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Calcium 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:

Sodium (Na) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at 0 and -1 Position, PDB code: 4ki4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4ki4

Go back to Calcium Binding Sites List in 4ki4
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca1002

b:27.3
occ:1.00
 O2B A:TTP1001 2.3 25.8 1.0
O2A A:TTP1001 2.3 36.0 1.0
OD2 A:ASP623 2.3 30.1 1.0
O A:LEU412 2.3 33.9 1.0
O1G A:TTP1001 2.4 20.3 1.0
OD2 A:ASP411 2.4 31.1 1.0
OD1 A:ASP411 2.7 32.4 1.0
CG A:ASP411 2.9 31.7 1.0
CG A:ASP623 3.4 30.1 1.0
PB A:TTP1001 3.4 23.8 1.0
PA A:TTP1001 3.5 25.5 1.0
C A:LEU412 3.5 34.6 1.0
PG A:TTP1001 3.6 22.6 1.0
O A:HOH1174 3.6 28.0 1.0
O3A A:TTP1001 3.6 49.6 1.0
OD1 A:ASP623 3.8 29.4 1.0
O3B A:TTP1001 4.0 40.4 1.0
N A:LEU412 4.0 33.9 1.0
O A:HOH1368 4.2 55.0 1.0
O2G A:TTP1001 4.2 42.1 1.0
C5' A:TTP1001 4.2 29.1 1.0
CA A:LEU412 4.3 34.3 1.0
CB A:ASP411 4.3 33.0 1.0
N A:SER414 4.4 31.6 0.5
N A:SER414 4.4 31.6 0.5
O5' A:TTP1001 4.5 31.9 1.0
O1A A:TTP1001 4.6 25.8 1.0
N A:THR413 4.6 35.7 1.0
C A:ASP411 4.6 34.5 1.0
N A:PHE415 4.6 29.6 1.0
CB A:ASP623 4.6 29.9 1.0
O1B A:TTP1001 4.6 22.9 1.0
CB A:LEU412 4.7 33.8 1.0
CA A:THR413 4.8 35.4 1.0
O3G A:TTP1001 4.8 69.2 1.0
CB A:PHE415 4.9 26.8 1.0
C A:THR413 4.9 33.3 1.0
CA A:ASP411 4.9 34.3 1.0

Calcium binding site 2 out of 4 in 4ki4

Go back to Calcium Binding Sites List in 4ki4
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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:Ca1003

b:87.1
occ:1.00
 OE1 A:GLU716 2.9 49.7 1.0
O A:HOH1368 3.1 55.0 1.0
CD A:GLU716 3.7 49.0 1.0
CG A:GLU716 3.8 47.4 1.0
O A:HOH1454 4.1 52.7 1.0
OE2 A:GLU686 4.1 50.9 1.0
CB A:ASP684 4.2 51.6 1.0
O A:ARG685 4.4 44.8 1.0
NZ A:LYS486 4.5 36.3 1.0
OD2 A:ASP411 4.6 31.1 1.0
CG A:GLU686 4.6 48.2 1.0
O A:ASP411 4.7 36.3 1.0
OD2 A:ASP684 4.7 53.9 1.0
NA A:NA1009 4.7 64.2 1.0
CD A:GLU686 4.8 50.2 1.0
O A:ASP684 4.8 48.4 1.0
CB A:ASP411 4.9 33.0 1.0
OE2 A:GLU716 4.9 49.1 1.0
CB A:GLU716 5.0 45.8 1.0
C A:ASP684 5.0 49.2 1.0
CG A:ASP684 5.0 53.6 1.0

Calcium binding site 3 out of 4 in 4ki4

Go back to Calcium Binding Sites List in 4ki4
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca 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:Ca1004

b:83.2
occ:1.00
 OD1 A:ASP684 2.6 54.9 1.0
OE1 A:GLU660 2.8 58.9 1.0
CD A:GLU660 3.8 58.4 1.0
CG A:ASP684 3.8 53.6 1.0
CB A:GLU660 4.2 59.7 1.0
O A:MET683 4.3 48.0 1.0
OD1 A:ASP664 4.3 62.5 1.0
CG A:GLU660 4.3 58.2 1.0
OD2 A:ASP684 4.5 53.9 1.0
OE2 A:GLU660 4.7 57.5 1.0
CB A:ASP684 4.8 51.6 1.0
CA A:ASP684 4.8 50.3 1.0
OD2 A:ASP664 4.8 64.9 1.0
C A:MET683 4.8 47.0 1.0
CG A:ASP664 5.0 63.4 1.0

Calcium binding site 4 out of 4 in 4ki4

Go back to Calcium Binding Sites List in 4ki4
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca 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:Ca1007

b:60.9
occ:1.00
 O A:HOH1269 2.5 44.0 1.0
OE1 A:GLU196 2.6 58.5 1.0
OD2 A:ASP192 2.6 64.9 1.0
OE2 A:GLU196 2.6 56.1 1.0
CD A:GLU196 3.0 55.7 1.0
CG A:ASP192 3.4 61.9 1.0
CB A:ASP192 3.5 57.7 1.0
ND2 A:ASN193 4.3 55.9 1.0
CG A:GLU196 4.5 52.3 1.0
OD1 A:ASP192 4.6 62.1 1.0
CA A:ASP192 4.9 52.4 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 Jul 14 09:04:37 2024

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