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Magnesium in PDB 1uvk: The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex

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

All present enzymatic activity of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End 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 Dead-End Complex, PDB code: 1uvk 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) 19.98 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.290, 93.800, 140.770, 90.00, 101.35, 90.00
R / Rfree (%) 24.3 / 26.5

Other elements in 1uvk:

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

Manganese (Mn) 3 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 1uvk

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:58.2
occ:1.00
 O A:POP703 2.6 0.5 1.0
O2 A:POP703 3.1 0.0 1.0
O4 A:POP703 3.1 0.5 1.0
O6 A:POP703 3.1 0.6 1.0
P2 A:POP703 3.1 0.8 1.0
P1 A:POP703 3.2 0.9 1.0
OD2 A:ASP324 3.5 61.1 1.0
O1 A:POP703 3.5 0.8 1.0
O3' A:G704 3.9 73.8 1.0
CG A:ASP324 4.3 59.4 1.0
OD1 A:ASP324 4.4 65.0 1.0
C3' A:G704 4.5 80.3 1.0
O5 A:POP703 4.6 0.1 1.0
O3 A:POP703 4.7 0.2 1.0
O A:VAL325 4.7 36.9 1.0

Magnesium binding site 2 out of 6 in 1uvk

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Magnesium binding site 2 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:35.9
occ:1.00
 O1B A:GTP706 1.8 57.9 1.0
O3G A:GTP706 2.3 75.0 1.0
PB A:GTP706 2.9 63.1 1.0
O3B A:GTP706 3.0 68.4 1.0
OD2 A:ASP624 3.1 52.6 1.0
OH A:TYR630 3.2 59.7 1.0
PG A:GTP706 3.2 60.0 1.0
O3A A:GTP706 3.8 62.2 1.0
CE2 A:TYR630 3.8 61.2 1.0
CZ A:TYR630 3.9 58.7 1.0
NZ A:LYS627 4.0 45.9 1.0
CG A:ASP624 4.1 49.5 1.0
O1G A:GTP706 4.1 71.7 1.0
O2B A:GTP706 4.2 59.0 1.0
OD1 A:ASP624 4.2 46.1 1.0
OD1 A:ASN626 4.2 60.1 1.0
O2G A:GTP706 4.4 68.7 1.0
ND2 A:ASN524 4.5 37.3 1.0
CB A:ASN626 4.6 54.1 1.0
OE1 A:GLU529 4.6 60.5 1.0
CD A:GLU529 4.7 59.2 1.0
CG A:LYS627 4.7 42.0 1.0
N7 A:GTP706 4.7 58.7 1.0
CG A:ASN626 4.8 59.8 1.0
CG A:GLU529 4.9 53.5 1.0
C8 A:GTP706 5.0 64.0 1.0
CE A:LYS627 5.0 35.9 1.0

Magnesium binding site 3 out of 6 in 1uvk

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Magnesium binding site 3 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:58.2
occ:1.00
 O C:POP701 2.6 0.5 1.0
O2 C:POP701 3.1 0.0 1.0
O4 C:POP701 3.1 0.5 1.0
O6 C:POP701 3.1 0.6 1.0
P2 C:POP701 3.1 0.8 1.0
P1 C:POP701 3.2 0.9 1.0
OD2 C:ASP324 3.5 61.1 1.0
O1 C:POP701 3.5 0.8 1.0
O3' C:G704 3.9 73.8 1.0
CG C:ASP324 4.3 59.4 1.0
OD1 C:ASP324 4.4 65.0 1.0
C3' C:G704 4.5 80.3 1.0
O5 C:POP701 4.6 0.1 1.0
O3 C:POP701 4.7 0.2 1.0
O C:VAL325 4.7 36.9 1.0

