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Magnesium in PDB 3ucw: Structure of MG2+ Bound N-Terminal Domain of Calmodulin

Protein crystallography data

The structure of Structure of MG2+ Bound N-Terminal Domain of Calmodulin, PDB code: 3ucw 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) 39.32 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.435, 43.040, 53.689, 68.44, 88.62, 79.44
R / Rfree (%) 19.6 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin (pdb code 3ucw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin, PDB code: 3ucw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3ucw

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Magnesium binding site 1 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg100

b:23.6
occ:1.00
 OD1 A:ASP20 2.0 24.8 1.0
O A:HOH224 2.1 24.2 1.0
O A:HOH208 2.1 23.9 1.0
OD1 A:ASP22 2.1 24.2 1.0
OD1 A:ASP24 2.1 29.1 1.0
O A:THR26 2.2 24.1 1.0
CG A:ASP22 3.1 33.7 1.0
CG A:ASP24 3.1 30.2 1.0
CG A:ASP20 3.2 29.8 1.0
C A:THR26 3.3 25.6 1.0
OD2 A:ASP22 3.3 29.5 1.0
OD2 A:ASP24 3.6 31.3 1.0
N A:THR26 3.8 26.1 1.0
CA A:ASP20 4.0 20.4 1.0
CA A:THR26 4.0 21.9 1.0
CB A:ASP20 4.0 24.5 1.0
OD2 A:ASP20 4.1 27.5 1.0
N A:ASP24 4.1 28.7 1.0
O D:HOH205 4.1 37.2 1.0
O A:HOH206 4.1 28.0 1.0
O A:HOH234 4.3 30.3 1.0
CB A:ASP24 4.3 29.1 1.0
N A:ILE27 4.3 21.7 1.0
CB A:THR26 4.4 39.5 1.0
C A:ASP20 4.4 24.9 1.0
N A:GLY23 4.5 25.4 1.0
CB A:ASP22 4.5 33.2 1.0
N A:GLY25 4.5 32.8 1.0
N A:ASP22 4.6 28.8 1.0
CA A:ASP24 4.6 32.2 1.0
CA A:ILE27 4.6 20.8 1.0
O A:ASP20 4.7 23.8 1.0
C A:ASP24 4.7 37.8 1.0
CA A:ASP22 4.8 28.4 1.0
C A:ASP22 4.9 34.3 1.0
N A:LYS21 4.9 22.4 0.8
CG2 A:ILE27 4.9 21.9 1.0
C A:GLY25 4.9 32.1 1.0

Magnesium binding site 2 out of 10 in 3ucw

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Magnesium binding site 2 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:20.4
occ:1.00
 O A:THR62 2.0 21.1 1.0
O A:HOH210 2.0 20.6 1.0
O A:HOH212 2.1 21.5 1.0
O A:HOH209 2.1 24.5 1.0
O A:HOH211 2.1 20.1 1.0
OG1 A:THR62 2.1 22.1 1.0
C A:THR62 2.9 22.9 1.0
CB A:THR62 3.2 26.6 1.0
CA A:THR62 3.4 19.9 1.0
N A:THR62 3.6 22.9 1.0
OE1 A:GLU67 4.0 22.0 1.0
N A:ILE63 4.0 23.5 1.0
OD1 A:ASP58 4.0 23.3 1.0
O A:HOH232 4.1 26.6 1.0
OE2 A:GLU67 4.2 25.3 1.0
OD2 A:ASP58 4.3 26.6 1.0
O A:HOH231 4.3 31.1 1.0
O A:HOH218 4.4 32.4 1.0
O A:VAL55 4.4 26.9 1.0
CA A:ILE63 4.4 21.4 1.0
CG2 A:THR62 4.5 24.6 1.0
CD A:GLU67 4.5 21.4 1.0
CG A:ASP58 4.6 25.9 1.0
CB A:ASN60 4.7 23.7 1.0
OD1 A:ASP56 4.8 29.9 1.0
CB B:PRO66 4.8 18.8 1.0
C A:GLY61 4.9 22.7 1.0

