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Calcium in PDB 1uvn: The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex

Enzymatic activity of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex

All present enzymatic activity of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex:
2.7.7.48;

Protein crystallography data

The structure of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex, PDB code: 1uvn was solved by P.S.Salgado, E.V.Makeyev, S.Butcher, D.Bamford, D.I.Stuart, J.M.Grimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.504, 92.134, 140.755, 90.00, 101.01, 90.00
R / Rfree (%) 23.4 / 25.7

Other elements in 1uvn:

The structure of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex (pdb code 1uvn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex, PDB code: 1uvn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1uvn

Go back to Calcium Binding Sites List in 1uvn
Calcium binding site 1 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1667

b:0.1
occ:1.00
 O2B A:GTP1665 2.7 0.3 1.0
O1A A:GTP1665 2.8 0.3 1.0
OH A:TYR630 3.0 0.9 1.0
O2G A:GTP1665 3.2 0.6 1.0
NH2 A:ARG204 3.3 89.3 1.0
O A:HOH2050 3.7 44.0 1.0
CZ A:TYR630 3.7 0.2 1.0
CE2 A:TYR630 4.0 0.1 1.0
PB A:GTP1665 4.0 0.3 1.0
PA A:GTP1665 4.1 0.3 1.0
N7 A:GTP1665 4.1 0.3 1.0
OE1 A:GLU529 4.2 79.6 1.0
C8 A:GTP1665 4.3 0.3 1.0
NE2 A:GLN206 4.4 97.1 1.0
O3A A:GTP1665 4.4 0.3 1.0
CZ A:ARG204 4.4 87.0 1.0
PG A:GTP1665 4.5 0.3 1.0
CE1 A:TYR630 4.6 0.3 1.0
O3B A:GTP1665 4.7 0.3 1.0
O5' A:GTP1665 4.7 0.2 1.0
NH1 A:ARG204 4.7 88.3 1.0

Calcium binding site 2 out of 6 in 1uvn

Go back to Calcium Binding Sites List in 1uvn
Calcium binding site 2 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1668

b:62.3
occ:1.00
 O A:VAL325 2.7 73.7 1.0
O1A A:GTP1666 2.8 0.5 1.0
OD2 A:ASP453 2.9 74.7 1.0
O2B A:GTP1666 3.0 93.0 1.0
O2G A:GTP1666 3.0 0.9 1.0
O3B A:GTP1666 3.3 96.4 1.0
OD1 A:ASP453 3.4 66.1 1.0
CG A:ASP453 3.4 69.0 1.0
PB A:GTP1666 3.5 94.4 1.0
PA A:GTP1666 3.6 0.6 1.0
O3A A:GTP1666 3.6 97.8 1.0
O5' A:GTP1666 3.8 0.7 1.0
PG A:GTP1666 3.8 0.9 1.0
C A:VAL325 3.8 66.9 1.0
O A:HOH2023 4.1 59.1 1.0
CA A:SER326 4.3 66.1 1.0
OD1 A:ASP324 4.4 88.1 1.0
N A:ASP327 4.6 59.5 1.0
CB A:HIS328 4.6 45.4 1.0
N A:SER326 4.6 67.0 1.0
O1G A:GTP1666 4.7 0.9 1.0
CB A:VAL325 4.7 62.2 1.0
CA A:VAL325 4.7 64.5 1.0
N A:VAL325 4.8 65.0 1.0
CB A:ASP453 4.8 67.8 1.0
N A:HIS328 4.8 47.6 1.0
C A:SER326 4.9 64.8 1.0
O3G A:GTP1666 5.0 97.2 1.0
C5' A:GTP1666 5.0 96.3 1.0

Calcium binding site 3 out of 6 in 1uvn

Go back to Calcium Binding Sites List in 1uvn
Calcium binding site 3 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1667

b:0.1
occ:1.00
 O2B C:GTP1665 2.7 0.3 1.0
O1A C:GTP1665 2.8 0.3 1.0
OH C:TYR630 3.0 0.9 1.0
O2G C:GTP1665 3.2 0.6 1.0
NH2 C:ARG204 3.3 89.3 1.0
O C:HOH2048 3.7 44.0 1.0
CZ C:TYR630 3.7 0.2 1.0
CE2 C:TYR630 4.0 0.1 1.0
PB C:GTP1665 4.0 0.3 1.0
PA C:GTP1665 4.1 0.3 1.0
N7 C:GTP1665 4.1 0.3 1.0
OE1 C:GLU529 4.2 79.6 1.0
C8 C:GTP1665 4.3 0.3 1.0
NE2 C:GLN206 4.4 97.1 1.0
O3A C:GTP1665 4.4 0.3 1.0
CZ C:ARG204 4.4 87.0 1.0
PG C:GTP1665 4.5 0.3 1.0
CE1 C:TYR630 4.6 0.3 1.0
O3B C:GTP1665 4.7 0.3 1.0
O5' C:GTP1665 4.7 0.2 1.0
NH1 C:ARG204 4.7 88.3 1.0

