Atomistry » Calcium » PDB 3q4y-3qgo » 3qew
Atomistry »
  Calcium »
    PDB 3q4y-3qgo »
      3qew »

Calcium in PDB 3qew: RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt

Enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt

All present enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt, PDB code: 3qew was solved by S.Xia, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.00 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.861, 120.342, 130.631, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.5

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt (pdb code 3qew). 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 (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt, PDB code: 3qew:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3qew

Go back to Calcium Binding Sites List in 3qew
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:20.1
occ:1.00
 OD1 A:ASP623 2.2 34.0 1.0
O1G A:DTP904 2.2 17.5 1.0
O2B A:DTP904 2.3 16.0 1.0
OD2 A:ASP411 2.3 27.8 1.0
O A:LEU412 2.3 15.6 1.0
O A:HOH1379 2.7 36.2 1.0
OD1 A:ASP411 2.8 32.2 1.0
CG A:ASP411 2.9 28.6 1.0
O2A A:DTP904 3.0 27.6 1.0
PB A:DTP904 3.4 18.3 1.0
CG A:ASP623 3.4 26.0 1.0
C A:LEU412 3.5 17.9 1.0
PG A:DTP904 3.5 21.0 1.0
O3A A:DTP904 3.7 24.4 1.0
O3B A:DTP904 3.8 18.2 1.0
CA A:CA906 3.9 32.8 1.0
PA A:DTP904 3.9 22.9 1.0
OD2 A:ASP623 4.1 23.6 1.0
N A:LEU412 4.1 17.2 1.0
O A:HOH1474 4.2 49.5 1.0
O2G A:DTP904 4.2 19.6 1.0
CB A:ASP411 4.3 24.9 1.0
CA A:LEU412 4.3 15.5 1.0
N A:SER414 4.4 14.6 1.0
CB A:ASP623 4.4 22.9 1.0
N A:THR413 4.4 17.0 1.0
O A:HOH1353 4.5 39.0 1.0
CA A:THR413 4.6 17.9 1.0
C A:ASP411 4.6 18.8 1.0
O3G A:DTP904 4.6 20.3 1.0
C5' A:DTP904 4.6 16.4 1.0
C A:THR413 4.7 16.2 1.0
O1B A:DTP904 4.8 21.4 1.0
N A:LEU415 4.8 14.1 1.0
O5' A:DTP904 4.8 18.6 1.0
CA A:ASP411 4.9 21.5 1.0
CB A:LEU412 4.9 14.8 1.0
O A:ASP623 4.9 19.1 1.0

Calcium binding site 2 out of 5 in 3qew

Go back to Calcium Binding Sites List in 3qew
Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:32.8
occ:1.00
 O A:HOH1377 2.3 31.7 1.0
O2A A:DTP904 2.4 27.6 1.0
O A:HOH1396 2.5 35.6 1.0
OD2 A:ASP623 2.6 23.6 1.0
O A:HOH1379 2.6 36.2 1.0
OD2 A:ASP411 3.1 27.8 1.0
CG A:ASP623 3.3 26.0 1.0
OD1 A:ASP623 3.3 34.0 1.0
C3' P:DOC115 3.8 21.2 1.0
PA A:DTP904 3.8 22.9 1.0
CA A:CA905 3.9 20.1 1.0
CB A:SER624 3.9 23.8 1.0
OG A:SER624 4.1 30.6 1.0
CG A:ASP411 4.2 28.6 1.0
O A:HOH1271 4.3 27.5 1.0
O1A A:DTP904 4.4 22.5 1.0
O A:HOH1353 4.5 39.0 1.0
O5' A:DTP904 4.6 18.6 1.0
N A:SER624 4.6 19.7 1.0
O A:ASP621 4.7 15.3 1.0
C5' P:DOC115 4.7 26.8 1.0
O5' P:DOC115 4.7 26.3 1.0
C5' A:DTP904 4.7 16.4 1.0
CB A:ASP623 4.7 22.9 1.0
O P:HOH511 4.7 30.3 1.0
C A:ASP623 4.8 19.7 1.0
C4' P:DOC115 4.8 21.2 1.0
CA A:SER624 4.9 20.9 1.0
O3A A:DTP904 4.9 24.4 1.0
C2' P:DOC115 5.0 22.7 1.0
OE2 A:GLU686 5.0 42.0 1.0
OD1 A:ASP411 5.0 32.2 1.0
CB A:ASP411 5.0 24.9 1.0