Magnesium binding site 3 out of 10 in 3ucw

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Magnesium binding site 3 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:22.6
occ:1.00
 O B:HOH201 2.0 20.4 1.0
O B:HOH202 2.1 25.8 1.0
O A:HOH217 2.1 22.8 1.0
O B:HOH212 2.1 26.5 1.0
OD2 B:ASP64 2.1 22.4 1.0
OD2 A:ASP64 2.1 20.9 1.0
CG A:ASP64 3.1 24.1 1.0
CG B:ASP64 3.1 20.1 1.0
OD1 A:ASP64 3.4 25.7 1.0
OD1 B:ASP64 3.5 23.5 1.0
O A:HOH218 4.0 32.4 1.0
O B:HOH203 4.0 28.7 1.0
O B:HOH225 4.3 29.4 1.0
CB A:ASP64 4.4 19.2 1.0
CB B:ASP64 4.4 26.7 1.0
OE2 B:GLU67 4.5 23.8 1.0
CD B:GLU67 4.5 24.2 1.0
OE2 A:GLU67 4.5 25.3 1.0
CD A:GLU67 4.5 21.4 1.0
CG B:GLU67 4.7 19.8 1.0
CG A:GLU67 4.8 16.1 1.0
OE1 B:GLU67 4.9 23.6 1.0
OE1 A:GLU67 4.9 22.0 1.0

Magnesium binding site 4 out of 10 in 3ucw

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Magnesium binding site 4 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg100

b:33.8
occ:1.00
 O B:HOH205 2.1 41.9 1.0
O B:HOH204 2.1 36.0 1.0
OD1 B:ASP20 2.1 32.9 1.0
OD1 B:ASP22 2.1 46.1 1.0
OD1 B:ASP24 2.1 38.4 1.0
O B:THR26 2.2 36.5 1.0
CG B:ASP22 3.0 44.4 1.0
CG B:ASP24 3.0 44.2 1.0
OD2 B:ASP22 3.2 46.4 1.0
CG B:ASP20 3.3 33.4 1.0
C B:THR26 3.4 37.1 1.0
OD2 B:ASP24 3.4 55.6 1.0
OG1 B:THR26 3.9 39.0 1.0
N B:THR26 3.9 34.2 1.0
CA B:ASP20 4.0 37.2 1.0
N B:ASP24 4.1 37.5 1.0
CA B:THR26 4.1 31.8 1.0
CB B:ASP20 4.1 33.0 1.0
OD2 B:ASP20 4.2 35.0 1.0
CB B:ASP24 4.2 38.0 1.0
O B:HOH215 4.3 42.5 1.0
N B:ASP22 4.3 39.9 1.0
CB B:ASP22 4.3 39.6 1.0
N B:ILE27 4.4 33.4 1.0
C B:ASP20 4.4 33.9 1.0
N B:LYS21 4.5 33.8 0.8
N B:GLY23 4.5 44.9 1.0
N B:GLY25 4.5 34.7 1.0
CA B:ASP24 4.5 38.9 1.0
CA B:ILE27 4.6 34.2 1.0
CB B:THR26 4.7 36.1 1.0
CA B:ASP22 4.7 42.9 1.0
C B:ASP24 4.8 43.5 1.0
C B:ASP22 4.8 46.9 1.0

Magnesium binding site 5 out of 10 in 3ucw

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Magnesium binding site 5 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:27.2
occ:1.00
 O B:HOH209 2.1 27.1 1.0
O B:HOH217 2.1 24.6 1.0
O B:HOH208 2.1 27.4 1.0
O B:HOH207 2.1 26.0 1.0
O B:THR62 2.1 25.4 1.0
OG1 B:THR62 2.2 27.7 1.0
C B:THR62 2.9 28.2 1.0
CB B:THR62 3.2 33.3 1.0
CA B:THR62 3.4 29.1 1.0
N B:THR62 3.5 30.6 1.0
OE1 B:GLU67 3.9 23.6 1.0
N B:ILE63 4.0 23.4 1.0
OD1 B:ASP58 4.1 31.1 1.0
OE2 B:GLU67 4.2 23.8 1.0
OD2 B:ASP58 4.2 29.6 1.0
O B:HOH203 4.4 28.7 1.0
O B:VAL55 4.4 27.8 1.0
CG2 B:THR62 4.5 32.2 1.0
CD B:GLU67 4.5 24.2 1.0
CA B:ILE63 4.5 28.0 1.0
CB B:ASN60 4.5 35.6 1.0
CG B:ASP58 4.6 31.9 1.0
OD1 B:ASP56 4.6 33.1 1.0
C B:GLY61 4.8 31.8 1.0
CB A:PRO66 4.9 25.2 1.0
N B:GLY61 4.9 31.9 1.0

Magnesium binding site 6 out of 10 in 3ucw

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Magnesium binding site 6 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg100

b:31.6
occ:1.00
 OD1 C:ASP20 2.0 28.1 1.0
O C:HOH209 2.0 33.5 1.0
OD1 C:ASP24 2.0 38.5 1.0
O C:HOH208 2.1 30.2 1.0
O C:THR26 2.1 29.2 1.0
OD1 C:ASP22 2.1 30.6 1.0
CG C:ASP24 3.0 40.1 1.0
CG C:ASP22 3.1 43.7 1.0
CG C:ASP20 3.2 31.9 1.0
C C:THR26 3.2 32.9 1.0
OD2 C:ASP22 3.4 31.1 1.0
OD2 C:ASP24 3.5 38.4 1.0
N C:THR26 3.7 30.0 1.0
OG1 C:THR26 3.9 52.1 1.0
CA C:THR26 4.0 26.9 1.0
OD2 C:ASP20 4.0 34.1 1.0
N C:ASP24 4.0 33.2 1.0
O C:HOH225 4.1 45.6 1.0
CA C:ASP20 4.1 27.7 1.0
CB C:ASP20 4.1 28.9 1.0
CB C:ASP24 4.2 41.3 1.0
N C:ILE27 4.3 24.7 1.0
C C:ASP20 4.4 28.0 1.0
N C:ASP22 4.4 35.0 1.0
CB C:ASP22 4.4 37.8 1.0
N C:GLY25 4.5 32.3 1.0
N C:GLY23 4.5 37.5 1.0
CA C:ASP24 4.5 38.1 1.0
CB C:THR26 4.5 40.0 1.0
CA C:ILE27 4.6 32.3 1.0
C C:ASP24 4.7 36.4 1.0
N C:LYS21 4.7 30.1 0.8
O C:ASP20 4.7 32.9 1.0
CA C:ASP22 4.8 36.1 1.0
C C:ASP22 4.8 42.2 1.0
C C:GLY25 4.9 36.8 1.0

Magnesium binding site 7 out of 10 in 3ucw

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Magnesium binding site 7 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:21.0
occ:1.00
 O C:THR62 2.1 21.2 1.0
O C:HOH205 2.1 18.2 1.0
O C:HOH216 2.1 20.4 1.0
O C:HOH204 2.1 20.0 1.0
O C:HOH206 2.1 18.9 1.0
OG1 C:THR62 2.2 20.3 1.0
C C:THR62 3.0 23.0 1.0
CB C:THR62 3.3 21.5 1.0
CA C:THR62 3.5 21.0 1.0
N C:THR62 3.6 21.1 1.0
OE1 C:GLU67 3.9 17.4 1.0
O C:HOH217 4.0 26.5 1.0
N C:ILE63 4.0 23.2 1.0
OD1 C:ASP58 4.0 19.7 1.0
OE2 C:GLU67 4.2 20.2 1.0
O C:HOH218 4.2 31.5 1.0
OD2 C:ASP58 4.3 25.4 1.0
O C:HOH207 4.3 28.4 1.0
O C:VAL55 4.3 21.6 1.0
CD C:GLU67 4.5 19.2 1.0
CA C:ILE63 4.5 23.0 1.0
CB C:ASN60 4.5 21.2 1.0
CG2 C:THR62 4.6 22.5 1.0
CG C:ASP58 4.6 24.5 1.0
OD1 C:ASP56 4.7 25.2 1.0
C C:GLY61 4.9 23.8 1.0

Magnesium binding site 8 out of 10 in 3ucw

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Magnesium binding site 8 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:22.4
occ:1.00
 OD2 C:ASP64 2.0 21.3 1.0
O C:HOH202 2.1 22.2 1.0
O C:HOH203 2.1 22.1 1.0
O C:HOH219 2.1 24.4 1.0
O C:HOH220 2.1 24.2 1.0
CG C:ASP64 3.1 25.0 1.0
OD1 C:ASP64 3.4 19.3 1.0
O C:HOH207 3.9 28.4 1.0
O C:HOH221 4.0 33.5 1.0
CB C:ASP64 4.3 19.0 1.0
OE2 C:GLU67 4.4 20.2 1.0
CD C:GLU67 4.5 19.2 1.0
OE1 C:GLU67 4.8 17.4 1.0
CG C:GLU67 4.8 19.3 1.0
O C:HOH218 4.9 31.5 1.0
O C:HOH216 5.0 20.4 1.0

Magnesium binding site 9 out of 10 in 3ucw

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Magnesium binding site 9 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg100

b:31.6
occ:1.00
 OD1 D:ASP20 2.0 35.8 1.0
O D:HOH201 2.1 29.0 1.0
OD1 D:ASP24 2.1 34.2 1.0
OD1 D:ASP22 2.1 31.2 1.0
O D:HOH202 2.1 33.1 1.0
O D:THR26 2.1 26.3 1.0
CG D:ASP22 3.0 27.8 1.0
CG D:ASP24 3.0 35.7 1.0
CG D:ASP20 3.2 32.1 1.0
C D:THR26 3.3 29.5 1.0
OD2 D:ASP22 3.3 41.4 1.0
OD2 D:ASP24 3.5 44.4 1.0
OG1 D:THR26 3.8 35.5 1.0
N D:THR26 3.9 29.1 1.0
OD2 D:ASP20 4.0 35.0 1.0
CA D:THR26 4.1 27.4 1.0
N D:ASP24 4.1 26.8 1.0
CA D:ASP20 4.1 30.5 1.0
CB D:ASP20 4.1 30.2 1.0
CB D:ASP24 4.2 32.9 1.0
N D:ILE27 4.3 24.0 1.0
C D:ASP20 4.4 31.7 1.0
CB D:ASP22 4.4 38.6 1.0
N D:ASP22 4.4 30.4 1.0
N D:GLY23 4.5 30.5 1.0
CA D:ILE27 4.5 30.2 1.0
N D:GLY25 4.5 35.2 1.0
CA D:ASP24 4.6 32.8 1.0
CB D:THR26 4.6 32.0 1.0
N D:LYS21 4.7 33.2 0.7
CA D:ASP22 4.7 30.6 1.0
C D:ASP22 4.8 34.0 1.0
O D:ASP20 4.8 30.3 1.0
C D:ASP24 4.8 37.7 1.0
C D:GLY25 5.0 34.0 1.0

Magnesium binding site 10 out of 10 in 3ucw

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Magnesium binding site 10 out of 10 in the Structure of MG2+ Bound N-Terminal Domain of Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of MG2+ Bound N-Terminal Domain of Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:25.9
occ:1.00
 O D:HOH203 2.0 26.7 1.0
O D:HOH204 2.1 23.9 1.0
O D:HOH212 2.1 23.3 1.0
O D:THR62 2.1 23.6 1.0
O D:HOH230 2.1 25.1 1.0
OG1 D:THR62 2.2 26.8 1.0
C D:THR62 2.9 23.4 1.0
CB D:THR62 3.2 27.9 1.0
CA D:THR62 3.4 26.0 1.0
N D:THR62 3.6 28.0 1.0
OE1 D:GLU67 3.9 20.8 1.0
N D:ILE63 4.0 26.6 1.0
OE2 D:GLU67 4.1 22.4 1.0
OD1 D:ASP58 4.1 27.2 1.0
OD2 D:ASP58 4.3 28.4 1.0
O D:VAL55 4.3 26.1 1.0
CA D:ILE63 4.4 23.5 1.0
CD D:GLU67 4.4 23.4 1.0
CG2 D:THR62 4.5 28.6 1.0
CG D:ASP58 4.7 30.6 1.0
OD1 D:ASP56 4.7 30.2 1.0
CB D:ASN60 4.8 32.8 1.0
C D:GLY61 4.9 32.6 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: Thu Aug 15 12:27:40 2024

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