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Manganese in PDB 1khw: Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+

Enzymatic activity of Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+

All present enzymatic activity of Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+, PDB code: 1khw was solved by K.K.Ng, M.M.Cherney, A.L.Vazquez, A.Machin, J.M.Alonso, F.Parra, M.N.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.16 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.694, 119.845, 159.498, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+ (pdb code 1khw). 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 Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+, PDB code: 1khw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1khw

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Manganese binding site 1 out of 4 in the Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+


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 Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:64.0
occ:1.00
 OD1 A:ASP250 2.2 46.9 1.0
OD1 A:ASP354 2.2 52.0 1.0
O A:HOH625 2.3 57.5 1.0
CG A:ASP354 2.8 42.0 1.0
OD2 A:ASP354 2.9 46.0 1.0
OD2 A:ASP355 3.3 49.0 1.0
CG A:ASP250 3.4 41.8 1.0
MN A:MN602 3.8 69.1 1.0
CG A:ASP355 3.8 45.5 1.0
CB A:ASP355 3.9 38.8 1.0
OD2 A:ASP250 3.9 43.7 1.0
C A:ASP354 4.0 37.2 1.0
N A:ASP355 4.0 37.6 1.0
O A:HOH607 4.1 44.8 1.0
CB A:ASP354 4.1 37.1 1.0
O A:ASP354 4.1 38.4 1.0
CA A:ASP355 4.2 37.6 1.0
CB A:ASP250 4.5 38.7 1.0
CA A:ASP354 4.5 37.1 1.0
O A:HOH608 4.6 60.4 1.0
OD1 A:ASP355 4.8 53.9 1.0
CA A:ASP250 4.9 37.0 1.0
N A:ASP354 4.9 36.3 1.0
N A:TYR251 4.9 36.3 1.0

Manganese binding site 2 out of 4 in 1khw

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Manganese binding site 2 out of 4 in the Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+


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 Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:69.1
occ:1.00
 O A:TYR251 2.2 44.0 1.0
OD2 A:ASP250 2.5 43.7 1.0
OD2 A:ASP354 2.8 46.0 1.0
O A:HOH608 3.1 60.4 1.0
OD1 A:ASP250 3.1 46.9 1.0
CG A:ASP250 3.1 41.8 1.0
O A:HOH625 3.2 57.5 1.0
C A:TYR251 3.2 34.6 1.0
O A:HOH604 3.3 30.7 1.0
O A:HOH603 3.7 40.7 1.0
N A:TYR251 3.7 36.3 1.0
MN A:MN601 3.8 64.0 1.0
CG A:ASP354 3.9 42.0 1.0
CA A:TYR251 4.1 35.5 1.0
N A:SER252 4.1 32.2 1.0
CA A:SER252 4.2 30.7 1.0
CB A:ASP250 4.5 38.7 1.0
OD1 A:ASP354 4.6 52.0 1.0
C A:ASP250 4.7 37.0 1.0
CB A:ASP354 4.8 37.1 1.0

Manganese binding site 3 out of 4 in 1khw

Go back to Manganese Binding Sites List in 1khw
Manganese binding site 3 out of 4 in the Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+


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 Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:84.0
occ:0.40
 O B:HOH617 2.5 61.4 1.0
OD1 B:ASP354 2.8 24.4 1.0
OD2 B:ASP354 2.9 22.1 1.0
CG B:ASP354 3.1 25.3 1.0
MN B:MN604 3.2 55.1 0.5
CB B:ASP355 4.3 27.3 1.0
CB B:ASP354 4.4 24.4 1.0
C B:ASP354 4.5 26.0 1.0
N B:ASP355 4.5 26.5 1.0
O B:ASP354 4.5 25.9 1.0
CA B:ASP355 4.5 27.2 1.0
CG B:ASP355 4.6 28.6 1.0
CE B:LYS403 4.6 49.0 1.0
OD2 B:ASP355 4.8 28.1 1.0

Manganese binding site 4 out of 4 in 1khw

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Manganese binding site 4 out of 4 in the Crystal Structure of Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+


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 Rabbit Hemorrhagic Disease Virus Rna-Dependent Rna Polymerase Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn604

b:55.1
occ:0.50
 O B:TYR251 2.2 45.4 1.0
O B:HOH617 2.7 61.4 1.0
OD2 B:ASP354 3.0 22.1 1.0
MN B:MN603 3.2 84.0 0.4
C B:TYR251 3.4 41.2 1.0
CG B:ASP354 3.7 25.3 1.0
N B:TYR251 4.0 40.1 1.0
CA B:TYR251 4.1 40.6 1.0
O B:HOH618 4.2 47.1 1.0
CB B:ASP354 4.4 24.4 1.0
N B:SER252 4.4 40.9 1.0
OD1 B:ASP354 4.5 24.4 1.0
CA B:SER252 4.5 39.9 1.0
CB B:TYR251 4.6 39.2 1.0
C B:ASP250 4.7 40.4 1.0

Reference:

K.K.Ng, M.M.Cherney, A.L.Vazquez, A.Machin, J.M.Alonso, F.Parra, M.N.James. Crystal Structures of Active and Inactive Conformations of A Caliciviral Rna-Dependent Rna Polymerase. J.Biol.Chem. V. 277 1381 2002.
ISSN: ISSN 0021-9258
PubMed: 11677245
DOI: 10.1074/JBC.M109261200
Page generated: Sat Oct 5 11:23:52 2024

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