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Manganese in PDB 4nyn: Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1

Enzymatic activity of Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1

All present enzymatic activity of Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1, PDB code: 4nyn was solved by D.J.You, C.Angkawidjaja, Y.Koga, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.94 / 1.41
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 115.802, 115.802, 38.282, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1 (pdb code 4nyn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1, PDB code: 4nyn:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 4nyn

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Manganese binding site 1 out of 5 in the Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1


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 Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:11.5
occ:1.00
 OD1 A:ASP75 2.1 10.2 1.0
OD1 A:ASP139 2.1 10.6 1.0
OE2 A:GLU115 2.1 13.5 1.0
O A:HOH530 2.3 11.5 1.0
O A:HOH540 2.6 14.1 1.0
CG A:ASP139 3.1 10.6 1.0
CD A:GLU115 3.1 13.3 1.0
CG A:ASP75 3.2 8.2 1.0
OE1 A:GLU115 3.3 13.1 1.0
OD2 A:ASP139 3.4 12.2 1.0
MN A:MN302 3.6 11.2 1.0
OD2 A:ASP75 3.7 10.1 1.0
O A:HOH526 4.0 11.9 1.0
O A:HOH432 4.0 18.9 1.0
O A:GLY76 4.2 14.7 1.0
CB A:ASP139 4.4 10.6 1.0
CG A:GLU115 4.5 11.3 1.0
CB A:ASP75 4.5 10.8 1.0
C A:ASP139 4.5 9.5 1.0
N A:GLY76 4.5 9.8 1.0
O A:ASP139 4.6 11.2 1.0
CA A:ASP75 4.7 9.8 1.0
N A:SER140 4.8 10.9 1.0
CA A:ASP139 4.9 9.2 1.0
O A:HOH528 5.0 12.2 1.0

Manganese binding site 2 out of 5 in 4nyn

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Manganese binding site 2 out of 5 in the Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1


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 Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:11.2
occ:1.00
 OD1 A:ASP189 2.1 13.3 1.0
O A:HOH540 2.1 14.1 1.0
OD2 A:ASP75 2.1 10.1 1.0
O A:HOH528 2.3 12.2 1.0
O A:HOH530 2.5 11.5 1.0
CG A:ASP75 3.1 8.2 1.0
CG A:ASP189 3.2 13.6 1.0
OD1 A:ASP75 3.3 10.2 1.0
MN A:MN301 3.6 11.5 1.0
CB A:ASP189 3.7 11.6 1.0
O A:GLY76 3.8 14.7 1.0
NH2 A:ARG182 4.1 22.9 1.0
ND2 A:ASN193 4.2 16.3 1.0
OD2 A:ASP189 4.2 15.9 1.0
CA A:ASP189 4.3 10.8 1.0
NE A:ARG182 4.4 22.4 1.0
CB A:ASP75 4.5 10.8 1.0
OD2 A:ASP139 4.5 12.2 1.0
CZ A:ARG182 4.7 25.3 1.0
C A:GLY76 4.9 12.5 1.0
OD1 A:ASP139 5.0 10.6 1.0

Manganese binding site 3 out of 5 in 4nyn

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Manganese binding site 3 out of 5 in the Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1


