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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

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