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Calcium in PDB 7y7p: Qde-1 in Complex with Rna Template, Rna Primer and Ampnpp

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

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

Protein crystallography data

The structure of Qde-1 in Complex with Rna Template, Rna Primer and Ampnpp, PDB code: 7y7p 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) 29.62 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.949, 120.201, 114.857, 90, 109.62, 90
R / Rfree (%) 22.3 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Qde-1 in Complex with Rna Template, Rna Primer and Ampnpp (pdb code 7y7p). 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 Rna Template, Rna Primer and Ampnpp, PDB code: 7y7p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7y7p

Go back to Calcium Binding Sites List in 7y7p
Calcium binding site 1 out of 7 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:42.8
occ:1.00
 OD1 A:ASP1007 1.9 40.9 1.0
O3' D:C7 2.3 51.8 1.0
OD1 A:ASP1011 2.3 55.0 1.0
OD1 A:ASP1009 2.3 56.4 1.0
O2A A:ZAN1504 2.3 41.3 1.0
O A:HOH1615 2.4 58.8 1.0
CG A:ASP1007 2.7 41.3 1.0
OD2 A:ASP1007 2.9 64.4 1.0
CG A:ASP1009 3.0 43.8 1.0
OD2 A:ASP1009 3.2 51.2 1.0
O A:HOH1636 3.2 46.8 1.0
CG A:ASP1011 3.2 44.5 1.0
PA A:ZAN1504 3.4 46.5 1.0
O2' D:C7 3.6 56.0 1.0
C3' D:C7 3.6 48.1 1.0
OD2 A:ASP1011 3.6 41.1 1.0
O5' A:ZAN1504 3.6 63.8 1.0
CA A:CA1503 3.8 46.8 1.0
O1A A:ZAN1504 4.0 49.7 1.0
C2' D:C7 4.0 52.0 1.0
CB A:ASP1007 4.2 41.5 1.0
C4' D:C7 4.4 47.3 1.0
CB A:ASP1009 4.4 39.1 1.0
O2B A:ZAN1504 4.4 55.0 1.0
N A:ASP1007 4.4 49.2 1.0
CB A:ASP1011 4.5 39.6 1.0
C5' A:ZAN1504 4.6 62.1 1.0
CA A:ASP1007 4.7 48.8 1.0
N3A A:ZAN1504 4.8 54.2 1.0
N A:ASP1011 4.8 44.1 1.0
C4' A:ZAN1504 4.9 59.6 1.0
N A:ASP1009 4.9 42.3 1.0
O4' A:ZAN1504 5.0 61.2 1.0
CA A:ASP1011 5.0 45.8 1.0

Calcium binding site 2 out of 7 in 7y7p

Go back to Calcium Binding Sites List in 7y7p
Calcium binding site 2 out of 7 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:85.4
occ:1.00
 O A:HOH1651 2.3 53.3 1.0
O A:HOH1636 2.4 46.8 1.0
O A:HOH1634 2.5 84.5 1.0
O A:GLY1005 2.5 59.0 1.0
O A:HOH1621 3.0 63.6 1.0
O2B A:ZAN1504 3.7 55.0 1.0
C A:GLY1005 3.7 57.4 1.0
O1B A:ZAN1504 4.0 64.0 1.0
O A:HOH1615 4.1 58.8 1.0
O5' A:ZAN1504 4.2 63.8 1.0
CA A:GLY1005 4.3 53.5 1.0
PB A:ZAN1504 4.3 50.5 1.0
O3' A:ZAN1504 4.4 59.9 1.0
OD2 A:ASP1007 4.7 64.4 1.0
N A:GLY1006 4.8 44.3 1.0
C4' A:ZAN1504 4.8 59.6 1.0

