1.0
CB A:ASN232 4.7 50.2 1.0
O A:SER127 5.0 50.6 1.0

Sodium binding site 4 out of 8 in 4khq

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Sodium binding site 4 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:96.4
occ:1.00
 O A:THR611 3.5 73.9 1.0
O A:GLY610 3.6 84.4 1.0
C A:GLY610 4.2 80.4 1.0
C A:THR611 4.2 74.2 1.0
CB A:GLU612 4.4 70.1 1.0
N A:THR611 4.7 79.4 1.0
CA A:THR611 4.8 78.4 1.0
CA A:GLY610 4.9 79.7 1.0
N A:GLU612 4.9 70.3 1.0

Sodium binding site 5 out of 8 in 4khq

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Sodium binding site 5 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1009

b:41.9
occ:1.00
 OD2 A:ASP623 2.4 32.6 1.0
O1A A:DUP1005 2.7 31.2 1.0
O3' P:DC115 2.8 32.7 1.0
CG A:ASP623 3.4 32.0 1.0
OD1 A:ASP411 3.5 42.4 1.0
C3' P:DC115 3.7 33.5 1.0
PA A:DUP1005 3.7 31.5 1.0
OD1 A:ASP623 3.7 32.3 1.0
O2A A:DUP1005 3.8 31.7 1.0
CA A:CA1001 3.9 33.5 1.0
CB A:SER624 4.0 35.6 1.0
OG A:SER624 4.1 36.1 1.0
CB A:ASP411 4.1 40.8 1.0
O5' A:DUP1005 4.2 34.8 1.0
O A:HOH1442 4.2 56.4 1.0
CG A:ASP411 4.2 42.7 1.0
C5' A:DUP1005 4.3 30.6 1.0
O A:HOH1218 4.3 33.3 1.0
O A:ASP621 4.6 31.9 1.0
N A:SER624 4.6 31.7 1.0
C5' P:DC115 4.7 34.4 1.0
O5' P:DC115 4.7 37.2 1.0
C4' P:DC115 4.7 33.4 1.0
C A:ASP623 4.8 35.7 1.0
CB A:ASP623 4.8 31.7 1.0
CA A:SER624 4.8 35.2 1.0
N A:ASP623 4.9 29.4 1.0
C2' P:DC115 4.9 32.5 1.0
O P:HOH236 4.9 60.3 1.0

Sodium binding site 6 out of 8 in 4khq

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Sodium binding site 6 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1010

b:41.2
occ:1.00
 OE1 A:GLU686 2.3 56.5 1.0
O A:HOH1323 2.4 37.9 1.0
O A:HOH1442 2.4 56.4 1.0
O A:HOH1134 2.6 44.0 1.0
OE1 A:GLU716 2.9 69.2 1.0
CD A:GLU686 3.2 59.1 1.0
CD A:GLU716 3.2 67.7 1.0
OE2 A:GLU716 3.3 71.0 1.0
OE2 A:GLU686 3.7 61.4 1.0
O P:HOH238 4.0 62.7 1.0
O3G A:DUP1005 4.2 28.5 1.0
CG A:GLU686 4.3 54.7 1.0
CG A:GLU716 4.3 61.9 1.0
NZ A:LYS486 4.3 57.4 1.0
OD2 A:ASP411 4.4 42.0 1.0
NA A:NA1011 4.4 59.8 1.0
O1G A:DUP1005 4.4 34.9 1.0
O A:HOH1449 4.5 35.8 1.0
OD1 A:ASP411 4.6 42.4 1.0
CG A:ASP411 4.9 42.7 1.0
CE A:MET715 4.9 76.5 1.0
PG A:DUP1005 5.0 33.8 1.0

Sodium binding site 7 out of 8 in 4khq

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Sodium binding site 7 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1011

b:59.8
occ:1.00
 O A:HOH1545 2.4 64.9 1.0
O A:HOH1452 2.4 67.2 1.0
O A:HOH1453 2.4 77.4 1.0
OE1 A:GLU716 2.7 69.2 1.0
O A:HOH1134 3.0 44.0 1.0
OE2 A:GLU686 3.2 61.4 1.0
CD A:GLU716 3.7 67.7 1.0
CG A:GLU716 3.9 61.9 1.0
OD2 A:ASP411 3.9 42.0 1.0
O A:HOH1530 4.0 50.2 1.0
NZ A:LYS486 4.0 57.4 1.0
CD A:GLU686 4.2 59.1 1.0
NA A:NA1010 4.4 41.2 1.0
OE1 A:GLU686 4.5 56.5 1.0
OG1 A:THR413 4.5 43.5 1.0
CB A:ASP684 4.7 59.8 1.0
OE2 A:GLU716 4.8 71.0 1.0
OD1 A:ASP684 4.8 72.1 1.0

Sodium binding site 8 out of 8 in 4khq

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Sodium binding site 8 out of 8 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1012

b:70.4
occ:1.00
 O A:HOH1568 2.4 64.9 1.0
O A:HOH1178 2.4 67.5 1.0
OD2 A:ASP684 2.4 68.7 1.0
OE1 A:GLU660 2.9 57.8 1.0
O A:HOH1570 3.2 62.4 1.0
O A:HOH1569 3.2 75.7 1.0
CG A:ASP684 3.6 67.1 1.0
CD A:GLU660 3.8 58.0 1.0
OD2 A:ASP664 4.1 71.5 1.0
CB A:GLU660 4.2 52.2 1.0
OD1 A:ASP664 4.3 68.9 1.0
OD1 A:ASP684 4.3 72.1 1.0
O A:MET683 4.3 47.3 1.0
CG A:GLU660 4.4 53.8 1.0
OE2 A:GLU660 4.6 61.5 1.0
CG A:ASP664 4.6 67.9 1.0
CB A:ASP684 4.7 59.8 1.0
CA A:ASP684 4.9 54.7 1.0
C A:MET683 4.9 48.2 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: Sun Aug 17 20:13:21 2025

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