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Calcium in PDB 4khw: Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position

Enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position

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

Protein crystallography data

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position, PDB code: 4khw 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) 44.64 / 2.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.355, 118.630, 126.310, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.4

Other elements in 4khw:

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -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 Ribonucleotide at -2 Position (pdb code 4khw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position, PDB code: 4khw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4khw

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Calcium binding site 1 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -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 Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:31.1
occ:1.00
 O2B A:TTP1001 2.1 34.2 1.0
O2A A:TTP1001 2.1 27.1 1.0
O1G A:TTP1001 2.2 22.8 1.0
O A:LEU412 2.4 34.8 1.0
OD1 A:ASP623 2.4 28.9 1.0
OD2 A:ASP411 2.4 45.7 1.0
OD1 A:ASP411 2.4 48.8 1.0
CG A:ASP411 2.7 43.5 1.0
PB A:TTP1001 3.4 27.1 1.0
CG A:ASP623 3.4 31.5 1.0
CA A:CA1003 3.5 75.1 1.0
PG A:TTP1001 3.5 22.5 1.0
C A:LEU412 3.5 33.8 1.0
PA A:TTP1001 3.5 28.6 1.0
OD2 A:ASP623 3.7 34.0 1.0
O3A A:TTP1001 3.8 59.8 1.0
N A:LEU412 3.9 34.0 1.0
O3B A:TTP1001 4.0 38.5 1.0
O2G A:TTP1001 4.1 35.7 1.0
C5' A:TTP1001 4.2 22.4 1.0
CB A:ASP411 4.2 38.5 1.0
CA A:LEU412 4.2 33.5 1.0
CA A:CA1010 4.3 0.4 1.0
O A:HOH1435 4.4 50.0 1.0
C A:ASP411 4.4 36.4 1.0
N A:SER414 4.5 36.0 1.0
O1A A:TTP1001 4.5 28.7 1.0
O5' A:TTP1001 4.5 25.7 1.0
O1B A:TTP1001 4.5 24.0 1.0
N A:THR413 4.6 35.3 1.0
CB A:ASP623 4.7 30.9 1.0
N A:PHE415 4.7 32.2 1.0
O3G A:TTP1001 4.8 55.7 1.0
CB A:LEU412 4.8 32.0 1.0
CA A:ASP411 4.8 37.2 1.0
CA A:THR413 4.8 37.1 1.0
CB A:PHE415 4.8 28.5 1.0
C A:THR413 4.9 37.6 1.0

Calcium binding site 2 out of 8 in 4khw

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Calcium binding site 2 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -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 Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:75.1
occ:1.00
 OD2 A:ASP411 2.4 45.7 1.0
O P:HOH208 2.4 37.7 1.0
O2A A:TTP1001 2.4 27.1 1.0
O A:HOH1435 2.4 50.0 1.0
OD2 A:ASP623 2.4 34.0 1.0
CG A:ASP623 3.4 31.5 1.0
O A:HOH1436 3.4 44.7 1.0
CA A:CA1002 3.5 31.1 1.0
PA A:TTP1001 3.5 28.6 1.0
O1A A:TTP1001 3.6 28.7 1.0
CG A:ASP411 3.6 43.5 1.0
OD1 A:ASP623 3.6 28.9 1.0
C3' P:DC115 3.8 26.9 1.0
O5' A:TTP1001 4.1 25.7 1.0
C5' A:TTP1001 4.2 22.4 1.0
CB A:SER624 4.2 33.5 1.0
C4' P:DC115 4.3 28.4 1.0
C5' P:DC115 4.3 29.3 1.0
OD1 A:ASP411 4.3 48.8 1.0
O A:ASP621 4.5 29.8 1.0
CB A:ASP411 4.5 38.5 1.0
C A:ASP623 4.6 29.5 1.0
N A:SER624 4.6 26.9 1.0
O2B A:TTP1001 4.7 34.2 1.0
CB A:ASP623 4.7 30.9 1.0
O1G A:TTP1001 4.7 22.8 1.0
O5' P:DC115 4.8 32.3 1.0
N A:ASP623 4.8 30.2 1.0
O A:ASP623 4.9 32.1 1.0
OG A:SER624 4.9 33.2 1.0
O A:HOH1170 4.9 30.6 1.0
CA A:SER624 4.9 32.7 1.0
O3A A:TTP1001 4.9 59.8 1.0
CA A:ASP623 5.0 31.4 1.0

Calcium binding site 3 out of 8 in 4khw

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Calcium binding site 3 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -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 Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:75.1
occ:1.00
 O A:HOH1391 2.4 45.5 1.0
OE2 A:GLU116 2.4 42.5 1.0
O A:HOH1163 2.4 51.9 1.0
O A:HOH1390 2.4 48.8 1.0
OE1 A:GLU116 2.5 34.4 1.0
CD A:GLU116 2.8 35.5 1.0
OD2 A:ASP114 3.8 40.2 1.0
O A:HOH1505 4.1 49.6 1.0
O A:HOH1191 4.2 35.0 1.0
CG A:GLU116 4.3 31.1 1.0
O A:HOH1238 4.5 36.0 1.0
O A:ILE115 4.5 32.7 1.0
CG A:ASP114 4.8 39.2 1.0

