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Manganese in PDB 3nai: Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase

Protein crystallography data

The structure of Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase, PDB code: 3nai was solved by K.H.Kim, J.H.Lee, I.Alam, Y.Park, S.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.53 / 2.56
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.246, 196.562, 109.598, 90.00, 114.81, 90.00
R / Rfree (%) 20.3 / 26.8

Other elements in 3nai:

The structure of Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase (pdb code 3nai). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase, PDB code: 3nai:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3nai

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Manganese binding site 1 out of 6 in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent 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 Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn522

b:47.7
occ:1.00
 SG A:CYS213 2.1 23.7 1.0
O A:LYS210 2.5 25.7 1.0
CB A:CYS213 3.1 23.9 1.0
MN A:MN3523 3.4 40.2 1.0
O A:GLY221 3.5 22.4 1.0
C A:LYS210 3.7 25.7 1.0
C A:GLY221 4.0 22.3 1.0
CA A:CYS213 4.4 23.9 1.0
N A:CYS213 4.4 24.2 1.0
CA A:GLU211 4.5 26.8 1.0
N A:MET222 4.5 22.6 1.0
N A:GLU211 4.5 26.2 1.0
CA A:MET222 4.6 22.8 1.0
OD2 A:ASP227 4.6 25.5 1.0
CA A:GLY221 4.6 21.9 1.0
CA A:LYS210 4.7 25.3 1.0
C A:GLU211 4.8 26.3 1.0
O A:VAL220 4.8 20.4 1.0

Manganese binding site 2 out of 6 in 3nai

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Manganese binding site 2 out of 6 in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent 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 Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn523

b:40.2
occ:1.00
 SG A:CYS213 2.2 23.7 1.0
O A:HOH539 2.8 2.0 1.0
O A:HOH656 2.9 13.0 1.0
N A:CYS213 3.2 24.2 1.0
N A:ILE214 3.3 23.5 1.0
MN A:MN3522 3.4 47.7 1.0
CG1 A:ILE214 3.4 23.3 1.0
O A:GLU211 3.5 26.6 1.0
CB A:CYS213 3.5 23.9 1.0
CA A:CYS213 3.7 23.9 1.0
C A:CYS213 3.9 23.9 1.0
C A:GLU211 3.9 26.3 1.0
CD1 A:ILE214 3.9 22.2 1.0
C A:THR212 4.0 24.9 1.0
CB A:ILE214 4.1 23.6 1.0
O A:LYS210 4.1 25.7 1.0
N A:THR212 4.3 26.0 1.0
CA A:ILE214 4.3 23.1 1.0
CA A:THR212 4.4 25.3 1.0
CA A:GLU211 4.6 26.8 1.0
O A:THR212 4.9 24.6 1.0
O A:CYS213 4.9 23.7 1.0

Manganese binding site 3 out of 6 in 3nai

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Manganese binding site 3 out of 6 in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent 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 Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn522

b:42.9
occ:1.00
 SG B:CYS213 2.2 28.9 1.0
O B:LYS210 2.6 29.5 1.0
O B:HOH551 2.6 32.1 1.0
MN B:MN3523 2.9 40.5 1.0
CB B:CYS213 3.2 27.4 1.0
O B:GLY221 3.4 28.8 1.0
C B:LYS210 3.8 29.2 1.0
C B:GLY221 3.9 28.5 1.0
N B:CYS213 4.1 27.8 1.0
CA B:CYS213 4.2 27.6 1.0
N B:MET222 4.3 28.5 1.0
CA B:MET222 4.3 28.5 1.0
CG B:LYS210 4.5 31.2 1.0
CA B:LYS210 4.6 28.8 1.0
N B:GLU211 4.7 29.6 1.0
OD2 B:ASP227 4.7 28.6 1.0
CA B:GLY221 4.7 28.0 1.0
CA B:GLU211 4.7 29.9 1.0
C B:GLU211 4.8 29.7 1.0
O B:VAL220 4.9 27.0 1.0