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 Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:11.7
occ:1.00
 O B:HOH429 2.1 12.7 1.0
OD1 B:ASP75 2.1 10.2 1.0
OE1 B:GLU115 2.1 11.7 1.0
OD1 B:ASP139 2.2 11.3 1.0
O A:HOH421 2.4 12.5 1.0
O B:HOH426 2.4 11.2 1.0
CD B:GLU115 3.0 10.8 1.0
OE2 B:GLU115 3.2 11.5 1.0
CG B:ASP75 3.2 9.4 1.0
CG B:ASP139 3.2 11.9 1.0
OD2 B:ASP139 3.4 12.9 1.0
MN B:MN202 3.5 12.2 1.0
OD2 B:ASP75 3.6 11.5 1.0
O A:HOH417 3.8 14.4 1.0
O B:HOH303 3.9 13.4 1.0
O A:HOH428 4.1 14.7 1.0
OD2 A:ASP198 4.3 14.0 1.0
CG B:GLU115 4.4 11.9 1.0
CB B:ASP75 4.4 9.9 1.0
OD1 A:ASP198 4.5 13.3 1.0
ND2 B:ASN185 4.5 11.9 1.0
CB B:ASP139 4.5 14.2 1.0
C B:ASP139 4.6 13.1 1.0
O B:GLY76 4.6 12.3 1.0
CA B:ASP75 4.7 11.1 1.0
CB B:SER140 4.7 12.4 1.0
N B:SER140 4.7 11.7 1.0
N B:GLY76 4.7 10.2 1.0
CG A:ASP198 4.8 14.6 1.0
O B:HOH305 4.8 13.6 1.0
N B:ASP139 4.8 11.5 1.0
CA B:ASP139 4.9 11.7 1.0
O A:HOH443 4.9 16.6 1.0
O B:ASP139 4.9 14.5 1.0

Manganese binding site 4 out of 5 in 4nyn

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Manganese binding site 4 out of 5 in the Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1


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 Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:12.2
occ:1.00
 OD1 B:ASP189 2.1 14.5 1.0
OD1 A:ASP198 2.1 13.3 1.0
OD2 B:ASP75 2.2 11.5 1.0
O B:HOH428 2.2 13.4 1.0
O B:HOH426 2.3 11.2 1.0
O A:HOH421 2.4 12.5 1.0
CG A:ASP198 3.1 14.6 1.0
CG B:ASP75 3.1 9.4 1.0
CG B:ASP189 3.1 12.8 1.0
OD1 B:ASP75 3.4 10.2 1.0
OD2 A:ASP198 3.4 14.0 1.0
MN B:MN201 3.5 11.7 1.0
CB B:ASP189 3.7 11.3 1.0
O B:HOH366 3.8 26.9 1.0
O B:GLY76 3.8 12.3 1.0
OD2 B:ASP189 4.1 16.8 1.0
CA B:ASP189 4.3 11.2 1.0
O A:HOH454 4.3 20.6 1.0
NE B:ARG182 4.4 17.0 1.0
O A:HOH417 4.4 14.4 1.0
OD2 B:ASP139 4.4 12.9 1.0
CB A:ASP198 4.4 15.7 1.0
CB B:ASP75 4.5 9.9 1.0
CD B:ARG182 4.6 15.8 1.0
O B:HOH429 4.6 12.7 1.0
CA A:ASP198 4.8 13.6 1.0
CZ B:ARG182 4.9 16.7 1.0
OD1 B:ASP139 4.9 11.3 1.0
C B:GLY76 5.0 11.2 1.0

Manganese binding site 5 out of 5 in 4nyn

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Manganese binding site 5 out of 5 in the Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:15.6
occ:1.00
 O B:HOH444 2.2 20.2 1.0
O B:GLY103 2.2 15.1 1.0
O B:HOH443 2.2 17.3 1.0
C B:GLY103 3.3 14.4 1.0
N B:GLY103 3.7 13.3 1.0
CA B:GLY103 3.9 13.3 1.0
O B:HOH422 4.1 30.4 1.0
O B:HOH311 4.2 18.8 1.0
O B:HOH358 4.2 30.9 1.0
OD1 B:ASP104 4.3 16.5 1.0
N B:ASP104 4.4 13.6 1.0
O B:HOH362 4.5 22.3 1.0
CG B:ASP104 4.6 14.8 1.0
CA B:ASP104 4.7 12.0 1.0
OD2 B:ASP104 4.8 16.8 1.0
C B:GLY102 4.9 10.4 1.0

Reference:

D.J.You, C.Angkawidjaja, Y.Koga, S.Kanaya. Crystal Structure of Rnase H1 From Halophilic Archaeon Halobacterium Salinarum Nrc-1 To Be Published.
Page generated: Sat Oct 5 20:39:06 2024

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