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Calcium in PDB 7y7s: Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp

Enzymatic activity of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp

All present enzymatic activity of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp:
2.7.7.48;

Protein crystallography data

The structure of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp, PDB code: 7y7s was solved by R.X.Cui, J.H.Gan, J.B.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.10 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.954, 120.412, 114.993, 90, 109.71, 90
R / Rfree (%) 20.8 / 24.5

Other elements in 7y7s:

The structure of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp (pdb code 7y7s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp, PDB code: 7y7s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 1 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:46.7
occ:1.00
 O3' D:C7 2.3 48.1 1.0
OD1 A:ASP1007 2.3 43.9 1.0
O2A A:ZAN1504 2.4 40.0 1.0
OD1 A:ASP1011 2.4 49.6 1.0
OD1 A:ASP1009 2.5 45.4 1.0
O A:HOH1631 2.5 46.5 1.0
OD2 A:ASP1007 2.6 48.2 1.0
CG A:ASP1007 2.8 43.0 1.0
OD2 A:ASP1009 3.1 43.0 1.0
CG A:ASP1009 3.1 45.0 1.0
CG A:ASP1011 3.3 46.4 1.0
PA A:ZAN1504 3.4 53.0 1.0
OD2 A:ASP1011 3.6 44.6 1.0
C3' D:C7 3.6 53.9 1.0
O5' A:ZAN1504 3.6 53.7 1.0
CA A:CA1502 3.7 50.6 1.0
O A:HOH1620 3.9 43.7 1.0
O2' D:C7 3.9 52.0 1.0
O1A A:ZAN1504 3.9 46.6 1.0
C4' D:C7 4.3 50.9 1.0
C2' D:C7 4.3 53.3 1.0
CB A:ASP1007 4.3 39.6 1.0
O2B A:ZAN1504 4.5 50.8 1.0
CB A:ASP1009 4.5 41.8 1.0
CB A:ASP1011 4.6 42.2 1.0
N A:ASP1007 4.7 39.7 1.0
N A:ASP1011 4.7 40.8 1.0
N A:ASP1009 4.7 42.6 1.0
N3A A:ZAN1504 4.8 49.5 1.0
C5' A:ZAN1504 4.8 42.9 1.0
C5' D:C7 4.9 38.4 1.0
CA A:ASP1007 4.9 44.7 1.0

Calcium binding site 2 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 2 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:50.6
occ:1.00
 O2B A:ZAN1504 2.2 50.8 1.0
OD2 A:ASP1007 2.2 48.2 1.0
O3G A:ZAN1504 2.2 42.4 1.0
O A:HOH1619 2.4 51.8 1.0
O A:HOH1601 2.4 46.7 1.0
O2A A:ZAN1504 2.5 40.0 1.0
OD2 A:ASP1009 2.5 43.0 1.0
CG A:ASP1007 3.4 43.0 1.0
PB A:ZAN1504 3.5 51.5 1.0
PG A:ZAN1504 3.6 42.9 1.0
O A:HOH1620 3.7 43.7 1.0
CG A:ASP1009 3.7 45.0 1.0
CA A:CA1501 3.7 46.7 1.0
PA A:ZAN1504 3.7 53.0 1.0
O3B A:ZAN1504 4.0 55.0 1.0
N3A A:ZAN1504 4.0 49.5 1.0
O A:HOH1626 4.1 47.6 1.0
OD1 A:ASP1007 4.1 43.9 1.0
NZ A:LYS743 4.2 58.9 1.0
NZ A:LYS767 4.2 53.9 1.0
CB A:ASP1007 4.3 39.6 1.0
OD1 A:ASP1009 4.3 45.4 1.0
OD1 A:ASP709 4.4 48.2 1.0
O2G A:ZAN1504 4.5 50.5 1.0
O5' A:ZAN1504 4.5 53.7 1.0
O1G A:ZAN1504 4.6 41.8 1.0
OD2 A:ASP709 4.6 41.8 1.0
CB A:ASP1009 4.7 41.8 1.0
CG A:ASP709 4.8 40.9 1.0
O1B A:ZAN1504 4.8 58.2 1.0
O A:HOH1631 4.9 46.5 1.0
O1A A:ZAN1504 5.0 46.6 1.0

Calcium binding site 3 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 3 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1503

b:82.6
occ:1.00
 O A:HOH1628 2.2 61.4 1.0
O A:GLY1005 2.2 62.1 1.0
O A:HOH1620 2.3 43.7 1.0
O A:HOH1625 2.6 59.1 1.0
O A:HOH1650 2.7 55.3 1.0
C A:GLY1005 3.3 53.9 1.0
CA A:GLY1005 3.9 42.5 1.0
O2B A:ZAN1504 4.3 50.8 1.0
N A:GLY1006 4.4 41.2 1.0
O3' A:ZAN1504 4.5 45.8 1.0
O A:HOH1631 4.5 46.5 1.0
O1B A:ZAN1504 4.5 58.2 1.0
O5' A:ZAN1504 4.6 53.7 1.0
CA A:GLY1006 4.8 50.1 1.0
O A:SER1004 4.9 52.8 1.0
O A:HOH1619 4.9 51.8 1.0
OD2 A:ASP1116 4.9 57.5 1.0
PB A:ZAN1504 4.9 51.5 1.0

