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Calcium in PDB 4du1: RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt, PDB code: 4du1 was solved by S.Xia, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.10 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.983, 119.836, 129.949, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt (pdb code 4du1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt, PDB code: 4du1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4du1

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Calcium binding site 1 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:30.4
occ:1.00
 O1G A:DTP1001 2.2 29.2 1.0
O A:LEU412 2.2 31.1 1.0
OD1 A:ASP623 2.3 41.3 1.0
O1B A:DTP1001 2.3 29.9 1.0
OD2 A:ASP411 2.3 38.3 1.0
OD1 A:ASP411 2.5 36.2 1.0
CG A:ASP411 2.7 35.1 1.0
O A:HOH1136 2.8 38.9 1.0
PB A:DTP1001 3.3 33.1 1.0
C A:LEU412 3.4 33.4 1.0
O3A A:DTP1001 3.4 34.7 1.0
CG A:ASP623 3.5 35.7 1.0
PG A:DTP1001 3.5 31.4 1.0
O1A A:DTP1001 3.7 39.2 1.0
O3B A:DTP1001 3.8 31.3 1.0
CA A:CA1003 3.9 38.7 1.0
O A:HOH1346 3.9 54.9 1.0
N A:LEU412 4.0 32.9 1.0
PA A:DTP1001 4.2 35.0 1.0
CB A:ASP411 4.2 34.4 1.0
CA A:LEU412 4.3 33.3 1.0
N A:SER414 4.3 30.7 1.0
N A:THR413 4.3 33.5 1.0
CB A:ASP623 4.3 32.4 1.0
O2G A:DTP1001 4.3 25.8 1.0
OD2 A:ASP623 4.3 35.8 1.0
CA A:THR413 4.4 33.4 1.0
C A:THR413 4.5 31.7 1.0
C A:ASP411 4.6 35.6 1.0
O3G A:DTP1001 4.6 31.7 1.0
OG A:SER624 4.7 45.0 1.0
O2B A:DTP1001 4.7 37.0 1.0
CB A:LEU412 4.8 32.5 1.0
C5' A:DTP1001 4.8 29.3 1.0
CA A:ASP411 4.9 34.9 1.0
N A:LEU415 4.9 27.4 1.0
O A:ASP623 4.9 28.6 1.0
O5' A:DTP1001 4.9 38.0 1.0

Calcium binding site 2 out of 7 in 4du1

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Calcium binding site 2 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:38.7
occ:1.00
 O A:HOH1171 2.2 26.4 1.0
O1A A:DTP1001 2.3 39.2 1.0
O A:HOH1136 2.4 38.9 1.0
O A:HOH1132 2.5 32.7 1.0
OD2 A:ASP623 2.5 35.8 1.0
OG A:SER624 2.7 45.0 1.0
OD1 A:ASP623 2.9 41.3 1.0
CG A:ASP623 3.1 35.7 1.0
OD2 A:ASP411 3.3 38.3 1.0
PA A:DTP1001 3.7 35.0 1.0
CB A:SER624 3.8 34.6 1.0
C3' P:2DT115 3.9 29.9 1.0
CA A:CA1002 3.9 30.4 1.0
CG A:ASP411 4.3 35.1 1.0
O3A A:DTP1001 4.4 34.7 1.0
CB A:ASP623 4.6 32.4 1.0
C5' P:2DT115 4.6 35.8 1.0
C5' A:DTP1001 4.6 29.3 1.0
O5' A:DTP1001 4.6 38.0 1.0
O2A A:DTP1001 4.7 43.4 1.0
N A:SER624 4.7 32.2 1.0
O5' P:2DT115 4.7 36.4 1.0
O A:ASP621 4.7 31.1 1.0
C A:ASP623 4.8 31.7 1.0
C4' P:2DT115 4.9 35.1 1.0
CA A:SER624 4.9 33.2 1.0
OE1 A:GLU686 5.0 55.5 1.0
OE2 A:GLU686 5.0 57.1 1.0
OD1 A:ASP411 5.0 36.2 1.0