Magnesium binding site 4 out of 6 in 1uvk

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Magnesium binding site 4 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:35.9
occ:1.00
 O1B C:GTP706 1.8 57.9 1.0
O3G C:GTP706 2.3 75.0 1.0
PB C:GTP706 2.9 63.1 1.0
O3B C:GTP706 3.0 68.4 1.0
OD2 C:ASP624 3.1 52.6 1.0
OH C:TYR630 3.2 59.7 1.0
PG C:GTP706 3.2 60.0 1.0
O3A C:GTP706 3.8 62.2 1.0
CE2 C:TYR630 3.8 61.2 1.0
CZ C:TYR630 3.9 58.7 1.0
NZ C:LYS627 4.0 45.9 1.0
CG C:ASP624 4.1 49.5 1.0
O1G C:GTP706 4.1 71.7 1.0
O2B C:GTP706 4.2 59.0 1.0
OD1 C:ASP624 4.2 46.1 1.0
OD1 C:ASN626 4.2 60.1 1.0
O2G C:GTP706 4.4 68.7 1.0
ND2 C:ASN524 4.5 37.3 1.0
CB C:ASN626 4.6 54.1 1.0
OE1 C:GLU529 4.6 60.5 1.0
CD C:GLU529 4.7 59.2 1.0
CG C:LYS627 4.7 42.0 1.0
N7 C:GTP706 4.7 58.7 1.0
CG C:ASN626 4.8 59.8 1.0
CG C:GLU529 4.9 53.5 1.0
C8 C:GTP706 5.0 64.0 1.0
CE C:LYS627 5.0 35.9 1.0

Magnesium binding site 5 out of 6 in 1uvk

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Magnesium binding site 5 out of 6 in the The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:58.2
occ:1.00
 O E:POP701 2.6 0.5 1.0
O2 E:POP701 3.1 0.0 1.0
O4 E:POP701 3.1 0.5 1.0
O6 E:POP701 3.1 0.6 1.0
P2 E:POP701 3.1 0.8 1.0
P1 E:POP701 3.2 0.9 1.0
OD2 E:ASP324 3.5 61.1 1.0
O1 E:POP701 3.5 0.8 1.0
O3' E:G704 3.9 73.8 1.0
CG E:ASP324 4.3 59.4 1.0
OD1 E:ASP324 4.4 65.0 1.0
C3' E:G704 4.5 80.3 1.0
O5 E:POP701 4.6 0.1 1.0
O3 E:POP701 4.7 0.2 1.0
O E:VAL325 4.7 36.9 1.0

Magnesium binding site 6 out of 6 in 1uvk

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structural Basis For Rna Specificity and CA2 Inhibition of An Rna- Dependent Rna Polymerase PHI6P2 Dead-End Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg705

b:35.9
occ:1.00
 O1B E:GTP706 1.8 57.9 1.0
O3G E:GTP706 2.3 75.0 1.0
PB E:GTP706 2.9 63.1 1.0
O3B E:GTP706 3.0 68.4 1.0
OD2 E:ASP624 3.1 52.6 1.0
OH E:TYR630 3.2 59.7 1.0
PG E:GTP706 3.2 60.0 1.0
O3A E:GTP706 3.8 62.2 1.0
CE2 E:TYR630 3.8 61.2 1.0
CZ E:TYR630 3.9 58.7 1.0
NZ E:LYS627 4.0 45.9 1.0
CG E:ASP624 4.1 49.5 1.0
O1G E:GTP706 4.1 71.7 1.0
O2B E:GTP706 4.2 59.0 1.0
OD1 E:ASP624 4.2 46.1 1.0
OD1 E:ASN626 4.2 60.1 1.0
O2G E:GTP706 4.4 68.7 1.0
ND2 E:ASN524 4.5 37.3 1.0
CB E:ASN626 4.6 54.1 1.0
OE1 E:GLU529 4.6 60.5 1.0
CD E:GLU529 4.7 59.2 1.0
CG E:LYS627 4.7 42.0 1.0
N7 E:GTP706 4.7 58.7 1.0
CG E:ASN626 4.8 59.8 1.0
CG E:GLU529 4.9 53.5 1.0
C8 E:GTP706 5.0 64.0 1.0
CE E:LYS627 5.0 35.9 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: Sun Aug 10 05:09:57 2025

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