Atomistry » Sodium » PDB 4jvl-4khs » 4khq
Atomistry »
  Sodium »
    PDB 4jvl-4khs »
      4khq »

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

Go back to Sodium Binding Sites List in 4khq
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

Go back to Sodium Binding Sites List in 4khq
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

Go back to Sodium Binding Sites List in 4khq
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

Go back to Sodium Binding Sites List in 4khq
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

Go back to Sodium Binding Sites List in 4khq
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

Go back to Sodium Binding Sites List in 4khq
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

Go back to Sodium Binding Sites List in 4khq
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

Go back to Sodium Binding Sites List in 4khq
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: Mon Oct 7 16:29:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy