Atomistry » Manganese » PDB 5nha-5raa » 5o1u
Atomistry »
  Manganese »
    PDB 5nha-5raa »
      5o1u »

Manganese in PDB 5o1u: Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+

Protein crystallography data

The structure of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+, PDB code: 5o1u was solved by G.Witte, D.Drexler, M.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.11 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.310, 106.790, 134.120, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.4

Other elements in 5o1u:

The structure of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ (pdb code 5o1u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+, PDB code: 5o1u:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5o1u

Go back to Manganese Binding Sites List in 5o1u
Manganese binding site 1 out of 6 in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:29.1
occ:1.00
 O A:HOH591 2.0 24.5 1.0
OD2 A:ASP23 2.1 30.0 1.0
OD2 A:ASP80 2.2 24.0 1.0
NE2 A:HIS19 2.3 27.8 1.0
O A:HOH673 2.5 29.6 1.0
OD1 A:ASP23 2.5 28.6 1.0
CG A:ASP23 2.7 33.9 1.0
CG A:ASP80 3.2 25.7 1.0
CD2 A:HIS19 3.2 26.5 1.0
CE1 A:HIS19 3.3 26.6 1.0
O A:HOH505 3.4 45.4 1.0
MN A:MN402 3.5 26.1 1.0
OD1 A:ASP80 3.7 22.5 1.0
MN A:MN403 4.1 55.3 0.8
CB A:ASP23 4.1 26.5 1.0
N A:CYS26 4.2 17.3 1.0
CB A:ASP25 4.2 17.6 1.0
O A:ASP80 4.3 25.5 1.0
ND1 A:HIS19 4.4 28.2 1.0
CG A:HIS19 4.4 25.7 1.0
CB A:CYS26 4.4 21.4 1.0
CB A:ASP80 4.5 17.1 1.0
O3' A:AMP404 4.5 50.2 0.7
OD1 A:ASP25 4.7 19.6 1.0
OD2 A:ASP154 4.7 25.4 1.0
CA A:CYS26 4.8 20.1 1.0
OD1 A:ASP154 4.8 25.6 1.0
N A:ASP23 4.8 25.0 1.0
C A:ASP25 4.9 22.1 1.0
O A:HOH517 4.9 19.8 1.0
CG A:ASP25 5.0 22.9 1.0
CA A:ASP23 5.0 24.6 1.0
CA A:ASP25 5.0 18.6 1.0
C3' A:AMP404 5.0 49.7 0.7

Manganese binding site 2 out of 6 in 5o1u

Go back to Manganese Binding Sites List in 5o1u
Manganese binding site 2 out of 6 in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:26.1
occ:1.00
 O A:HOH591 2.0 24.5 1.0
OD1 A:ASP25 2.2 19.6 1.0
NE2 A:HIS104 2.2 20.9 1.0
OD1 A:ASP80 2.3 22.5 1.0
OD1 A:ASP154 2.3 25.6 1.0
CE1 A:HIS104 3.0 21.8 1.0
CG A:ASP80 3.0 25.7 1.0
OD2 A:ASP80 3.1 24.0 1.0
O A:HOH505 3.2 45.4 1.0
CG A:ASP25 3.2 22.9 1.0
CD2 A:HIS104 3.4 19.7 1.0
CG A:ASP154 3.4 25.5 1.0
CB A:ASP25 3.5 17.6 1.0
MN A:MN401 3.5 29.1 1.0
MN A:MN403 3.8 55.3 0.8
OD2 A:ASP154 3.8 25.4 1.0
OG1 A:THR124 4.1 19.1 1.0
N A:THR124 4.2 16.2 1.0
ND1 A:HIS104 4.2 23.2 1.0
O A:HOH673 4.2 29.6 1.0
CE1 A:HIS105 4.3 41.3 1.0
OD2 A:ASP25 4.3 20.9 1.0
CG A:HIS104 4.4 21.7 1.0
CB A:ASP80 4.4 17.1 1.0
NE2 A:HIS286 4.5 47.8 1.0
CB A:ASP154 4.6 15.2 1.0
CA A:ALA123 4.7 16.3 1.0
CB A:THR124 4.7 17.0 1.0
CE1 A:HIS286 4.8 42.3 1.0
NE2 A:HIS105 4.8 47.2 1.0
OD2 A:ASP23 4.9 30.0 1.0
CA A:ASP25 4.9 18.6 1.0
O3' A:AMP404 4.9 50.2 0.7
C A:ALA123 5.0 20.2 1.0
O A:ALA122 5.0 20.8 1.0

Manganese binding site 3 out of 6 in 5o1u

Go back to Manganese Binding Sites List in 5o1u
Manganese binding site 3 out of 6 in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:55.3
occ:0.77
 O3' A:AMP404 2.0 50.2 0.7
NE2 A:HIS105 2.1 47.2 1.0
O2' A:AMP404 2.3 44.4 0.7
NE2 A:HIS286 2.5 47.8 1.0
O A:HOH673 2.5 29.6 1.0
O A:HOH505 2.7 45.4 1.0
CE1 A:HIS105 2.8 41.3 1.0
C3' A:AMP404 3.0 49.7 0.7
C2' A:AMP404 3.0 44.2 0.7
CD2 A:HIS105 3.3 44.4 1.0
CE1 A:HIS286 3.4 42.3 1.0
CD2 A:HIS286 3.5 39.2 1.0
O A:HOH591 3.6 24.5 1.0
MN A:MN402 3.8 26.1 1.0
ND1 A:HIS105 4.0 41.4 1.0
MN A:MN401 4.1 29.1 1.0
C4' A:AMP404 4.2 49.9 0.7
CG A:HIS105 4.2 42.3 1.0
NE2 A:HIS104 4.2 20.9 1.0
C1' A:AMP404 4.3 40.4 0.7
O A:HOH522 4.4 40.0 1.0
OD1 A:ASP80 4.4 22.5 1.0
ND1 A:HIS286 4.5 38.0 1.0
CG A:HIS286 4.6 37.5 1.0
OD1 A:ASP154 4.8 25.6 1.0
CE1 A:HIS104 4.8 21.8 1.0
O4' A:AMP404 4.8 42.0 0.7
OD2 A:ASP23 4.9 30.0 1.0
OD2 A:ASP80 5.0 24.0 1.0

Manganese binding site 4 out of 6 in 5o1u

Go back to Manganese Binding Sites List in 5o1u
Manganese binding site 4 out of 6 in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:28.4
occ:1.00
 O B:HOH589 2.1 31.9 1.0
OD2 B:ASP80 2.1 26.9 1.0
NE2 B:HIS19 2.3 24.2 1.0
O B:HOH662 2.4 31.3 1.0
OD2 B:ASP23 2.4 27.6 1.0
OD1 B:ASP23 2.5 23.6 1.0
CG B:ASP23 2.8 24.5 1.0
CG B:ASP80 3.1 25.5 1.0
CD2 B:HIS19 3.2 24.7 1.0
CE1 B:HIS19 3.3 25.5 1.0
OD1 B:ASP80 3.5 26.2 1.0
MN B:MN402 3.6 25.4 0.9
O B:HOH502 3.9 36.6 1.0
MN B:MN403 4.1 70.7 1.0
O3' B:AMP405 4.1 62.6 0.6
N B:CYS26 4.1 22.7 1.0
CB B:ASP25 4.3 20.8 1.0
O B:ASP80 4.3 25.3 1.0
CB B:ASP23 4.3 23.2 1.0
CB B:CYS26 4.3 25.0 1.0
CG B:HIS19 4.4 26.3 1.0
ND1 B:HIS19 4.4 24.0 1.0
CB B:ASP80 4.4 18.1 1.0
OD1 B:ASP25 4.7 20.7 1.0
OD1 B:ASP154 4.7 22.1 1.0
CA B:CYS26 4.7 20.5 1.0
N B:ASP23 4.9 26.0 1.0
O B:HOH645 4.9 68.3 1.0
C B:ASP25 4.9 21.1 1.0
C3' B:AMP405 4.9 64.1 0.6
NH2 B:ARG86 5.0 37.5 1.0
O B:HOH564 5.0 22.8 1.0