Calcium binding site 4 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 4 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1502

b:46.7
occ:1.00
 OD1 B:ASP1007 2.1 37.7 1.0
O2A B:ZAN1504 2.2 40.1 1.0
O3' J:C7 2.3 54.9 1.0
OD1 B:ASP1011 2.5 51.4 1.0
OD1 B:ASP1009 2.5 52.5 1.0
O B:HOH1639 2.6 43.4 1.0
CG B:ASP1007 2.8 40.5 1.0
OD2 B:ASP1007 2.9 53.2 1.0
OD2 B:ASP1009 2.9 58.3 1.0
CG B:ASP1009 3.0 61.6 1.0
PA B:ZAN1504 3.3 57.4 1.0
O5' B:ZAN1504 3.3 58.5 1.0
CG B:ASP1011 3.3 49.6 1.0
OD2 B:ASP1011 3.6 45.8 1.0
C3' J:C7 3.6 60.1 1.0
CA B:CA1503 3.8 51.0 1.0
O1A B:ZAN1504 3.8 50.8 1.0
O B:HOH1625 3.9 41.9 1.0
O2' J:C7 4.0 64.3 1.0
CB B:ASP1007 4.3 43.0 1.0
C2' J:C7 4.3 52.3 1.0
C4' J:C7 4.4 59.8 1.0
CB B:ASP1009 4.5 48.3 1.0
N B:ASP1007 4.5 45.0 1.0
C5' B:ZAN1504 4.6 56.0 1.0
O2B B:ZAN1504 4.6 63.0 1.0
CB B:ASP1011 4.7 36.9 1.0
N3A B:ZAN1504 4.7 63.0 1.0
N B:ASP1009 4.8 42.8 1.0
CA B:ASP1007 4.8 46.8 1.0
N B:ASP1011 4.8 43.8 1.0
NZ B:LYS743 5.0 57.5 1.0
C4' B:ZAN1504 5.0 55.9 1.0
O2G B:ZAN1504 5.0 69.8 1.0

Calcium binding site 5 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 5 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1503

b:51.0
occ:1.00
 O2G B:ZAN1504 2.0 69.8 1.0
O B:HOH1644 2.3 60.7 1.0
OD2 B:ASP1007 2.3 53.2 1.0
O B:HOH1611 2.3 46.5 1.0
OD2 B:ASP1009 2.4 58.3 1.0
O2B B:ZAN1504 2.5 63.0 1.0
O2A B:ZAN1504 2.6 40.1 1.0
CG B:ASP1007 3.2 40.5 1.0
PG B:ZAN1504 3.4 54.0 1.0
CG B:ASP1009 3.6 61.6 1.0
PB B:ZAN1504 3.6 59.2 1.0
OD1 B:ASP1007 3.8 37.7 1.0
CA B:CA1502 3.8 46.7 1.0
O3B B:ZAN1504 3.8 72.8 1.0
PA B:ZAN1504 3.8 57.4 1.0
O B:HOH1625 4.0 41.9 1.0
N3A B:ZAN1504 4.0 63.0 1.0
O B:HOH1638 4.1 51.8 1.0
O1G B:ZAN1504 4.1 50.6 1.0
CB B:ASP1007 4.1 43.0 1.0
NZ B:LYS743 4.2 57.5 1.0
NZ B:LYS767 4.3 51.5 1.0
OD1 B:ASP1009 4.4 52.5 1.0
O3G B:ZAN1504 4.5 42.6 1.0
CB B:ASP1009 4.6 48.3 1.0
OD1 B:ASP709 4.6 55.6 1.0
O5' B:ZAN1504 4.7 58.5 1.0
O B:HOH1639 4.9 43.4 1.0
O1A B:ZAN1504 4.9 50.8 1.0
OD2 B:ASP709 5.0 63.8 1.0
CG B:ASP709 5.0 55.6 1.0
O1B B:ZAN1504 5.0 71.3 1.0

Calcium binding site 6 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 6 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:91.2
occ:1.00
 O C:HOH205 2.2 75.5 1.0
O C:HOH209 2.3 95.2 1.0
O C:HOH207 2.6 110.5 1.0
O C:HOH201 2.7 63.6 1.0
O C:HOH206 2.9 57.3 1.0
N7 C:DG4 3.2 55.4 1.0
O6 C:DG4 3.6 47.3 1.0
C5 C:DG4 4.0 59.5 1.0
O C:HOH202 4.0 63.7 1.0
C6 C:DG4 4.1 55.5 1.0
C8 C:DG4 4.2 57.0 1.0
O6 C:DG5 4.2 68.6 1.0
N7 C:DG5 4.4 52.7 1.0

Calcium binding site 7 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 7 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca101

b:109.9
occ:1.00
 O I:HOH203 2.2 75.0 1.0
O I:HOH202 2.3 101.1 1.0
O I:HOH205 2.4 71.8 1.0
O I:HOH206 2.5 103.3 1.0
O I:HOH201 2.9 72.4 1.0
N7 I:DG8 4.1 64.2 1.0
O6 I:DG8 4.4 52.4 1.0
O6 I:DG9 4.4 73.6 1.0
C5 I:DG8 4.9 60.2 1.0
O4 I:DT7 4.9 65.6 1.0
N7 I:DG9 5.0 66.5 1.0

Reference:

R.Cui, H.Li, J.Zhao, X.Li, J.Gan, J.Ma. Structural Insights Into the Dual Activities of the Two-Barrel Rna Polymerase Qde-1. Nucleic Acids Res. V. 50 10169 2022.
ISSN: ESSN 1362-4962
PubMed: 36039765
DOI: 10.1093/NAR/GKAC727
Page generated: Fri Jul 19 06:11:44 2024

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