Atomistry » Calcium » PDB 3ljz-3lzk » 3lzi
Atomistry »
  Calcium »
    PDB 3ljz-3lzk »
      3lzi »

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

Go back to Calcium Binding Sites List in 3lzi
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

Go back to Calcium Binding Sites List in 3lzi
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

Go back to Calcium Binding Sites List in 3lzi
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

Go back to Calcium Binding Sites List in 3lzi
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

Go back to Calcium Binding Sites List in 3lzi
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: Sat Jul 13 13:21:39 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy