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Calcium in PDB 4ki6: Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position

Enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position, PDB code: 4ki6 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) 35.95 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.853, 118.400, 127.970, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.3

Other elements in 4ki6:

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position (pdb code 4ki6). 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 Ribonucleotides at -1 and -2 Position, PDB code: 4ki6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4ki6

Go back to Calcium Binding Sites List in 4ki6
Calcium binding site 1 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 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 -1 and -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:48.0
occ:1.00
 O1G A:TTP1001 2.3 37.2 1.0
OD2 A:ASP623 2.3 53.6 1.0
O2B A:TTP1001 2.4 37.6 1.0
OD2 A:ASP411 2.4 54.5 1.0
O A:LEU412 2.4 52.5 1.0
O2A A:TTP1001 2.4 59.5 1.0
OD1 A:ASP411 2.4 53.7 1.0
CG A:ASP411 2.7 52.8 1.0
CG A:ASP623 3.4 53.4 1.0
C A:LEU412 3.4 51.4 1.0
PB A:TTP1001 3.5 41.1 1.0
PG A:TTP1001 3.6 39.1 1.0
PA A:TTP1001 3.6 42.8 1.0
O3A A:TTP1001 3.7 68.3 1.0
N A:LEU412 3.8 50.7 1.0
OD1 A:ASP623 3.9 51.6 1.0
CA A:CA1003 3.9 89.9 1.0
O3B A:TTP1001 4.0 54.9 1.0
CA A:LEU412 4.1 51.2 1.0
CB A:ASP411 4.2 52.4 1.0
O2G A:TTP1001 4.3 73.8 1.0
C5' A:TTP1001 4.4 48.1 1.0
C A:ASP411 4.4 51.7 1.0
N A:SER414 4.4 46.7 1.0
N A:THR413 4.5 54.1 1.0
O A:HOH1249 4.6 63.5 1.0
O5' A:TTP1001 4.6 54.0 1.0
N A:PHE415 4.6 45.5 1.0
CB A:ASP623 4.6 53.0 1.0
O1A A:TTP1001 4.7 43.8 1.0
CB A:LEU412 4.7 51.0 1.0
CA A:THR413 4.7 55.3 1.0
O1B A:TTP1001 4.7 40.0 1.0
O A:HOH1168 4.7 47.0 1.0
CA A:ASP411 4.8 52.8 1.0
CB A:PHE415 4.8 42.9 1.0
O3G A:TTP1001 4.8 56.0 1.0
C A:THR413 4.9 51.6 1.0

Calcium binding site 2 out of 6 in 4ki6

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Calcium binding site 2 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 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 -1 and -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:89.9
occ:1.00
 O A:HOH1168 2.5 47.0 1.0
O2A A:TTP1001 2.7 59.5 1.0
OD1 A:ASP411 2.8 53.7 1.0
OD1 A:ASP623 3.1 51.6 1.0
O1A A:TTP1001 3.4 43.8 1.0
PA A:TTP1001 3.6 42.8 1.0
CA A:CA1002 3.9 48.0 1.0
CG A:ASP411 3.9 52.8 1.0
CG A:ASP623 4.0 53.4 1.0
OD2 A:ASP623 4.1 53.6 1.0
C3' P:DC115 4.1 55.2 1.0
C5' P:DC115 4.2 55.3 1.0
C4' P:DC115 4.3 55.4 1.0
CB A:SER624 4.4 50.2 1.0
O5' P:DC115 4.5 56.6 1.0
C5' A:TTP1001 4.6 48.1 1.0
OD2 A:ASP411 4.7 54.5 1.0
O5' A:TTP1001 4.7 54.0 1.0
O3A A:TTP1001 4.8 68.3 1.0
OG A:SER624 4.8 52.9 1.0
O A:ASP621 4.9 44.2 1.0
CB A:ASP411 4.9 52.4 1.0
O1G A:TTP1001 4.9 37.2 1.0

Calcium binding site 3 out of 6 in 4ki6

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Calcium binding site 3 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 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 -1 and -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:79.8
occ:1.00
 OE2 A:GLU116 2.5 58.6 1.0
O A:HOH1126 2.5 45.4 1.0
O A:HOH1240 2.5 62.8 1.0
OE1 A:GLU116 2.6 56.7 1.0
CD A:GLU116 2.9 56.0 1.0
OD2 A:ASP114 3.9 62.7 1.0
CG A:GLU116 4.4 51.6 1.0
O A:ILE115 4.5 41.9 1.0

Calcium binding site 4 out of 6 in 4ki6

Go back to Calcium Binding Sites List in 4ki6
Calcium binding site 4 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 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 -1 and -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:98.5
occ:1.00
 O A:HOH1251 2.7 72.8 1.0
OD1 A:ASP684 3.0 84.2 1.0
OE1 A:GLU660 3.3 86.5 1.0
OD2 A:ASP664 3.7 90.8 1.0
OD1 A:ASP664 3.9 87.1 1.0
O A:MET683 4.2 67.6 1.0
CG A:ASP664 4.3 86.7 1.0
CG A:ASP684 4.3 82.6 1.0
CD A:GLU660 4.3 85.8 1.0
CB A:GLU660 4.4 81.2 1.0
C A:MET683 4.7 66.8 1.0
CG A:GLU660 4.7 83.3 1.0
CA A:ASP684 4.9 78.2 1.0
N A:MET683 5.0 66.1 1.0

Calcium binding site 5 out of 6 in 4ki6

Go back to Calcium Binding Sites List in 4ki6
Calcium binding site 5 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 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 Ribonucleotides at -1 and -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:89.7
occ:1.00
 OE2 A:GLU177 2.7 65.0 1.0
O A:HOH1202 2.8 64.3 1.0
OE1 A:GLU172 3.0 60.8 1.0
OE1 A:GLU177 3.2 69.4 1.0
CD A:GLU177 3.3 64.6 1.0
OE2 A:GLU172 3.4 61.2 1.0
CD A:GLU172 3.6 59.8 1.0
CG A:GLN171 4.7 67.3 1.0
CB A:GLN171 4.8 60.7 1.0
CG A:GLU177 4.8 59.0 1.0

Calcium binding site 6 out of 6 in 4ki6

Go back to Calcium Binding Sites List in 4ki6
Calcium binding site 6 out of 6 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 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 Ribonucleotides at -1 and -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:96.5
occ:1.00
 OE2 A:GLU196 2.5 89.0 1.0
OD2 A:ASP192 2.7 95.4 1.0
OE1 A:GLU196 2.9 85.6 1.0
CD A:GLU196 3.0 85.0 1.0
CG A:ASP192 3.5 92.2 1.0
CB A:ASP192 3.6 84.6 1.0
CG A:GLU196 4.5 79.2 1.0
ND2 A:ASN193 4.6 77.2 1.0
OD1 A:ASP192 4.7 93.8 1.0
CA A:ASP192 4.9 75.8 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 09:05:19 2024

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