Manganese binding site 4 out of 6 in 3nai

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Manganese binding site 4 out of 6 in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent 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 Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn523

b:40.5
occ:1.00
 SG B:CYS213 2.5 28.9 1.0
O B:HOH554 2.8 13.1 1.0
MN B:MN3522 2.9 42.9 1.0
O B:HOH634 2.9 16.4 1.0
N B:CYS213 3.1 27.8 1.0
CD1 B:ILE214 3.5 24.7 1.0
N B:ILE214 3.6 26.4 1.0
CB B:CYS213 3.6 27.4 1.0
CG1 B:ILE214 3.7 25.0 1.0
CA B:CYS213 3.7 27.6 1.0
O B:GLU211 3.9 30.2 1.0
O B:LYS210 3.9 29.5 1.0
C B:CYS213 3.9 27.1 1.0
C B:THR212 4.0 27.9 1.0
C B:GLU211 4.1 29.7 1.0
CA B:THR212 4.3 28.2 1.0
CB B:ILE214 4.3 25.6 1.0
N B:THR212 4.3 29.0 1.0
CA B:ILE214 4.5 25.6 1.0
OD1 B:ASP227 4.9 31.8 1.0
CA B:GLU211 4.9 29.9 1.0
O B:CYS213 4.9 27.3 1.0
O B:THR212 4.9 28.1 1.0

Manganese binding site 5 out of 6 in 3nai

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Manganese binding site 5 out of 6 in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn522

b:46.9
occ:1.00
 SG C:CYS213 2.2 27.7 1.0
O C:LYS210 2.3 28.8 1.0
CB C:CYS213 2.8 26.4 1.0
C C:LYS210 3.5 28.6 1.0
MN C:MN3523 3.6 55.9 1.0
N C:MET222 4.0 27.0 1.0
CA C:CYS213 4.1 26.6 1.0
C C:GLY221 4.1 26.9 1.0
N C:CYS213 4.1 26.8 1.0
CG C:LYS210 4.2 30.0 1.0
CA C:MET222 4.2 27.1 1.0
CA C:LYS210 4.3 28.4 1.0
O C:GLY221 4.3 27.4 1.0
CE C:LYS210 4.5 34.2 1.0
OD2 C:ASP227 4.5 27.6 1.0
N C:GLU211 4.5 28.8 1.0
CA C:GLY221 4.6 26.4 1.0
O C:VAL220 4.6 25.0 1.0
CA C:GLU211 4.8 29.2 1.0
CB C:LYS210 4.8 28.4 1.0
C C:GLU211 4.9 28.9 1.0
CD C:LYS210 5.0 33.1 1.0

Manganese binding site 6 out of 6 in 3nai

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Manganese binding site 6 out of 6 in the Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structures and Functional Analysis of Murine Norovirus Rna- Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn523

b:55.9
occ:1.00
 SG C:CYS213 2.2 27.7 1.0
O C:GLU211 3.4 29.0 1.0
N C:ILE214 3.5 25.3 1.0
O C:HOH527 3.5 21.9 1.0
N C:CYS213 3.5 26.8 1.0
CG1 C:ILE214 3.6 23.3 1.0
MN C:MN3522 3.6 46.9 1.0
CB C:CYS213 3.8 26.4 1.0
C C:GLU211 3.8 28.9 1.0
CD1 C:ILE214 3.9 22.0 1.0
CA C:CYS213 4.0 26.6 1.0
CB C:ILE214 4.1 24.3 1.0
O C:LYS210 4.1 28.8 1.0
C C:THR212 4.1 27.3 1.0
N C:THR212 4.2 28.4 1.0
C C:CYS213 4.2 26.1 1.0
CA C:THR212 4.2 27.8 1.0
CA C:ILE214 4.4 24.5 1.0
CA C:GLU211 4.6 29.2 1.0
O C:THR212 5.0 27.3 1.0

Reference:

K.H.Kim, J.H.Lee, I.Alam, Y.Park, S.Kang. Crystal Structures and Functional Analysis of Murine Norovirus Rna-Dependent Rna Polymerase To Be Published.
Page generated: Sat Oct 5 17:18:07 2024

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