Calcium binding site 3 out of 7 in 7y7p

Go back to Calcium Binding Sites List in 7y7p
Calcium binding site 3 out of 7 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1503

b:46.8
occ:1.00
 OD2 A:ASP1007 1.9 64.4 1.0
O3G A:ZAN1504 2.2 55.8 1.0
O2B A:ZAN1504 2.2 55.0 1.0
OD2 A:ASP1009 2.5 51.2 1.0
O2A A:ZAN1504 2.6 41.3 1.0
O A:HOH1640 2.6 42.9 1.0
O A:HOH1616 2.6 45.6 1.0
CG A:ASP1007 3.1 41.3 1.0
PB A:ZAN1504 3.4 50.5 1.0
CG A:ASP1009 3.4 43.8 1.0
O A:HOH1636 3.5 46.8 1.0
PG A:ZAN1504 3.6 42.1 1.0
CA A:CA1501 3.8 42.8 1.0
PA A:ZAN1504 3.8 46.5 1.0
OD1 A:ASP1007 3.8 40.9 1.0
N3A A:ZAN1504 3.9 54.2 1.0
O3B A:ZAN1504 3.9 61.6 1.0
O A:HOH1637 4.0 45.4 1.0
NZ A:LYS743 4.0 53.5 1.0
CB A:ASP1007 4.1 41.5 1.0
OD1 A:ASP1009 4.1 56.4 1.0
CB A:ASP1009 4.3 39.1 1.0
O2G A:ZAN1504 4.5 60.7 1.0
O1G A:ZAN1504 4.5 41.5 1.0
O5' A:ZAN1504 4.6 63.8 1.0
NZ A:LYS767 4.6 56.0 1.0
OD2 A:ASP709 4.7 43.2 1.0
O1B A:ZAN1504 4.8 64.0 1.0
OD1 A:ASP709 4.9 51.2 1.0
O A:HOH1615 4.9 58.8 1.0

Calcium binding site 4 out of 7 in 7y7p

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Calcium binding site 4 out of 7 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1503

b:44.8
occ:1.00
 OD1 B:ASP1007 1.6 41.7 1.0
OD1 B:ASP1009 1.9 61.3 1.0
O2A B:ZAN1506 2.1 42.0 1.0
O3' J:C7 2.4 46.5 1.0
CG B:ASP1007 2.5 46.0 1.0
OD1 B:ASP1011 2.5 57.5 1.0
O B:HOH1618 2.6 42.4 1.0
CG B:ASP1009 2.6 45.9 1.0
OD2 B:ASP1007 2.7 68.0 1.0
OD2 B:ASP1009 3.0 55.0 1.0
CG B:ASP1011 3.3 40.5 1.0
PA B:ZAN1506 3.4 54.3 1.0
OD2 B:ASP1011 3.6 43.6 1.0
CA B:CA1505 3.7 51.0 1.0
C3' J:C7 3.8 62.7 1.0
O5' B:ZAN1506 3.8 63.0 1.0
CB B:ASP1007 3.8 42.6 1.0
CB B:ASP1009 3.9 45.0 1.0
O1A B:ZAN1506 4.0 53.1 1.0
O2' J:C7 4.2 63.1 1.0
N B:ASP1007 4.3 45.4 1.0
C4' J:C7 4.4 60.8 1.0
N B:ASP1009 4.5 40.2 1.0
CA B:ASP1007 4.5 54.2 1.0
C2' J:C7 4.5 45.0 1.0
CB B:ASP1011 4.6 39.9 1.0
CA B:ASP1009 4.6 39.9 1.0
O2B B:ZAN1506 4.6 59.6 1.0
N3A B:ZAN1506 4.7 55.3 1.0
N B:ASP1011 4.7 56.2 1.0
C B:ASP1007 4.7 54.2 1.0
C B:ASP1009 4.7 43.1 1.0
O B:HOH1636 4.9 51.6 1.0
O B:ASP1007 4.9 49.9 1.0
C5' B:ZAN1506 5.0 63.8 1.0
C5' J:C7 5.0 38.9 1.0