Calcium binding site 4 out of 6 in 1uvn

Go back to Calcium Binding Sites List in 1uvn
Calcium binding site 4 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1668

b:62.3
occ:1.00
 O C:VAL325 2.7 73.7 1.0
O1A C:GTP1666 2.8 0.5 1.0
OD2 C:ASP453 2.9 74.7 1.0
O2B C:GTP1666 3.0 93.0 1.0
O2G C:GTP1666 3.0 0.9 1.0
O3B C:GTP1666 3.3 96.4 1.0
OD1 C:ASP453 3.4 66.1 1.0
CG C:ASP453 3.4 69.0 1.0
PB C:GTP1666 3.5 94.4 1.0
PA C:GTP1666 3.6 0.6 1.0
O3A C:GTP1666 3.6 97.8 1.0
O5' C:GTP1666 3.8 0.7 1.0
PG C:GTP1666 3.8 0.9 1.0
C C:VAL325 3.8 66.9 1.0
O C:HOH2023 4.1 59.1 1.0
CA C:SER326 4.3 66.1 1.0
OD1 C:ASP324 4.4 88.1 1.0
N C:ASP327 4.6 59.5 1.0
N C:SER326 4.6 67.0 1.0
CB C:HIS328 4.6 45.4 1.0
O1G C:GTP1666 4.7 0.9 1.0
CB C:VAL325 4.7 62.2 1.0
CA C:VAL325 4.7 64.5 1.0
N C:VAL325 4.8 65.0 1.0
CB C:ASP453 4.8 67.8 1.0
N C:HIS328 4.8 47.6 1.0
C C:SER326 4.9 64.8 1.0
O3G C:GTP1666 5.0 97.2 1.0
C5' C:GTP1666 5.0 96.3 1.0

Calcium binding site 5 out of 6 in 1uvn

Go back to Calcium Binding Sites List in 1uvn
Calcium binding site 5 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1667

b:0.1
occ:1.00
 O2B E:GTP1665 2.7 0.3 1.0
O1A E:GTP1665 2.8 0.3 1.0
OH E:TYR630 3.0 0.9 1.0
O2G E:GTP1665 3.2 0.6 1.0
NH2 E:ARG204 3.3 89.3 1.0
O E:HOH2049 3.7 44.0 1.0
CZ E:TYR630 3.7 0.2 1.0
CE2 E:TYR630 4.0 0.1 1.0
PB E:GTP1665 4.0 0.3 1.0
PA E:GTP1665 4.1 0.3 1.0
N7 E:GTP1665 4.1 0.3 1.0
OE1 E:GLU529 4.2 79.6 1.0
C8 E:GTP1665 4.3 0.3 1.0
NE2 E:GLN206 4.4 97.1 1.0
O3A E:GTP1665 4.4 0.3 1.0
CZ E:ARG204 4.4 87.0 1.0
PG E:GTP1665 4.5 0.3 1.0
CE1 E:TYR630 4.6 0.3 1.0
O3B E:GTP1665 4.7 0.3 1.0
O5' E:GTP1665 4.7 0.2 1.0
NH1 E:ARG204 4.7 88.3 1.0

Calcium binding site 6 out of 6 in 1uvn

Go back to Calcium Binding Sites List in 1uvn
Calcium binding site 6 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 CA2+ Inhibition Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1668

b:62.3
occ:1.00
 O E:VAL325 2.7 73.7 1.0
O1A E:GTP1666 2.8 0.5 1.0
OD2 E:ASP453 2.9 74.7 1.0
O2B E:GTP1666 3.0 93.0 1.0
O2G E:GTP1666 3.0 0.9 1.0
O3B E:GTP1666 3.3 96.4 1.0
OD1 E:ASP453 3.4 66.1 1.0
CG E:ASP453 3.4 69.0 1.0
PB E:GTP1666 3.5 94.4 1.0
PA E:GTP1666 3.6 0.6 1.0
O3A E:GTP1666 3.6 97.8 1.0
O5' E:GTP1666 3.8 0.7 1.0
PG E:GTP1666 3.8 0.9 1.0
C E:VAL325 3.8 66.9 1.0
O E:HOH2023 4.1 59.1 1.0
CA E:SER326 4.3 66.1 1.0
OD1 E:ASP324 4.4 88.1 1.0
N E:ASP327 4.6 59.5 1.0
CB E:HIS328 4.6 45.4 1.0
N E:SER326 4.6 67.0 1.0
O1G E:GTP1666 4.7 0.9 1.0
CB E:VAL325 4.7 62.2 1.0
CA E:VAL325 4.7 64.5 1.0
N E:VAL325 4.8 65.0 1.0
CB E:ASP453 4.8 67.8 1.0
N E:HIS328 4.8 47.6 1.0
C E:SER326 4.9 64.8 1.0
O3G E:GTP1666 5.0 97.2 1.0
C5' E:GTP1666 5.0 96.3 1.0

Reference:

P.S.Salgado, E.V.Makeyev, S.J.Butcher, D.H.Bamford, D.I.Stuart, J.M.Grimes. The Structural Basis For Rna Specificity and CA2+ Inhibition of An Rna-Dependent Rna Polymerase. Structure V. 12 307 2004.
ISSN: ISSN 0969-2126
PubMed: 14962391
DOI: 10.1016/J.STR.2004.01.012
Page generated: Sat Dec 12 03:23:41 2020

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