Calcium binding site 3 out of 7 in 4du1

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Calcium binding site 3 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:51.1
occ:1.00
 OD1 A:ASN507 2.2 60.9 1.0
O A:HOH1255 2.2 37.3 1.0
O A:LYS531 2.2 55.2 1.0
O A:ASN505 2.4 56.8 1.0
O A:HOH1324 2.5 36.3 1.0
O A:HOH1301 2.6 44.9 1.0
C A:LYS531 3.2 55.1 1.0
CG A:ASN507 3.4 63.6 1.0
C A:ASN505 3.6 58.6 1.0
CA A:LYS531 4.0 54.5 1.0
ND2 A:ASN507 4.1 61.5 1.0
N A:LYS532 4.1 53.6 1.0
N A:ASN507 4.1 63.6 1.0
CA A:LYS532 4.3 53.9 1.0
CB A:ASN505 4.3 60.1 1.0
C A:PRO506 4.4 62.4 1.0
CA A:PRO506 4.4 60.7 1.0
N A:PRO506 4.5 59.2 1.0
O A:LEU533 4.5 48.6 1.0
CB A:ASN507 4.6 63.5 1.0
CA A:ASN505 4.6 59.4 1.0
C A:LYS532 4.7 52.5 1.0
N A:LEU533 4.7 50.8 1.0
CA A:ASN507 4.7 65.0 1.0
O A:ALA502 4.8 46.4 1.0
CB A:LYS531 4.8 54.4 1.0
O A:ILE530 4.8 50.6 1.0

Calcium binding site 4 out of 7 in 4du1

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Calcium binding site 4 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:76.8
occ:1.00
 O A:HOH1358 2.0 63.5 1.0
O A:HOH1346 2.1 54.9 1.0
O A:HOH1263 2.7 39.6 1.0
O A:HOH1404 2.8 46.0 1.0
OD1 A:ASP411 3.0 36.2 1.0
OE1 A:GLU716 3.3 45.7 1.0
CG A:ASP411 3.9 35.1 1.0
CD A:GLU716 4.0 48.3 1.0
CB A:ASP411 4.1 34.4 1.0
O A:HOH1286 4.1 30.0 1.0
NZ A:LYS486 4.1 30.1 1.0
OE1 A:GLU686 4.2 55.5 1.0
CG A:GLU716 4.4 46.6 1.0
O1G A:DTP1001 4.4 29.2 1.0
O A:ASP411 4.7 33.6 1.0
CD A:GLU686 4.8 56.1 1.0
CG A:GLU686 4.9 46.9 1.0
OG1 A:THR413 4.9 40.2 1.0
OE2 A:GLU716 4.9 47.2 1.0

Calcium binding site 5 out of 7 in 4du1

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Calcium binding site 5 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:78.3
occ:1.00
 O A:HOH1117 2.6 38.6 1.0
OE1 A:GLU116 2.8 42.5 1.0
OE2 A:GLU116 3.0 41.4 1.0
CD A:GLU116 3.3 40.9 1.0
OD2 A:ASP114 4.4 49.0 1.0
O A:HOH1259 4.6 42.5 1.0
O A:ILE115 4.8 30.4 1.0
CG A:GLU116 4.8 32.4 1.0
CD1 A:ILE309 4.9 49.6 1.0

Calcium binding site 6 out of 7 in 4du1

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Calcium binding site 6 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:74.3
occ:1.00
 O A:LEU857 2.6 60.1 1.0
OD1 A:ASP861 2.9 60.2 1.0
OD2 A:ASP860 2.9 62.6 1.0
OD1 A:ASP860 3.3 63.5 1.0
CG A:ASP860 3.5 60.7 1.0
CG A:ASP861 3.6 56.4 1.0
C A:LEU857 3.8 58.3 1.0
OD2 A:ASP861 3.9 57.6 1.0
CB A:ASP861 4.5 51.5 1.0
CA A:ILE858 4.6 51.7 1.0
N A:ILE858 4.7 53.9 1.0
CA A:LEU857 4.7 59.9 1.0
N A:ASP861 4.7 47.9 1.0
CB A:ASP860 5.0 55.2 1.0

Calcium binding site 7 out of 7 in 4du1

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Calcium binding site 7 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:74.8
occ:1.00
 OD1 A:ASP684 2.4 54.4 1.0
OE1 A:GLU660 2.9 47.2 1.0
CG A:ASP684 3.6 54.0 1.0
CD A:GLU660 3.7 43.4 1.0
CG A:GLU660 4.2 40.6 1.0
CB A:GLU660 4.2 41.1 1.0
OD2 A:ASP684 4.2 57.4 1.0
OD1 A:ASP664 4.3 53.1 1.0
OD2 A:ASP664 4.4 51.2 1.0
O A:MET683 4.5 38.8 1.0
OE2 A:GLU660 4.6 43.3 1.0
CB A:ASP684 4.7 46.5 1.0
CG A:ASP664 4.8 47.8 1.0
CA A:ASP684 4.8 44.4 1.0

Reference:

S.Xia, T.D.Christian, J.Wang, W.H.Konigsberg. Probing Minor Groove Hydrogen Bonding Interactions Between RB69 Dna Polymerase and Dna. Biochemistry V. 51 4343 2012.
ISSN: ISSN 0006-2960
PubMed: 22571765
DOI: 10.1021/BI300416Z
Page generated: Sat Jul 13 23:40:28 2024

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