Calcium in PDB 4khq: Ternary Complex of RB69 Mutant L415F Wit Dumpnpp

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp:
2.7.7.7;

The structure of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp, PDB code: 4khq 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)	46.24 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.659, 119.360, 128.070, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.2

The structure of Ternary Complex of RB69 Mutant L415F Wit Dumpnpp also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Calcium atom in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp (pdb code 4khq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp, PDB code: 4khq:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:33.5 occ:1.00 O2B A:DUP1005 2.2 29.9 1.0 O3G A:DUP1005 2.3 28.5 1.0 OD1 A:ASP411 2.3 42.4 1.0 O1A A:DUP1005 2.3 31.2 1.0 O A:LEU412 2.4 36.4 1.0 OD1 A:ASP623 2.4 32.3 1.0 PB A:DUP1005 3.4 30.4 1.0 CG A:ASP411 3.4 42.7 1.0 CG A:ASP623 3.5 32.0 1.0 PG A:DUP1005 3.5 33.8 1.0 PA A:DUP1005 3.6 31.5 1.0 C A:LEU412 3.6 37.6 1.0 O3B A:DUP1005 3.7 35.6 1.0 OD2 A:ASP623 3.8 32.6 1.0 N3A A:DUP1005 3.9 35.9 1.0 NA A:NA1009 3.9 41.9 1.0 O A:HOH1442 3.9 56.4 1.0 N A:LEU412 4.1 37.0 1.0 C5' A:DUP1005 4.1 30.6 1.0 O A:HOH1134 4.1 44.0 1.0 OD2 A:ASP411 4.2 42.0 1.0 O2G A:DUP1005 4.2 32.1 1.0 CB A:ASP411 4.3 40.8 1.0 CA A:LEU412 4.4 36.7 1.0 N A:SER414 4.4 35.9 0.5 N A:SER414 4.4 35.9 0.5 O5' A:DUP1005 4.5 34.8 1.0 N A:PHE415 4.5 30.3 1.0 N A:THR413 4.6 37.5 1.0 O1B A:DUP1005 4.7 32.1 1.0 O1G A:DUP1005 4.7 34.9 1.0 CB A:PHE415 4.7 30.7 1.0 O2A A:DUP1005 4.7 31.7 1.0 CA A:THR413 4.8 38.9 1.0 CB A:ASP623 4.8 31.7 1.0 C A:ASP411 4.8 39.4 1.0 C A:THR413 4.9 38.9 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:46.4 occ:1.00 OD2 A:ASP192 2.4 56.5 1.0 O A:HOH1458 2.4 39.2 1.0 O A:HOH1443 2.4 50.3 1.0 OE2 A:GLU196 2.4 50.0 1.0 OE1 A:GLU196 2.5 46.4 1.0 OD1 A:ASP192 2.5 52.6 1.0 CG A:ASP192 2.8 54.6 1.0 CD A:GLU196 2.8 47.5 1.0 O A:HOH1286 3.8 49.3 1.0 ND2 A:ASN193 4.1 62.2 1.0 CB A:ASP192 4.3 50.5 1.0 CG A:GLU196 4.3 44.1 1.0 CG A:ASN193 5.0 61.1 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of RB69 Mutant L415F Wit Dumpnpp


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 Wit Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:79.0 occ:1.00 O A:LYS531 2.3 71.5 1.0 O A:HOH1472 2.4 62.6 1.0 O A:HOH1471 2.4 94.5 1.0 O A:HOH1554 2.4 54.3 1.0 O A:ASN505 2.5 85.8 0.5 O A:ASN505 2.5 85.8 0.5 OD1 A:ASN507 2.5 75.1 1.0 C A:LYS531 2.9 72.4 1.0 CG A:ASN507 3.5 78.7 1.0 CA A:LYS531 3.5 73.0 1.0 C A:ASN505 3.6 86.1 0.5 C A:ASN505 3.6 86.1 0.5 N A:LYS532 3.9 73.2 1.0 ND2 A:ASN507 3.9 81.4 1.0 CB A:ASN505 4.0 91.1 0.5 CB A:ASN505 4.0 91.1 0.5 CB A:LYS531 4.1 71.8 1.0 CA A:LYS532 4.3 78.1 1.0 N A:ASN507 4.3 81.4 1.0 CA A:ASN505 4.4 88.4 0.5 CA A:ASN505 4.4 88.4 0.5 O A:ILE530 4.5 75.1 1.0 O A:ALA502 4.6 72.0 1.0 N A:PRO506 4.6 84.2 1.0 O A:LEU533 4.7 70.7 1.0 CA A:PRO506 4.7 83.2 1.0 N A:LEU533 4.8 75.8 1.0 CB A:ASN507 4.8 81.1 1.0 N A:LYS531 4.8 72.5 1.0 C A:LYS532 4.9 77.8 1.0 C A:PRO506 4.9 83.1 1.0

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