Atomistry » Manganese » PDB 4dky-4ee1 » 4e19
Atomistry »
  Manganese »
    PDB 4dky-4ee1 »
      4e19 »

Manganese in PDB 4e19: 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: 4e19 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 (%) 17.2 / 20.7

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 4e19). 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: 4e19:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 4e19

Go back to Manganese Binding Sites List in 4e19
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
 OE2 A:GLU115 2.0 13.4 1.0
OD1 A:ASP75 2.1 10.1 1.0
OD1 A:ASP139 2.1 10.6 1.0
O A:HOH530 2.3 11.6 1.0
O A:HOH540 2.6 14.0 1.0
CD A:GLU115 2.9 13.4 1.0
CG A:ASP139 3.1 10.7 1.0
CG A:ASP75 3.3 8.2 1.0
OE1 A:GLU115 3.3 13.1 1.0
OD2 A:ASP139 3.4 12.3 1.0
MN A:MN302 3.6 11.3 1.0
OD2 A:ASP75 3.7 10.2 1.0
O A:HOH432 4.0 18.9 1.0
O A:HOH526 4.0 11.8 1.0
O A:GLY76 4.2 14.5 1.0
CG A:GLU115 4.3 11.4 1.0
CB A:ASP139 4.4 10.7 1.0
CB A:ASP75 4.5 10.4 1.0
N A:GLY76 4.5 10.0 1.0
C A:ASP139 4.5 9.5 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 11.0 1.0
CA A:ASP139 4.9 9.5 1.0
O A:HOH528 5.0 12.1 1.0

Manganese binding site 2 out of 5 in 4e19

Go back to Manganese Binding Sites List in 4e19
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:11.3
occ:1.00
 OD1 A:ASP189 2.1 13.2 1.0
O A:HOH540 2.1 14.0 1.0
OD2 A:ASP75 2.2 10.2 1.0
O A:HOH528 2.3 12.1 1.0
O A:HOH530 2.4 11.6 1.0
CG A:ASP75 3.1 8.2 1.0
CG A:ASP189 3.2 13.2 1.0
OD1 A:ASP75 3.3 10.1 1.0
MN A:MN301 3.6 11.5 1.0
CB A:ASP189 3.7 11.4 1.0
O A:GLY76 3.8 14.5 1.0
NH2 A:ARG182 4.1 23.2 1.0
OD2 A:ASP189 4.2 16.0 1.0
ND2 A:ASN193 4.3 15.9 1.0
CA A:ASP189 4.3 11.1 1.0
NE A:ARG182 4.4 22.6 1.0
CB A:ASP75 4.5 10.4 1.0
OD2 A:ASP139 4.5 12.3 1.0
CZ A:ARG182 4.7 25.4 1.0
C A:GLY76 5.0 12.5 1.0

Manganese binding site 3 out of 5 in 4e19

Go back to Manganese Binding Sites List in 4e19
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:11.8
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 11.6 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
CG B:ASP75 3.2 9.4 1.0
OE2 B:GLU115 3.2 11.5 1.0
CG B:ASP139 3.2 11.7 1.0
OD2 B:ASP139 3.4 12.9 1.0
MN B:MN202 3.5 12.3 1.0
OD2 B:ASP75 3.6 11.5 1.0
O A:HOH417 3.8 14.7 1.0
O B:HOH303 3.9 13.4 1.0
O A:HOH428 4.1 15.0 1.0
OD2 A:ASP198 4.3 14.0 1.0
CG B:GLU115 4.4 12.2 1.0
CB B:ASP75 4.4 10.2 1.0
OD1 A:ASP198 4.5 13.4 1.0
CB B:ASP139 4.5 14.2 1.0
ND2 B:ASN185 4.5 12.0 1.0
C B:ASP139 4.6 13.2 1.0
O B:GLY76 4.6 12.4 1.0
CA B:ASP75 4.7 10.9 1.0
CB B:SER140 4.7 12.6 1.0
N B:GLY76 4.7 10.4 1.0
N B:SER140 4.7 11.7 1.0
CG A:ASP198 4.8 14.5 1.0
O B:HOH305 4.8 13.8 1.0
N B:ASP139 4.8 11.6 1.0
O A:HOH443 4.9 16.9 1.0
CA B:ASP139 4.9 11.8 1.0
O B:ASP139 4.9 14.6 1.0

Manganese binding site 4 out of 5 in 4e19

Go back to Manganese Binding Sites List in 4e19
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:12.3
occ:1.00
 OD1 B:ASP189 2.1 14.7 1.0
OD1 A:ASP198 2.1 13.4 1.0
OD2 B:ASP75 2.2 11.5 1.0
O B:HOH428 2.2 13.3 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 14.5 1.0
CG B:ASP75 3.1 9.4 1.0
CG B:ASP189 3.2 12.9 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 11.8 1.0
CB B:ASP189 3.7 11.3 1.0
O B:HOH366 3.8 27.1 1.0
O B:GLY76 3.8 12.4 1.0
OD2 B:ASP189 4.1 16.7 1.0
CA B:ASP189 4.3 11.3 1.0
O A:HOH454 4.3 20.8 1.0
O A:HOH417 4.4 14.7 1.0
NE B:ARG182 4.4 16.6 1.0
OD2 B:ASP139 4.4 12.9 1.0
CB A:ASP198 4.4 16.0 1.0
CB B:ASP75 4.5 10.2 1.0
CD B:ARG182 4.5 15.8 1.0
O B:HOH429 4.6 12.7 1.0
CA A:ASP198 4.8 14.4 1.0
CZ B:ARG182 4.9 16.5 1.0
OD1 B:ASP139 4.9 11.3 1.0

Manganese binding site 5 out of 5 in 4e19

Go back to Manganese Binding Sites List in 4e19
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 15.0 1.0
O B:HOH443 2.3 17.3 1.0
C B:GLY103 3.3 14.2 1.0
N B:GLY103 3.7 13.4 1.0
CA B:GLY103 3.9 13.1 1.0
O B:HOH422 4.1 30.9 1.0
O B:HOH358 4.2 31.4 1.0
O B:HOH311 4.2 19.2 1.0
OD1 B:ASP104 4.3 16.6 1.0
N B:ASP104 4.4 13.8 1.0
O B:HOH362 4.5 22.4 1.0
CG B:ASP104 4.6 14.9 1.0
CA B:ASP104 4.7 12.5 1.0
OD2 B:ASP104 4.8 16.7 1.0
C B:GLY102 4.9 10.5 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 Aug 16 13:46:17 2025

Last articles

Mn in 5HWU
Mn in 5HRM
Mn in 5HUE
Mn in 5HUD
Mn in 5HUC
Mn in 5HRL
Mn in 5HRK
Mn in 5HRI
Mn in 5HRH
Mn in 5HRG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy