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Manganese in PDB 3uct: Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+

Protein crystallography data

The structure of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+, PDB code: 3uct was solved by F.T.Senguen, Z.Grabarek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.23 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.288, 35.463, 58.343, 90.00, 93.12, 90.00
R / Rfree (%) 20.2 / 23.4

Other elements in 3uct:

The structure of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ (pdb code 3uct). 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 MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+, PDB code: 3uct:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3uct

Go back to Manganese Binding Sites List in 3uct
Manganese binding site 1 out of 6 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn100

b:41.7
occ:1.00
 OD1 A:ASP20 2.1 37.1 1.0
O A:HOH92 2.1 43.0 1.0
OD1 A:ASP22 2.1 47.4 1.0
OD1 A:ASP24 2.2 44.7 1.0
O A:THR26 2.2 35.3 1.0
O A:HOH91 2.2 33.1 1.0
CG A:ASP22 3.1 50.0 1.0
CG A:ASP24 3.1 51.5 1.0
CG A:ASP20 3.2 38.4 1.0
OD2 A:ASP22 3.3 52.7 1.0
C A:THR26 3.3 31.9 1.0
MN A:MN102 3.4 53.8 1.0
OD2 A:ASP24 3.4 44.6 1.0
OG1 A:THR26 3.6 48.5 1.0
N A:THR26 3.8 34.8 1.0
CA A:THR26 4.0 32.6 1.0
CB A:ASP20 4.1 30.8 1.0
OD2 A:ASP20 4.1 37.5 1.0
CA A:ASP20 4.1 34.4 1.0
N A:ASP24 4.1 45.8 1.0
CB A:ASP24 4.4 46.0 1.0
CB A:THR26 4.4 41.8 1.0
N A:ILE27 4.4 29.4 1.0
CB A:ASP22 4.4 51.2 1.0
O A:HOH138 4.5 49.2 1.0
C A:ASP20 4.5 38.8 1.0
O A:HOH95 4.5 50.7 1.0
N A:GLY25 4.5 43.4 1.0
N A:ASP22 4.6 47.5 1.0
CA A:ASP24 4.6 43.0 1.0
O A:HOH137 4.6 54.5 1.0
N A:GLY23 4.6 46.6 1.0
O A:HOH93 4.6 40.9 1.0
CA A:ILE27 4.7 29.2 1.0
C A:ASP24 4.7 44.3 1.0
C A:ASP22 4.8 54.0 1.0
CA A:ASP22 4.8 48.2 1.0
N A:LYS21 4.9 36.5 1.0
C A:GLY25 4.9 32.7 1.0

Manganese binding site 2 out of 6 in 3uct

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Manganese binding site 2 out of 6 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn101

b:40.4
occ:1.00
 O A:HOH123 2.2 46.4 1.0
O A:HOH106 2.2 39.4 1.0
OD1 A:ASN60 2.2 42.5 1.0
OD1 A:ASP58 2.2 51.9 1.0
OD1 A:ASP56 2.2 48.8 1.0
O A:THR62 2.2 35.6 1.0
CG A:ASN60 3.1 47.4 1.0
CG A:ASP58 3.2 55.0 1.0
CG A:ASP56 3.3 47.8 1.0
C A:THR62 3.3 35.7 1.0
OD2 A:ASP58 3.4 58.9 1.0
ND2 A:ASN60 3.5 47.1 1.0
N A:THR62 3.7 39.6 1.0
OG1 A:THR62 3.9 41.1 1.0
OD2 A:ASP56 4.0 49.6 1.0
CA A:THR62 4.0 37.6 1.0
O A:HOH120 4.1 51.9 1.0
O A:HOH119 4.1 46.6 1.0
N A:ASN60 4.1 45.7 1.0
CB A:ASP56 4.2 42.5 1.0
CA A:ASP56 4.2 42.6 1.0
CB A:ASN60 4.4 44.1 1.0
N A:ILE63 4.4 31.3 1.0
N A:GLY61 4.4 39.1 1.0
N A:GLY59 4.5 50.4 1.0
CB A:ASP58 4.5 55.4 1.0
CB A:THR62 4.6 39.9 1.0
CA A:ASN60 4.6 42.1 1.0
N A:ASP58 4.7 52.9 1.0
C A:ASN60 4.7 38.8 1.0
CD1 A:ILE63 4.8 37.4 1.0
CA A:ILE63 4.8 28.1 1.0
C A:ASP56 4.8 48.5 1.0
C A:GLY61 4.8 39.2 1.0
C A:ASP58 4.9 55.9 1.0
CA A:ASP58 4.9 55.4 1.0
OE1 A:GLU67 4.9 41.3 1.0

Manganese binding site 3 out of 6 in 3uct

Go back to Manganese Binding Sites List in 3uct
Manganese binding site 3 out of 6 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn102

b:53.8
occ:1.00
 OD2 A:ASP22 2.1 52.7 1.0
O A:HOH137 2.1 54.5 1.0
OD2 A:ASP24 2.1 44.6 1.0
O A:HOH138 2.2 49.2 1.0
O A:HOH92 2.3 43.0 1.0
CG A:ASP24 3.2 51.5 1.0
CG A:ASP22 3.2 50.0 1.0
MN A:MN100 3.4 41.7 1.0
OD1 A:ASP24 3.5 44.7 1.0
OD1 A:ASP22 3.6 47.4 1.0
OG1 A:THR26 3.9 48.5 1.0
O A:HOH91 4.4 33.1 1.0
CB A:ASP22 4.4 51.2 1.0
CB A:ASP24 4.5 46.0 1.0
O A:THR26 4.8 35.3 1.0

Manganese binding site 4 out of 6 in 3uct

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Manganese binding site 4 out of 6 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn103

b:34.8
occ:0.74
 OE2 A:GLU31 2.1 42.4 1.0
O A:HOH94 2.2 42.7 1.0
O A:HOH114 2.2 43.3 1.0
O A:PHE19 2.2 34.9 1.0
O A:HOH93 2.3 40.9 1.0
CD A:GLU31 3.1 41.0 1.0
C A:PHE19 3.2 32.7 1.0
OE1 A:GLU31 3.4 41.7 1.0
CA A:PHE19 3.8 35.8 1.0
O A:HOH91 4.0 33.1 1.0
CB A:PHE19 4.1 31.2 1.0
N A:ASP20 4.2 32.9 1.0
N A:LYS21 4.3 36.5 1.0
O A:HOH130 4.4 46.3 1.0
O A:HOH95 4.4 50.7 1.0
CG A:GLU31 4.5 36.9 1.0
CA A:ASP20 4.6 34.4 1.0
CG A:LYS21 4.7 41.7 1.0
CB A:LYS21 4.9 45.6 1.0
C A:ASP20 5.0 38.8 1.0

Manganese binding site 5 out of 6 in 3uct

Go back to Manganese Binding Sites List in 3uct
Manganese binding site 5 out of 6 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn100

b:29.9
occ:1.00
 OD1 B:ASP20 2.1 33.9 1.0
O B:THR26 2.1 29.5 1.0
OD1 B:ASP24 2.1 31.5 1.0
O B:HOH85 2.1 35.8 1.0
OD1 B:ASP22 2.2 36.6 1.0
O A:HOH110 2.2 33.4 1.0
CG B:ASP20 3.1 33.1 1.0
CG B:ASP24 3.2 33.4 1.0
C B:THR26 3.2 32.2 1.0
CG B:ASP22 3.2 38.4 1.0
ZN B:ZN102 3.4 42.4 1.0
OD2 B:ASP22 3.6 35.9 1.0
OD2 B:ASP24 3.6 32.4 1.0
N B:THR26 3.8 32.0 1.0
OG1 B:THR26 3.9 31.8 1.0
OD2 B:ASP20 3.9 36.4 1.0
N B:ASP24 4.0 36.3 1.0
CA B:THR26 4.0 32.0 1.0
CA B:ASP20 4.1 31.1 1.0
CB B:ASP20 4.1 30.3 1.0
N B:ILE27 4.1 30.7 1.0
CA B:ILE27 4.2 33.4 1.0
OE2 A:GLU45 4.3 44.9 1.0
N B:ASP22 4.3 33.5 1.0
C B:ASP20 4.3 34.8 1.0
N B:GLY23 4.4 38.5 1.0
CB B:ASP24 4.4 31.3 1.0
CB B:ASP22 4.5 34.8 1.0
N B:GLY25 4.5 30.1 1.0
O B:HOH92 4.6 43.2 1.0
CB B:THR26 4.6 27.5 1.0
N B:LYS21 4.6 35.3 1.0
CA B:ASP24 4.6 32.2 1.0
OE1 B:GLU31 4.6 35.9 1.0
C B:ASP22 4.7 36.5 1.0
CA B:ASP22 4.7 35.1 1.0
C B:ASP24 4.8 34.7 1.0
O B:ASP20 4.9 37.1 1.0
C B:GLY25 5.0 33.7 1.0

Manganese binding site 6 out of 6 in 3uct

Go back to Manganese Binding Sites List in 3uct
Manganese binding site 6 out of 6 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn101

b:39.8
occ:1.00
 OD1 B:ASP56 2.2 40.7 1.0
OD1 B:ASP58 2.2 48.7 1.0
OD1 B:ASN60 2.2 46.0 1.0
O B:HOH88 2.2 36.3 1.0
O B:HOH89 2.2 47.0 1.0
O B:THR62 2.2 30.3 1.0
CG B:ASN60 3.1 42.9 1.0
CG B:ASP58 3.2 54.7 1.0
CG B:ASP56 3.3 47.8 1.0
C B:THR62 3.4 34.4 1.0
ND2 B:ASN60 3.5 47.2 1.0
OD2 B:ASP58 3.6 50.6 1.0
OG1 B:THR62 3.8 35.9 1.0
N B:THR62 3.9 35.5 1.0
O B:HOH94 4.0 42.7 1.0
N B:ASN60 4.0 46.6 1.0
OD2 B:ASP56 4.1 50.9 1.0
CA B:ASP56 4.1 50.8 1.0
O B:HOH93 4.1 47.9 1.0
CA B:THR62 4.2 34.8 1.0
CB B:ASP56 4.3 48.9 1.0
CB B:ASN60 4.3 48.9 1.0
N B:ILE63 4.4 32.1 1.0
N B:ASP58 4.5 53.6 1.0
N B:GLY59 4.5 57.1 1.0
CB B:ASP58 4.5 53.3 1.0
CA B:ILE63 4.6 33.3 1.0
C B:ASP56 4.6 61.2 1.0
CA B:ASN60 4.6 40.3 1.0
OE1 B:GLU67 4.6 32.1 1.0
CB B:THR62 4.6 32.1 1.0
N B:GLY61 4.7 44.0 1.0
C B:ASP58 4.7 54.5 1.0
N B:ALA57 4.7 55.4 1.0
CA B:ASP58 4.8 53.1 1.0
C B:ASN60 4.9 44.5 1.0
CG2 B:ILE63 5.0 41.3 1.0

Reference:

F.T.Senguen, Z.Grabarek. X-Ray Structures of Magnesium and Manganese Complexes with the N-Terminal Domain of Calmodulin: Insights Into the Mechanism and Specificity of Metal Ion Binding to An Ef-Hand. Biochemistry V. 51 6182 2012.
ISSN: ISSN 0006-2960
PubMed: 22803592
DOI: 10.1021/BI300698H
Page generated: Sat Oct 5 18:05:13 2024

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