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Manganese in PDB 3h5x: Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase

Enzymatic activity of Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase

All present enzymatic activity of Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase, PDB code: 3h5x was solved by D.F.Zamyatkin, F.Parra, A.Machin, P.Grochulski, K.K.S.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.600, 93.700, 96.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase (pdb code 3h5x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase, PDB code: 3h5x:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3h5x

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Manganese binding site 1 out of 4 in the Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn511

b:43.3
occ:1.00
 OD2 A:ASP343 2.2 38.4 1.0
O2B A:CSG515 2.2 46.9 1.0
O3G A:CSG515 2.2 48.3 1.0
O A:TYR243 2.3 37.3 1.0
O1A A:CSG515 2.5 48.3 1.0
O A:HOH882 2.6 47.5 1.0
PB A:CSG515 3.2 50.0 1.0
CG A:ASP343 3.3 35.9 1.0
O3A A:CSG515 3.3 48.5 1.0
PG A:CSG515 3.4 52.1 1.0
PA A:CSG515 3.5 49.0 1.0
C A:TYR243 3.5 37.3 1.0
O3B A:CSG515 3.6 49.6 1.0
MN A:MN512 3.7 47.0 1.0
OD1 A:ASP343 3.8 32.2 1.0
O1G A:CSG515 4.2 46.7 1.0
C5' A:CSG515 4.3 39.3 1.0
N A:TYR243 4.3 44.9 1.0
O5' A:CSG515 4.4 43.4 1.0
CA A:TYR243 4.4 37.9 1.0
O2G A:CSG515 4.5 47.1 1.0
CB A:ASP343 4.5 28.6 1.0
N A:SER244 4.5 36.1 1.0
O1B A:CSG515 4.5 47.4 1.0
CA A:SER244 4.6 35.3 1.0
N A:ARG245 4.7 33.6 1.0
O2A A:CSG515 4.7 45.9 1.0
CB A:TYR243 4.9 34.7 1.0
CB A:TRP246 4.9 26.3 1.0
C A:SER244 4.9 33.9 1.0
N A:TRP246 4.9 29.3 1.0

Manganese binding site 2 out of 4 in 3h5x

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Manganese binding site 2 out of 4 in the Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn512

b:47.0
occ:1.00
 OD1 A:ASP343 2.2 32.2 1.0
O1A A:CSG515 2.2 48.3 1.0
O3' P:G8 2.6 35.6 1.0
CG A:ASP343 3.1 35.9 1.0
OD2 A:ASP343 3.3 38.4 1.0
O A:HOH882 3.3 47.5 1.0
PA A:CSG515 3.5 49.0 1.0
MN A:MN511 3.7 43.3 1.0
C3' P:G8 3.9 31.1 1.0
O2A A:CSG515 3.9 45.9 1.0
N A:ASP344 4.0 25.4 1.0
CB A:ASP344 4.1 28.0 1.0
C5' A:CSG515 4.2 39.3 1.0
O5' A:CSG515 4.2 43.4 1.0
CA A:ASP344 4.2 25.5 1.0
O P:HOH671 4.2 41.6 1.0
CG A:ASP344 4.3 35.1 1.0
C A:ASP343 4.3 24.5 1.0
OD2 A:ASP344 4.4 36.4 1.0
CB A:ASP343 4.5 28.6 1.0
C4' P:G8 4.5 32.5 1.0
C5' P:G8 4.6 28.5 1.0
O3A A:CSG515 4.8 48.5 1.0
OD1 A:ASP344 4.8 42.9 1.0
CA A:ASP343 4.8 27.6 1.0
O A:ASP343 4.8 29.1 1.0
O2' P:G8 4.9 29.6 1.0
N A:ASP343 5.0 25.1 1.0
C2' P:G8 5.0 30.9 1.0

Manganese binding site 3 out of 4 in 3h5x

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Manganese binding site 3 out of 4 in the Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn513

b:57.5
occ:1.00
 OD1 A:ASP344 2.1 42.9 1.0
O A:HOH563 2.2 53.9 1.0
O A:HOH637 2.2 28.7 1.0
CG A:ASP344 3.1 35.1 1.0
O A:ALA241 3.3 53.4 1.0
OD2 A:ASP344 3.7 36.4 1.0
CA A:ASP344 4.1 25.5 1.0
N A:GLU345 4.1 25.1 1.0
O A:THR389 4.2 35.6 1.0
CB A:ASP344 4.2 28.0 1.0
C A:ALA241 4.2 52.2 1.0
O P:HOH671 4.3 41.6 1.0
OG1 A:THR389 4.5 42.9 1.0
O A:GLU345 4.6 30.0 1.0
C A:ASP344 4.7 25.4 1.0
CA A:PHE390 4.8 31.9 1.0
C A:THR389 4.8 35.6 1.0
N A:ALA241 4.8 49.6 1.0
CA A:ASP242 4.9 51.6 1.0
N A:ASP242 4.9 52.0 1.0
O A:HOH882 5.0 47.5 1.0
CB A:ASP242 5.0 51.9 1.0

Manganese binding site 4 out of 4 in 3h5x

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Manganese binding site 4 out of 4 in the Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of 2'-Amino-2'-Deoxy-Cytidine-5'-Triphosphate Bound to Norovirus Gii Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn514

b:28.5
occ:1.00
 OE2 A:GLU205 2.1 30.3 1.0
NE2 A:HIS209 2.1 28.8 1.0
OD2 A:ASP99 2.1 35.9 1.0
CD A:GLU205 3.0 35.0 1.0
CD2 A:HIS209 3.0 27.8 1.0
CE1 A:HIS209 3.1 28.0 1.0
CG A:ASP99 3.2 34.6 1.0
OE1 A:GLU205 3.3 33.9 1.0
CB A:ASP99 3.6 33.1 1.0
N A:ASP99 3.8 30.9 1.0
CG A:HIS209 4.2 27.1 1.0
ND1 A:HIS209 4.2 29.9 1.0
OD1 A:ASP99 4.2 37.2 1.0
CG A:GLU205 4.3 33.9 1.0
CA A:ASP99 4.4 31.6 1.0
CG2 A:THR208 4.4 35.3 1.0
CA A:ILE98 4.5 28.6 1.0
C A:ILE98 4.5 31.1 1.0
O A:THR97 4.7 30.4 1.0
CB A:THR208 4.8 31.1 1.0
O A:GLU205 4.9 26.7 1.0

Reference:

D.F.Zamyatkin, F.Parra, A.Machin, P.Grochulski, K.K.Ng. Binding of 2'-Amino-2'-Deoxycytidine-5'-Triphosphate to Norovirus Polymerase Induces Rearrangement of the Active Site. J.Mol.Biol. V. 390 10 2009.
ISSN: ISSN 0022-2836
PubMed: 19426741
DOI: 10.1016/J.JMB.2009.04.069
Page generated: Sat Oct 5 16:25:50 2024

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