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Calcium in PDB 3lzi: RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine

Enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine

All present enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine, PDB code: 3lzi was solved by M.Wang, J.Beckman, G.Blaha, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.15 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.148, 117.603, 130.681, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine (pdb code 3lzi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine, PDB code: 3lzi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3lzi

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Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:42.0
occ:1.00
 O2B A:DTP904 2.1 30.4 1.0
OD1 A:ASP623 2.2 43.6 1.0
O2G A:DTP904 2.3 28.4 1.0
O A:LEU412 2.3 31.9 1.0
OD2 A:ASP411 2.4 46.6 1.0
O2A A:DTP904 2.6 30.1 1.0
OD1 A:ASP411 2.7 49.0 1.0
CG A:ASP411 2.9 42.4 1.0
PB A:DTP904 3.3 30.2 1.0
CG A:ASP623 3.3 40.8 1.0
O A:HOH1068 3.5 64.1 1.0
C A:LEU412 3.5 30.4 1.0
PG A:DTP904 3.6 29.7 1.0
PA A:DTP904 3.7 28.9 1.0
O3A A:DTP904 3.8 32.8 1.0
O3B A:DTP904 3.8 28.6 1.0
CA A:CA907 3.8 74.7 1.0
OD2 A:ASP623 3.9 45.3 1.0
N A:LEU412 4.1 34.8 1.0
O3G A:DTP904 4.3 28.2 1.0
N A:SER414 4.3 29.7 1.0
CB A:ASP411 4.3 39.0 1.0
C5' A:DTP904 4.3 26.9 1.0
CA A:LEU412 4.4 31.8 1.0
CB A:ASP623 4.5 39.4 1.0
N A:THR413 4.5 29.8 1.0
O5' A:DTP904 4.6 26.9 1.0
CA A:THR413 4.6 31.5 1.0
O1B A:DTP904 4.6 30.4 1.0
C A:ASP411 4.6 36.1 1.0
O1G A:DTP904 4.7 30.8 1.0
C A:THR413 4.7 30.9 1.0
N A:LEU415 4.9 30.7 1.0
CB A:LEU412 4.9 27.9 1.0
CA A:ASP411 5.0 36.3 1.0

Calcium binding site 2 out of 5 in 3lzi

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:63.6
occ:1.00
 O A:ASN505 2.3 49.2 1.0
O A:HOH983 2.3 45.8 1.0
O A:LYS531 2.4 54.0 1.0
OD1 A:ASN507 2.6 53.5 1.0
O A:HOH933 2.7 48.0 1.0
C A:LYS531 3.3 53.8 1.0
C A:ASN505 3.5 51.6 1.0
CG A:ASN507 3.6 55.1 1.0
CA A:LYS531 3.9 55.3 1.0
CB A:ASN505 4.0 53.0 1.0
ND2 A:ASN507 4.1 52.7 1.0
N A:ASN507 4.3 55.6 1.0
N A:LYS532 4.3 53.5 1.0
CA A:ASN505 4.4 51.8 1.0
C A:PRO506 4.4 54.8 1.0
N A:PRO506 4.5 52.0 1.0
CA A:PRO506 4.5 53.9 1.0
CB A:LYS531 4.6 55.0 1.0
O A:LEU533 4.6 43.1 1.0
CA A:LYS532 4.6 53.6 1.0
O A:ALA502 4.7 46.9 1.0
CB A:ASN507 4.8 55.3 1.0
O A:ILE530 4.9 52.7 1.0
CA A:ASN507 4.9 55.6 1.0
N A:LEU533 5.0 49.4 1.0
C A:LYS532 5.0 52.4 1.0

Calcium binding site 3 out of 5 in 3lzi

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:74.7
occ:1.00
 O2A A:DTP904 2.6 30.1 1.0
OD2 A:ASP623 2.8 45.3 1.0
OD1 A:ASP411 2.8 49.0 1.0
O A:HOH1069 3.1 36.6 1.0
O A:HOH1068 3.4 64.1 1.0
CG A:ASP623 3.7 40.8 1.0
C3' P:DOC115 3.7 29.4 1.0
OD1 A:ASP623 3.7 43.6 1.0
CG A:ASP411 3.8 42.4 1.0
PA A:DTP904 3.8 28.9 1.0
CA A:CA905 3.8 42.0 1.0
O A:HOH951 4.0 38.2 1.0
CB A:SER624 4.2 40.5 1.0
O1A A:DTP904 4.3 31.9 1.0
C5' P:DOC115 4.3 31.4 1.0
OD2 A:ASP411 4.3 46.6 1.0
O5' A:DTP904 4.4 26.9 1.0
C4' P:DOC115 4.6 30.2 1.0
O5' P:DOC115 4.6 32.8 1.0
OG A:SER624 4.7 45.5 1.0
C5' A:DTP904 4.7 26.9 1.0
CB A:ASP411 4.8 39.0 1.0
O A:ASP621 4.9 34.7 1.0
OE2 A:GLU686 4.9 65.3 1.0
C2' P:DOC115 5.0 27.0 1.0
O2G A:DTP904 5.0 28.4 1.0

Calcium binding site 4 out of 5 in 3lzi

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:87.5
occ:1.00
 OE1 A:GLU716 2.6 58.4 1.0
OE1 A:GLU686 3.5 60.2 1.0
CD A:GLU716 3.7 56.5 1.0
OD2 A:ASP411 3.7 46.6 1.0
NZ A:LYS486 3.9 41.7 1.0
CG A:GLU716 4.2 49.6 1.0
CD A:GLU686 4.5 59.7 1.0
CB A:ASP411 4.5 39.0 1.0
CG A:ASP411 4.6 42.4 1.0
O A:ASP411 4.6 36.5 1.0
O2G A:DTP904 4.7 28.4 1.0
OE2 A:GLU716 4.7 56.3 1.0
CG A:GLU686 4.8 50.4 1.0
OG1 A:THR413 4.9 38.7 1.0
O A:HOH1068 4.9 64.1 1.0
O3G A:DTP904 5.0 28.2 1.0

Calcium binding site 5 out of 5 in 3lzi

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Calcium binding site 5 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:62.7
occ:1.00
 O A:HOH1070 2.5 43.9 1.0
OE2 A:GLU116 2.7 43.1 1.0
OE1 A:GLU116 2.8 40.9 1.0
O A:HOH910 2.9 39.4 1.0
O A:HOH1019 3.0 38.7 1.0
CD A:GLU116 3.1 39.6 1.0
OD2 A:ASP114 4.4 51.9 1.0
CG A:GLU116 4.6 38.0 1.0
O A:ILE115 4.7 33.3 1.0

Reference:

J.Beckman, M.Wang, G.Blaha, J.Wang, W.H.Konigsberg. Substitution of Ala For TYR567 in RB69 Dna Polymerase Allows Damp to Be Inserted Opposite 7,8-Dihydro-8-Oxoguanine . Biochemistry V. 49 4116 2010.
ISSN: ISSN 0006-2960
PubMed: 20411947
DOI: 10.1021/BI100102S
Page generated: Tue Jul 8 14:26:46 2025

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