Calcium binding site 3 out of 5 in 3qew

Go back to Calcium Binding Sites List in 3qew
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:36.2
occ:1.00
 OD1 A:ASN507 2.2 44.6 1.0
O A:HOH1409 2.2 42.7 1.0
O A:LYS531 2.3 39.3 1.0
O A:ASN505 2.4 41.7 1.0
O A:HOH1338 2.4 30.6 1.0
O A:HOH1372 2.5 30.3 1.0
O A:HOH1509 2.6 42.0 1.0
C A:LYS531 3.3 38.4 1.0
CG A:ASN507 3.4 45.3 1.0
C A:ASN505 3.6 42.5 1.0
ND2 A:ASN507 4.0 42.8 1.0
CA A:LYS531 4.1 37.8 1.0
N A:LYS532 4.2 38.1 1.0
N A:ASN507 4.2 45.1 1.0
CB A:ASN505 4.3 42.3 0.5
CB A:ASN505 4.3 42.8 0.5
C A:PRO506 4.3 44.3 1.0
CA A:PRO506 4.3 43.0 1.0
CA A:LYS532 4.4 38.8 1.0
O A:HOH1426 4.4 36.5 1.0
N A:PRO506 4.5 42.6 1.0
CA A:ASN505 4.6 42.7 0.5
CA A:ASN505 4.6 42.8 0.5
CB A:ASN507 4.6 45.5 1.0
O A:LEU533 4.6 34.2 1.0
O A:ALA502 4.6 33.3 1.0
C A:LYS532 4.7 38.0 1.0
CB A:LYS531 4.8 39.8 1.0
CA A:ASN507 4.8 46.6 1.0
N A:LEU533 4.8 35.5 1.0
O A:ILE530 4.9 31.7 1.0
O A:PRO506 4.9 44.9 1.0

Calcium binding site 4 out of 5 in 3qew

Go back to Calcium Binding Sites List in 3qew
Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:62.1
occ:1.00
 O A:HOH1474 2.3 49.5 1.0
O A:HOH1068 2.6 30.2 1.0
O A:HOH1369 2.6 34.5 1.0
O A:HOH1711 3.0 49.0 1.0
OD1 A:ASP411 3.2 32.2 1.0
OE1 A:GLU716 3.5 39.6 1.0
NZ A:LYS486 4.1 28.8 1.0
O A:HOH1104 4.2 23.6 1.0
CG A:ASP411 4.2 28.6 1.0
OE1 A:GLU686 4.3 38.5 1.0
CD A:GLU716 4.4 37.2 1.0
CB A:ASP411 4.4 24.9 1.0
CG A:GLU716 4.5 33.3 1.0
O A:ASP411 4.7 21.0 1.0
OG1 A:THR413 4.8 23.9 1.0
O1G A:DTP904 4.8 17.5 1.0
CD A:GLU686 5.0 39.2 1.0

Calcium binding site 5 out of 5 in 3qew

Go back to Calcium Binding Sites List in 3qew
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:41.7
occ:1.00
 O A:HOH1561 2.3 32.2 1.0
O A:HOH1562 2.5 24.6 1.0
OE2 A:GLU116 2.6 27.4 1.0
OE1 A:GLU116 2.6 27.6 1.0
CD A:GLU116 3.0 26.2 1.0
OD2 A:ASP114 4.1 37.1 1.0
O A:HOH1505 4.3 30.5 1.0
O A:HOH1387 4.4 34.2 1.0
CG A:GLU116 4.5 19.8 1.0
O A:ILE115 4.6 18.1 1.0
OD1 A:ASP114 4.9 34.4 1.0
CG A:ASP114 4.9 31.5 1.0
CD1 A:ILE309 4.9 43.4 1.0

Reference:

S.Xia, W.H.Konigsberg, J.Wang. Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes To Be Published.
Page generated: Sat Jul 13 17:29:18 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