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Calcium in PDB 3erc: Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp

Enzymatic activity of Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp

All present enzymatic activity of Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp:
2.1.1.57; 2.7.7.19;

Protein crystallography data

The structure of Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp, PDB code: 3erc was solved by C.Li, H.Li, S.Zhou, T.L.Poulos, P.D.Gershon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.55 / 3.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.925, 77.153, 108.030, 89.52, 73.45, 63.76
R / Rfree (%) 24.5 / 30.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp (pdb code 3erc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp, PDB code: 3erc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3erc

Go back to Calcium Binding Sites List in 3erc
Calcium binding site 1 out of 4 in the Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca901

b:79.8
occ:1.00
 OD2 C:ASP253 2.5 77.6 1.0
OD1 C:ASP204 2.7 78.3 1.0
OD1 C:ASP202 2.7 71.2 1.0
O3' F:DC610 2.8 0.2 1.0
OD1 C:ASP253 2.9 77.6 1.0
CG C:ASP253 3.1 77.6 1.0
O C:HOH1001 3.4 79.8 1.0
C3' F:DC610 3.4 0.2 1.0
C4' F:DC610 3.5 0.2 1.0
CA C:CA902 3.8 79.8 1.0
CG C:ASP204 3.8 78.3 1.0
CG C:ASP202 3.9 71.2 1.0
C5' F:DC610 4.2 0.2 1.0
CB C:ASP253 4.6 77.6 1.0
O4' F:DC610 4.6 0.2 1.0
CB C:ASP204 4.6 78.3 1.0
OD2 C:ASP202 4.7 71.2 1.0
OD2 C:ASP204 4.7 78.3 1.0
CB C:ASP202 4.8 71.2 1.0
O1A C:3AT801 4.9 93.1 1.0
C2' F:DC610 4.9 0.2 1.0
CE1 C:HIS250 4.9 0.7 1.0

Calcium binding site 2 out of 4 in 3erc

Go back to Calcium Binding Sites List in 3erc
Calcium binding site 2 out of 4 in the Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca902

b:79.8
occ:1.00
 O1B C:3AT801 2.3 93.1 1.0
O1A C:3AT801 2.3 93.1 1.0
OD2 C:ASP204 2.4 78.3 1.0
O1G C:3AT801 2.6 93.1 1.0
OD2 C:ASP202 2.6 71.2 1.0
OD1 C:ASP204 2.7 78.3 1.0
CG C:ASP204 2.8 78.3 1.0
OD1 C:ASP202 2.8 71.2 1.0
O5' C:3AT801 3.1 93.1 1.0
PA C:3AT801 3.1 93.1 1.0
CG C:ASP202 3.1 71.2 1.0
C5' C:3AT801 3.3 97.4 1.0
O3' F:DC610 3.3 0.2 1.0
PB C:3AT801 3.5 93.1 1.0
CA C:CA901 3.8 79.8 1.0
O3A C:3AT801 3.9 93.1 1.0
OG C:SER188 3.9 55.8 1.0
PG C:3AT801 4.0 93.1 1.0
CB C:ASP204 4.1 78.3 1.0
N C:SER188 4.3 0.9 1.0
O3B C:3AT801 4.4 93.1 1.0
O C:ASP202 4.4 83.7 1.0
O2A C:3AT801 4.4 93.1 1.0
CA C:GLY187 4.5 82.3 1.0
C3' F:DC610 4.5 0.2 1.0
CB C:ASP202 4.6 71.2 1.0
O2G C:3AT801 4.7 93.1 1.0
O2B C:3AT801 4.7 93.1 1.0
C4' C:3AT801 4.8 97.4 1.0
CB C:SER188 4.8 55.8 1.0
C C:GLY187 5.0 82.3 1.0

Calcium binding site 3 out of 4 in 3erc

Go back to Calcium Binding Sites List in 3erc
Calcium binding site 3 out of 4 in the Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca903

b:79.8
occ:1.00
 OD2 D:ASP253 2.4 73.5 1.0
OD1 D:ASP253 2.5 73.5 1.0
OD1 D:ASP204 2.5 78.0 1.0
OD1 D:ASP202 2.6 85.6 1.0
O3' E:DC605 2.7 0.9 1.0
CG D:ASP253 2.8 73.5 1.0
C3' E:DC605 3.4 0.9 1.0
C4' E:DC605 3.6 0.9 1.0
CG D:ASP202 3.7 85.6 1.0
CG D:ASP204 3.7 78.0 1.0
CA D:CA904 4.0 79.8 1.0
CB D:ASP253 4.3 73.5 1.0
CB D:ASP202 4.4 85.6 1.0
C5' E:DC605 4.5 0.9 1.0
CB D:ASP204 4.5 78.0 1.0
OD2 D:ASP202 4.6 85.6 1.0
OD2 D:ASP204 4.6 78.0 1.0
O4' E:DC605 4.7 0.9 1.0
CE1 D:HIS250 4.7 82.5 1.0
NE2 D:HIS250 4.8 82.5 1.0
O D:ASP253 4.8 75.8 1.0
C2' E:DC605 4.8 0.9 1.0
CA D:ASP204 5.0 93.5 1.0

Calcium binding site 4 out of 4 in 3erc

Go back to Calcium Binding Sites List in 3erc
Calcium binding site 4 out of 4 in the Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase with Three Fragments of Rna and 3'-Deoxy Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca904

b:79.8
occ:1.00
 OD2 D:ASP204 2.3 78.0 1.0
O1B D:3AT800 2.4 0.8 1.0
O1G D:3AT800 2.6 0.8 1.0
O1A D:3AT800 2.6 0.8 1.0
OD1 D:ASP204 2.7 78.0 1.0
CG D:ASP204 2.7 78.0 1.0
OD2 D:ASP202 2.8 85.6 1.0
OD1 D:ASP202 3.0 85.6 1.0
O5' D:3AT800 3.1 0.8 1.0
CG D:ASP202 3.2 85.6 1.0
O3' E:DC605 3.3 0.9 1.0
PA D:3AT800 3.3 0.8 1.0
C5' D:3AT800 3.3 0.5 1.0
PB D:3AT800 3.7 0.8 1.0
OG D:SER188 4.0 70.8 1.0
CA D:CA903 4.0 79.8 1.0
CB D:ASP204 4.1 78.0 1.0
PG D:3AT800 4.1 0.8 1.0
O3A D:3AT800 4.1 0.8 1.0
C3' E:DC605 4.2 0.9 1.0
N D:SER188 4.3 0.7 1.0
CA D:GLY187 4.4 90.9 1.0
O3B D:3AT800 4.5 0.8 1.0
O D:ASP202 4.5 0.7 1.0
C4' D:3AT800 4.6 0.5 1.0
O2A D:3AT800 4.7 0.8 1.0
O2G D:3AT800 4.7 0.8 1.0
CB D:ASP202 4.7 85.6 1.0
C2' E:DC605 4.8 0.9 1.0
CB D:SER188 4.9 70.8 1.0
C D:GLY187 4.9 90.9 1.0
O2B D:3AT800 5.0 0.8 1.0

Reference:

C.Li, H.Li, S.Zhou, E.Sun, J.Yoshizawa, T.L.Poulos, P.D.Gershon. Polymerase Translocation with Respect to Single-Stranded Nucleic Acid: Looping or Wrapping of Primer Around A Poly(A) Polymerase Structure V. 17 680 2009.
ISSN: ISSN 0969-2126
PubMed: 19446524
DOI: 10.1016/J.STR.2009.03.012
Page generated: Sat Jul 13 09:34:01 2024

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