Calcium binding site 4 out of 8 in 4khw

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Calcium binding site 4 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -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 Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:0.1
occ:1.00
 O A:HOH1339 2.4 51.3 1.0
O A:HOH1454 2.4 53.9 1.0
OD2 A:ASP684 2.4 67.7 1.0
OE1 A:GLU660 2.4 60.1 1.0
CD A:GLU660 3.5 58.1 1.0
CG A:ASP684 3.7 67.1 1.0
CB A:GLU660 4.0 57.4 1.0
OD2 A:ASP664 4.1 73.2 1.0
CG A:GLU660 4.2 57.4 1.0
OE2 A:GLU660 4.4 57.5 1.0
OD1 A:ASP684 4.5 70.5 1.0
O A:MET683 4.5 47.5 1.0
CB A:ASP684 4.5 61.7 1.0
CA A:ASP684 4.7 56.6 1.0
C A:MET683 4.9 47.6 1.0

Calcium binding site 5 out of 8 in 4khw

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Calcium binding site 5 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -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 Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:92.0
occ:1.00
 O A:ASN505 2.3 68.8 1.0
O A:HOH1387 2.4 59.7 1.0
O A:LYS531 2.4 65.8 1.0
O A:HOH1455 2.4 72.6 1.0
O A:HOH1388 2.4 81.8 1.0
OD1 A:ASN507 2.4 72.1 1.0
O A:HOH1389 2.4 56.0 1.0
CG A:ASN507 3.3 71.0 1.0
C A:LYS531 3.4 68.3 1.0
C A:ASN505 3.5 72.1 1.0
ND2 A:ASN507 3.8 69.9 1.0
CB A:ASN505 3.9 80.3 1.0
CA A:LYS531 4.1 69.1 1.0
N A:ASN507 4.1 72.8 1.0
CA A:ASN505 4.3 77.5 1.0
N A:PRO506 4.4 70.5 1.0
CA A:PRO506 4.4 70.4 1.0
C A:PRO506 4.5 71.8 1.0
N A:LYS532 4.5 70.1 1.0
CB A:LYS531 4.5 68.9 1.0
CB A:ASN507 4.6 71.5 1.0
O A:ALA502 4.6 68.8 1.0
CA A:ASN507 4.7 73.5 1.0
CA A:LYS532 4.8 73.4 1.0
O A:LEU533 5.0 70.1 1.0

Calcium binding site 6 out of 8 in 4khw

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Calcium binding site 6 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -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 Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:70.3
occ:1.00
 OE2 A:GLU196 2.4 64.0 1.0
OE1 A:GLU196 2.4 62.4 1.0
OD2 A:ASP192 2.4 72.9 1.0
CD A:GLU196 2.7 60.9 1.0
OD1 A:ASP192 2.9 74.6 1.0
CG A:ASP192 3.1 70.6 1.0
O A:HOH1251 4.0 35.4 1.0
CG A:GLU196 4.2 54.7 1.0
CB A:ASP192 4.6 63.3 1.0
ND2 A:ASN193 4.9 52.6 1.0

Calcium binding site 7 out of 8 in 4khw

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Calcium binding site 7 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:90.5
occ:1.00
 OE2 A:GLU177 2.4 59.5 1.0
O A:HOH1405 2.4 48.3 1.0
OE1 A:GLU172 2.5 57.4 1.0
CD A:GLU177 3.2 57.1 1.0
OE1 A:GLU177 3.3 60.9 1.0
CD A:GLU172 3.3 55.5 1.0
OE2 A:GLU172 3.5 55.5 1.0
CG A:GLU177 4.6 48.8 1.0
CB A:GLN171 4.7 48.9 1.0
CG A:GLU172 4.7 51.8 1.0
N A:GLN171 5.0 40.5 1.0

Calcium binding site 8 out of 8 in 4khw

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Calcium binding site 8 out of 8 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1010

b:0.4
occ:1.00
 OE1 A:GLU686 2.4 62.7 1.0
O A:HOH1546 2.4 55.4 1.0
OD1 A:ASP411 2.5 48.8 1.0
CG A:ASP411 3.2 43.5 1.0
O A:HOH1547 3.4 43.1 1.0
O1G A:TTP1001 3.4 22.8 1.0
CD A:GLU686 3.5 60.9 1.0
OE1 A:GLU716 3.6 66.1 1.0
CB A:ASP411 3.8 38.5 1.0
CG A:GLU686 4.0 55.1 1.0
NZ A:LYS486 4.1 44.5 1.0
OD2 A:ASP411 4.1 45.7 1.0
CD A:GLU716 4.2 63.0 1.0
O A:HOH1186 4.2 56.2 1.0
PG A:TTP1001 4.2 22.5 1.0
O3G A:TTP1001 4.3 55.7 1.0
O2G A:TTP1001 4.3 35.7 1.0
CA A:CA1002 4.3 31.1 1.0
OE2 A:GLU686 4.5 63.2 1.0
OE2 A:GLU716 4.7 63.3 1.0
O A:HOH1435 4.8 50.0 1.0
O A:HOH1436 4.9 44.7 1.0
CG A:GLU716 4.9 56.9 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: Sat Dec 12 04:55:00 2020

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