Atomistry » Sodium » PDB 4khu-4kxx » 4ki4
Atomistry »
  Sodium »
    PDB 4khu-4kxx »
      4ki4 »

Sodium in PDB 4ki4: Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 Position

Enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 Position:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 Position, PDB code: 4ki4 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) 38.48 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.734, 118.840, 127.520, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.1

Other elements in 4ki4:

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 Position also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 Position (pdb code 4ki4). 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 Ribonucleotides at 0 and -1 Position, PDB code: 4ki4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4ki4

Go back to Sodium Binding Sites List in 4ki4
Sodium binding site 1 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -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 Ribonucleotides at 0 and -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:71.6
occ:1.00
 OE1 A:GLU172 2.9 51.5 1.0
OE2 A:GLU177 3.2 50.8 1.0
OE1 A:GLU177 3.7 50.5 1.0
CD A:GLU172 3.8 50.6 1.0
CD A:GLU177 3.9 49.1 1.0
OE2 A:GLU172 4.0 49.5 1.0

Sodium binding site 2 out of 6 in 4ki4

Go back to Sodium Binding Sites List in 4ki4
Sodium binding site 2 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -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 Ribonucleotides at 0 and -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1008

b:59.8
occ:1.00
 O A:ASN505 2.3 76.6 1.0
O A:LYS531 2.3 71.3 1.0
OD1 A:ASN507 2.4 74.9 1.0
C A:LYS531 3.2 75.1 1.0
CG A:ASN507 3.5 73.4 1.0
C A:ASN505 3.5 76.6 1.0
CB A:ASN505 3.8 83.0 1.0
CA A:LYS531 4.0 73.4 1.0
N A:LYS532 4.0 74.4 1.0
ND2 A:ASN507 4.0 79.5 1.0
CA A:LYS532 4.2 75.8 1.0
N A:ASN507 4.2 76.3 1.0
CA A:ASN505 4.3 79.6 1.0
N A:PRO506 4.5 74.1 1.0
CA A:PRO506 4.6 73.4 1.0
CB A:LYS531 4.6 75.0 1.0
C A:PRO506 4.6 76.0 1.0
CB A:ASN507 4.7 79.6 1.0
C A:LYS532 4.7 74.0 1.0
O A:LEU533 4.7 68.7 1.0
O A:ALA502 4.9 71.4 1.0
CA A:ASN507 4.9 78.7 1.0
O A:ILE530 4.9 69.9 1.0

Sodium binding site 3 out of 6 in 4ki4

Go back to Sodium Binding Sites List in 4ki4
Sodium binding site 3 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -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 Ribonucleotides at 0 and -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:98.2
occ:1.00
 CA A:GLY610 4.1 90.5 1.0
O A:GLY610 4.4 91.4 1.0
C A:GLY610 4.7 89.6 1.0

Sodium binding site 4 out of 6 in 4ki4

Go back to Sodium Binding Sites List in 4ki4
Sodium binding site 4 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -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 Ribonucleotides at 0 and -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1009

b:64.2
occ:1.00
 OE2 A:GLU686 2.5 50.9 1.0
O A:HOH1368 2.8 55.0 1.0
OE1 A:GLU716 3.4 49.7 1.0
CD A:GLU686 3.6 50.2 1.0
CD A:GLU716 4.0 49.0 1.0
NZ A:LYS486 4.0 36.3 1.0
O1G A:TTP1001 4.1 20.3 1.0
O3G A:TTP1001 4.1 69.2 1.0
OE2 A:GLU716 4.2 49.1 1.0
OD2 A:ASP411 4.3 31.1 1.0
OE1 A:GLU686 4.3 50.9 1.0
CG A:GLU686 4.5 48.2 1.0
PG A:TTP1001 4.7 22.6 1.0
O A:HOH1233 4.7 30.5 1.0
CA A:CA1003 4.7 87.1 1.0
CG A:ASP411 4.9 31.7 1.0

Sodium binding site 5 out of 6 in 4ki4

Go back to Sodium Binding Sites List in 4ki4
Sodium binding site 5 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 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 Ribonucleotides at 0 and -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1010

b:57.0
occ:1.00
 O A:HOH1343 2.4 49.5 1.0
O A:HOH1387 2.4 54.5 1.0
O A:HOH1389 2.4 51.4 1.0
OD1 A:ASN232 2.5 50.4 1.0
O A:HOH1388 2.5 47.3 1.0
CG A:ASN232 3.4 48.5 1.0
ND2 A:ASN232 3.8 48.0 1.0
CD A:LYS231 4.2 48.1 1.0
OD1 A:ASN228 4.7 34.6 1.0
O A:SER127 4.8 44.8 1.0
CB A:ASN232 4.8 47.3 1.0
CG A:LYS231 5.0 46.9 1.0
O A:ASN228 5.0 35.1 1.0

Sodium binding site 6 out of 6 in 4ki4

Go back to Sodium Binding Sites List in 4ki4
Sodium binding site 6 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 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 Ribonucleotides at 0 and -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1011

b:48.8
occ:1.00
 O A:HOH1171 2.5 27.7 1.0
O A:HOH1191 2.5 32.4 1.0
O A:HOH1329 2.6 29.6 1.0
O A:ILE115 2.7 26.7 1.0
OE1 A:GLU116 2.9 27.1 1.0
OD2 A:ASP114 2.9 31.9 1.0
O A:HOH1193 3.0 44.1 1.0
OE2 A:GLU116 3.1 29.8 1.0
CD A:GLU116 3.2 28.0 1.0
CG A:ASP114 3.7 30.2 1.0
OD1 A:ASP114 3.8 31.6 1.0
C A:ILE115 3.9 26.4 1.0
O A:HOH1156 3.9 22.5 1.0
CG A:GLU116 4.3 27.9 1.0
CA A:GLU116 4.5 28.3 1.0
N A:GLU116 4.6 28.2 1.0
N A:ILE115 4.7 22.8 1.0
CB A:GLU116 4.9 27.9 1.0
ND2 A:ASN324 4.9 23.6 1.0
CA A:ILE115 5.0 24.3 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 16:31:36 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy