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Calcium 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:

Sodium (Na) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -3 Position, PDB code: 4khy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4khy

Go back to Calcium Binding Sites List in 4khy
Calcium 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 Calcium with other atoms in the Ca 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:Ca1002

b:30.0
occ:1.00
 O1B A:TTP1001 2.2 25.5 1.0
O1A A:TTP1001 2.2 34.9 1.0
O2G A:TTP1001 2.3 24.4 1.0
OD1 A:ASP623 2.3 34.2 1.0
O A:LEU412 2.3 36.0 1.0
OD1 A:ASP411 2.4 45.0 1.0
OD2 A:ASP411 2.4 45.0 1.0
CG A:ASP411 2.7 42.9 1.0
PB A:TTP1001 3.4 31.3 1.0
CG A:ASP623 3.4 35.8 1.0
PA A:TTP1001 3.5 32.3 1.0
C A:LEU412 3.5 34.8 1.0
PG A:TTP1001 3.6 31.1 1.0
NA A:NA1013 3.6 61.1 1.0
O3A A:TTP1001 3.7 46.3 1.0
OD2 A:ASP623 3.7 33.8 1.0
O3B A:TTP1001 3.9 42.4 1.0
N A:LEU412 4.0 32.5 1.0
C5' A:TTP1001 4.2 28.9 1.0
CB A:ASP411 4.2 39.0 1.0
CA A:LEU412 4.3 33.6 1.0
O1G A:TTP1001 4.4 55.8 1.0
N A:SER414 4.4 34.3 0.5
N A:SER414 4.5 34.2 0.5
O2A A:TTP1001 4.5 35.1 1.0
N A:THR413 4.5 35.0 1.0
O5' A:TTP1001 4.5 36.5 1.0
C A:ASP411 4.6 35.0 1.0
O2B A:TTP1001 4.6 33.6 1.0
N A:PHE415 4.6 30.2 1.0
CB A:ASP623 4.6 33.1 1.0
CA A:THR413 4.7 36.3 1.0
O3G A:TTP1001 4.7 48.7 1.0
O A:HOH1424 4.8 57.8 1.0
CB A:PHE415 4.8 28.8 1.0
CB A:LEU412 4.8 36.2 1.0
C A:THR413 4.8 35.4 1.0
CA A:ASP411 4.9 35.5 1.0

Calcium binding site 2 out of 6 in 4khy

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1003

b:87.6
occ:1.00
 OE1 A:GLU716 3.2 64.2 1.0
OE1 A:GLU686 3.5 65.8 1.0
CD A:GLU716 4.2 62.0 1.0
OD1 A:ASP411 4.2 45.0 1.0
NZ A:LYS486 4.2 49.3 1.0
OG1 A:THR413 4.4 45.0 1.0
CG A:GLU716 4.5 57.8 1.0
CD A:GLU686 4.5 61.9 1.0
CB A:ASP684 4.6 55.3 1.0
O A:ASP411 4.6 37.7 1.0
OE2 A:GLU686 4.7 61.3 1.0
O A:ARG685 4.8 41.8 1.0
OD1 A:ASP684 4.9 62.8 1.0
CB A:ASP411 5.0 39.0 1.0

Calcium binding site 3 out of 6 in 4khy

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1004

b:0.7
occ:1.00
 O A:ARG668 3.8 46.1 1.0
SG A:CYS671 3.8 45.8 1.0
CB A:CYS671 4.2 33.8 1.0
OE1 A:GLU672 4.4 76.5 1.0
N A:GLU672 4.6 44.3 1.0
CB A:HIS679 4.6 38.2 1.0
C A:ARG668 4.7 48.1 1.0
NH1 A:ARG668 4.8 74.3 1.0
CA A:ARG668 4.8 51.1 1.0
C A:CYS671 4.9 39.1 1.0
CA A:GLU672 4.9 49.4 1.0
CB A:GLU672 5.0 56.1 1.0

Calcium binding site 4 out of 6 in 4khy

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1005

b:91.0
occ:1.00
 O A:HOH1404 2.4 52.0 1.0
O A:HOH1405 2.4 72.4 1.0
OD2 A:ASP684 2.4 63.4 1.0
OE1 A:GLU660 3.1 58.4 1.0
O A:HOH1406 3.1 64.5 1.0
CG A:ASP684 3.6 60.7 1.0
CD A:GLU660 4.1 59.0 1.0
OD2 A:ASP664 4.2 77.4 1.0
OD1 A:ASP684 4.2 62.8 1.0
OD1 A:ASP664 4.3 74.7 1.0
O A:MET683 4.3 51.8 1.0
CB A:GLU660 4.5 54.9 1.0
CG A:ASP664 4.7 73.2 1.0
CG A:GLU660 4.7 55.8 1.0
CB A:ASP684 4.7 55.3 1.0
CA A:ASP684 4.9 51.0 1.0
C A:MET683 4.9 50.1 1.0
OE2 A:GLU660 4.9 61.1 1.0

Calcium binding site 5 out of 6 in 4khy

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1009

b:57.6
occ:1.00
 OD2 A:ASP192 2.4 61.6 1.0
OE1 A:GLU196 2.4 43.6 1.0
O A:HOH1383 2.4 49.3 1.0
OE2 A:GLU196 2.4 47.2 1.0
OD1 A:ASP192 2.5 56.1 1.0
CD A:GLU196 2.8 43.9 1.0
CG A:ASP192 2.8 58.8 1.0
O A:HOH1220 3.8 33.6 1.0
ND2 A:ASN193 4.1 58.8 1.0
CB A:ASP192 4.3 54.7 1.0
CG A:GLU196 4.3 39.2 1.0
O A:HOH1384 4.6 56.8 1.0
CG A:ASN193 4.9 54.7 1.0

Calcium binding site 6 out of 6 in 4khy

Go back to Calcium Binding Sites List in 4khy
Calcium 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 Calcium with other atoms in the Ca 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:Ca1010

b:85.9
occ:1.00
 O A:LYS531 2.1 74.5 1.0
OD1 A:ASN507 2.3 0.5 1.0
O A:ASN505 2.4 75.9 1.0
ND2 A:ASN507 2.6 0.1 1.0
CG A:ASN507 2.8 1.0 1.0
C A:LYS531 3.0 75.2 1.0
O A:HOH1452 3.2 51.3 1.0
CB A:ASN505 3.3 90.8 1.0
C A:ASN505 3.5 79.1 1.0
CA A:LYS531 3.8 76.1 1.0
N A:LYS532 3.8 74.4 1.0
CA A:ASN505 4.0 85.0 1.0
NA A:NA1007 4.0 0.3 1.0
CA A:LYS532 4.1 75.5 1.0
CB A:ASN507 4.3 99.0 1.0
N A:ASN507 4.3 92.2 1.0
CB A:LYS531 4.4 75.9 1.0
O A:LEU533 4.4 83.5 1.0
C A:LYS532 4.5 76.6 1.0
O A:HOH1453 4.5 46.8 1.0
CG A:ASN505 4.6 96.2 1.0
N A:PRO506 4.6 79.2 1.0
N A:LEU533 4.7 76.2 1.0
O A:ALA502 4.7 72.2 1.0
ND2 A:ASN505 4.7 98.0 1.0
O A:ILE530 4.8 69.0 1.0
CA A:ASN507 4.8 96.2 1.0
C A:PRO506 5.0 89.1 1.0
CA A:PRO506 5.0 81.7 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 09:04:17 2024

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