Calcium binding site 5 out of 7 in 7y7p

Go back to Calcium Binding Sites List in 7y7p
Calcium binding site 5 out of 7 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1504

b:79.4
occ:1.00
 O B:HOH1628 2.8 53.9 1.0
O B:GLY1005 2.8 53.0 1.0
O2B B:ZAN1506 2.9 59.6 1.0
O B:HOH1606 3.1 53.8 1.0
O B:HOH1618 3.4 42.4 1.0
O B:HOH1652 3.9 55.5 1.0
PB B:ZAN1506 3.9 57.6 1.0
O5' B:ZAN1506 4.0 63.0 1.0
O1B B:ZAN1506 4.0 56.7 1.0
OD2 B:ASP1007 4.0 68.0 1.0
C B:GLY1005 4.0 65.4 1.0
CA B:CA1505 4.3 51.0 1.0
CG B:ASP1007 4.3 46.0 1.0
O2A B:ZAN1506 4.4 42.0 1.0
O B:HOH1631 4.4 54.3 1.0
OD1 B:ASP1007 4.6 41.7 1.0
PA B:ZAN1506 4.7 54.3 1.0
N3A B:ZAN1506 4.8 55.3 1.0
C B:GLY1006 4.8 53.7 1.0
CA B:GLY1006 4.8 54.3 1.0
N B:GLY1006 4.9 51.5 1.0
CA B:GLY1005 4.9 55.7 1.0
O B:GLY1006 5.0 47.5 1.0
O3' B:ZAN1506 5.0 51.5 1.0

Calcium binding site 6 out of 7 in 7y7p

Go back to Calcium Binding Sites List in 7y7p
Calcium binding site 6 out of 7 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1505

b:51.0
occ:1.00
 OD2 B:ASP1007 1.7 68.0 1.0
O2G B:ZAN1506 2.2 55.4 1.0
O B:HOH1636 2.3 51.6 1.0
O B:HOH1631 2.3 54.3 1.0
O2B B:ZAN1506 2.3 59.6 1.0
O2A B:ZAN1506 2.8 42.0 1.0
CG B:ASP1007 2.9 46.0 1.0
OD2 B:ASP1009 3.2 55.0 1.0
PB B:ZAN1506 3.4 57.6 1.0
PG B:ZAN1506 3.5 61.1 1.0
O3B B:ZAN1506 3.7 81.5 1.0
CA B:CA1503 3.7 44.8 1.0
OD1 B:ASP1007 3.7 41.7 1.0
CG B:ASP1009 3.7 45.9 1.0
N3A B:ZAN1506 3.8 55.3 1.0
PA B:ZAN1506 3.8 54.3 1.0
CB B:ASP1007 3.9 42.6 1.0
OD1 B:ASP1009 4.3 61.3 1.0
O1G B:ZAN1506 4.3 60.0 1.0
CA B:CA1504 4.3 79.4 1.0
OD1 B:ASP709 4.4 60.8 1.0
NZ B:LYS767 4.4 62.9 1.0
CB B:ASP1009 4.4 45.0 1.0
OD2 B:ASP709 4.5 51.3 1.0
O3G B:ZAN1506 4.6 43.0 1.0
CG B:ASP709 4.7 47.4 1.0
O5' B:ZAN1506 4.7 63.0 1.0
O B:HOH1618 4.7 42.4 1.0
NZ B:LYS743 4.8 66.2 1.0
O1B B:ZAN1506 4.8 56.7 1.0

Calcium binding site 7 out of 7 in 7y7p

Go back to Calcium Binding Sites List in 7y7p
Calcium binding site 7 out of 7 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:122.1
occ:1.00
 O C:HOH204 2.3 47.0 1.0
O C:HOH205 2.4 74.6 1.0
O C:HOH201 2.6 61.9 1.0
O C:HOH206 2.7 89.5 1.0
O6 C:G2 3.4 49.5 1.0
O6 C:G3 3.5 61.7 1.0
N7 C:G2 3.5 67.2 1.0
C6 C:G2 4.1 54.5 1.0
C5 C:G2 4.1 60.9 1.0
N7 C:G3 4.2 66.3 1.0
C6 C:G3 4.3 56.4 1.0
C5 C:G3 4.6 55.9 1.0
C8 C:G2 4.6 67.4 1.0
O4 C:U1 4.8 55.4 1.0
C4 C:U1 5.0 63.4 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 06:09:34 2024

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