Manganese binding site 5 out of 6 in 5o1u

Go back to Manganese Binding Sites List in 5o1u
Manganese binding site 5 out of 6 in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:25.4
occ:0.95
 O B:HOH589 1.9 31.9 1.0
OD1 B:ASP25 2.1 20.7 1.0
OD2 B:ASP154 2.2 21.4 1.0
NE2 B:HIS104 2.3 24.5 1.0
OD1 B:ASP80 2.4 26.2 1.0
CE1 B:HIS104 3.1 21.9 1.0
CG B:ASP25 3.2 24.7 1.0
CG B:ASP80 3.2 25.5 1.0
CG B:ASP154 3.2 26.8 1.0
OD2 B:ASP80 3.3 26.9 1.0
CD2 B:HIS104 3.4 25.9 1.0
CB B:ASP25 3.5 20.8 1.0
OD1 B:ASP154 3.5 22.1 1.0
MN B:MN401 3.6 28.4 1.0
O B:HOH502 3.6 36.6 1.0
MN B:MN403 3.6 70.7 1.0
O B:HOH662 4.0 31.3 1.0
OG1 B:THR124 4.1 21.8 1.0
N B:THR124 4.2 19.7 1.0
CE1 B:HIS105 4.3 38.2 1.0
ND1 B:HIS104 4.3 24.4 1.0
OD2 B:ASP25 4.3 18.1 1.0
CG B:HIS104 4.4 24.7 1.0
CB B:ASP80 4.5 18.1 1.0
CB B:ASP154 4.6 20.6 1.0
CA B:ALA123 4.6 23.4 1.0
NE2 B:HIS105 4.7 37.2 1.0
CB B:THR124 4.7 21.7 1.0
NE2 B:HIS286 4.8 45.7 1.0
CA B:ASP25 4.9 17.2 1.0
O B:ALA122 5.0 23.7 1.0
C B:ALA123 5.0 22.4 1.0

Manganese binding site 6 out of 6 in 5o1u

Go back to Manganese Binding Sites List in 5o1u
Manganese binding site 6 out of 6 in the Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Wildtype T.Maritima Pde (TM1595) with Amp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:70.7
occ:1.00
 O2' B:AMP405 2.1 62.0 0.6
NE2 B:HIS105 2.3 37.2 1.0
O3' B:AMP405 2.5 62.6 0.6
O B:HOH662 2.6 31.3 1.0
O B:HOH502 2.6 36.6 1.0
NE2 B:HIS286 2.7 45.7 1.0
CE1 B:HIS105 3.0 38.2 1.0
C2' B:AMP405 3.1 63.2 0.6
C3' B:AMP405 3.3 64.1 0.6
CD2 B:HIS286 3.3 48.9 1.0
CD2 B:HIS105 3.4 35.4 1.0
O B:HOH589 3.4 31.9 1.0
MN B:MN402 3.6 25.4 0.9
CE1 B:HIS286 3.9 47.1 1.0
MN B:MN401 4.1 28.4 1.0
NE2 B:HIS104 4.1 24.5 1.0
C4' B:AMP405 4.1 58.6 0.6
ND1 B:HIS105 4.2 38.0 1.0
C1' B:AMP405 4.3 58.8 0.6
CG B:HIS105 4.4 35.2 1.0
OD1 B:ASP80 4.4 26.2 1.0
CG B:HIS286 4.6 48.9 1.0
CE1 B:HIS104 4.7 21.9 1.0
OD2 B:ASP154 4.7 21.4 1.0
O B:HOH534 4.7 52.5 1.0
O4' B:AMP405 4.8 54.1 0.6
ND1 B:HIS286 4.8 47.6 1.0
OD1 B:ASP154 4.9 22.1 1.0
OD2 B:ASP23 5.0 27.6 1.0
CD2 B:HIS104 5.0 25.9 1.0

Reference:

D.J.Drexler, M.Muller, C.A.Rojas-Cordova, A.M.Bandera, G.Witte. Structural and Biophysical Analysis of the Soluble Dhh/DHHA1-Type Phosphodiesterase TM1595 From Thermotoga Maritima. Structure V. 25 1887 2017.
ISSN: ISSN 1878-4186
PubMed: 29107484
DOI: 10.1016/J.STR.2017.10.001
Page generated: Sun Oct 6 02:07:51 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy