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Magnesium in PDB 5mfm: Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5

Protein crystallography data

The structure of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5, PDB code: 5mfm was solved by S.Hansen, P.Ernst, C.Reichen, C.Ewald, P.Mittl, A.Plueckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.69 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.760, 89.390, 123.850, 90.00, 97.07, 90.00
R / Rfree (%) 21.7 / 25.1

Other elements in 5mfm:

The structure of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 also contains other interesting chemical elements:

Calcium (Ca) 23 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 (pdb code 5mfm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5, PDB code: 5mfm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5mfm

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Magnesium binding site 1 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:58.8
occ:1.00
 ND2 A:ASN192 3.0 52.1 1.0
OD1 A:ASN192 3.7 53.7 1.0
CG A:ASN192 3.8 59.6 1.0
CB A:GLU151 4.2 51.2 1.0
CB A:GLN194 4.5 41.4 1.0
OE1 A:GLN194 4.6 86.7 1.0
CG A:GLU151 4.6 60.5 1.0
CD A:GLN194 4.6 88.0 1.0
NE2 A:GLN194 4.7 82.1 1.0

Magnesium binding site 2 out of 10 in 5mfm

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Magnesium binding site 2 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:55.4
occ:1.00
 ND2 A:ASN234 2.9 43.0 1.0
OD1 A:ASN234 3.4 46.9 1.0
CG A:ASN234 3.6 55.5 1.0
OE1 A:GLN236 3.7 76.3 1.0
CB A:GLU193 3.9 42.1 1.0
CB A:GLN236 4.1 42.8 1.0
CG A:GLU193 4.2 53.1 1.0
CD A:GLN236 4.3 79.8 1.0
CG A:GLN236 4.7 60.0 1.0
CG1 A:ILE237 4.8 46.1 1.0
CD1 A:ILE237 4.9 54.3 1.0

Magnesium binding site 3 out of 10 in 5mfm

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Magnesium binding site 3 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:63.0
occ:1.00
 OE1 B:GLN236 3.1 89.6 1.0
ND2 B:ASN234 3.3 60.6 1.0
OD1 B:ASN234 3.4 56.7 1.0
CG B:ASN234 3.8 67.7 1.0
CD B:GLN236 3.9 93.8 1.0
CB B:GLU193 3.9 47.2 1.0
CB B:GLN236 4.1 51.1 1.0
CG B:GLU193 4.4 57.0 1.0
CG B:GLN236 4.5 70.0 1.0
NE2 B:GLN236 4.6 88.4 1.0
O B:GLU193 4.7 48.4 1.0
C B:GLU193 5.0 49.0 1.0
CA B:GLU193 5.0 45.6 1.0

Magnesium binding site 4 out of 10 in 5mfm

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Magnesium binding site 4 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:70.7
occ:1.00
 NE2 B:GLN71 2.2 74.9 1.0
CD B:GLN71 3.2 86.8 1.0
ND2 B:ASN108 3.4 60.8 1.0
OD1 B:ASN108 3.5 60.3 1.0
OE1 B:GLN71 3.5 83.4 1.0
CB B:GLN110 3.9 47.0 1.0
CG B:ASN108 3.9 67.0 1.0
CG B:GLN110 4.3 63.9 1.0
CB B:GLU67 4.3 56.0 1.0
CG B:GLN71 4.5 70.6 1.0
CG B:GLU67 4.7 66.7 1.0
CD1 B:ILE111 4.9 58.5 1.0

Magnesium binding site 5 out of 10 in 5mfm

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Magnesium binding site 5 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:80.0
occ:1.00
 O C:GLU151 2.6 52.2 1.0
OE1 C:GLN194 2.8 84.5 1.0
O C:HOH515 2.9 43.7 1.0
C C:GLU151 3.3 54.2 1.0
OE1 E:GLN194 3.3 83.7 1.0
CD1 C:ILE195 3.4 59.0 1.0
CB C:GLN155 3.4 51.8 1.0
CB C:GLU151 3.6 53.2 1.0
CD E:GLN194 3.6 85.9 1.0
NE2 E:GLN194 3.8 77.4 1.0
CA C:GLU151 3.9 51.6 1.0
CD C:GLN194 3.9 86.7 1.0
CG C:GLN155 4.0 73.9 1.0
N C:GLN152 4.0 52.1 1.0
CB E:GLN194 4.2 50.4 1.0
CG1 C:ILE195 4.3 52.2 1.0
CA C:GLN152 4.4 51.5 1.0
CG C:GLU151 4.5 64.1 1.0
CG E:GLN194 4.5 63.0 1.0
CG C:GLN194 4.6 63.0 1.0
CA C:GLN155 4.6 50.1 1.0
OD1 E:ASN192 4.7 58.5 1.0
N C:GLN155 4.8 51.4 1.0
CB C:GLN194 4.8 46.3 1.0
ND2 C:ASN192 4.8 57.3 1.0
CD C:GLN155 4.8 99.9 1.0
NE2 C:GLN194 4.9 79.0 1.0
OD1 C:ASN192 5.0 54.4 1.0

Magnesium binding site 6 out of 10 in 5mfm

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Magnesium binding site 6 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg406

b:52.1
occ:1.00
 ND2 C:ASN150 2.8 64.2 1.0
ND2 E:ASN234 2.9 67.2 1.0
OD1 C:ASN150 3.2 65.5 1.0
CG C:ASN150 3.4 73.1 1.0
OD1 E:ASN234 3.5 67.6 1.0
CG E:ASN234 3.6 78.0 1.0
OE1 E:GLN236 3.6 97.9 1.0
CB C:GLN152 3.8 53.7 1.0
CB C:GLU109 3.9 67.6 1.0
CB E:GLU193 4.1 58.4 1.0
CG C:GLU109 4.1 76.5 1.0
CG C:GLN152 4.2 69.2 1.0
CG1 C:ILE153 4.4 60.2 1.0
CB E:GLN236 4.5 67.5 1.0
CD E:GLN236 4.6 0.1 1.0
CD1 C:ILE153 4.6 66.2 1.0
CG E:GLU193 4.6 71.4 1.0
OE1 C:GLN113 4.7 0.8 1.0
CB C:ASN150 4.9 55.4 1.0
O C:GLU109 5.0 68.0 1.0

Magnesium binding site 7 out of 10 in 5mfm

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Magnesium binding site 7 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg406

b:77.4
occ:1.00
 NE2 D:GLN71 2.9 98.5 1.0
ND2 D:ASN108 3.0 64.4 1.0
ND2 F:ASN276 3.1 70.5 1.0
NE2 F:GLN239 3.2 86.1 1.0
OD1 D:ASN108 3.2 59.7 1.0
CG D:ASN108 3.5 70.5 1.0
CB D:GLN110 3.8 53.6 1.0
OD1 F:ASN276 3.8 65.8 1.0
CB F:GLU235 3.9 53.6 1.0
CG F:ASN276 3.9 75.7 1.0
CD D:GLN71 4.1 0.2 1.0
CG D:GLN110 4.2 71.3 1.0
CD F:GLN239 4.2 95.0 1.0
CG F:GLU235 4.3 65.5 1.0
CB D:GLU67 4.3 64.4 1.0
CG D:GLU67 4.6 76.0 1.0
CD1 D:ILE111 4.6 64.2 1.0
CG1 D:ILE111 4.7 59.0 1.0
OE1 F:GLN239 4.7 90.9 1.0
CB F:GLN278 4.7 51.9 1.0
OE1 D:GLN71 4.7 0.7 1.0
CG D:GLN71 4.9 83.2 1.0
CG1 F:ILE279 5.0 56.6 1.0
O F:GLU235 5.0 52.3 1.0

Magnesium binding site 8 out of 10 in 5mfm

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Magnesium binding site 8 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:62.5
occ:1.00
 ND2 E:ASN108 2.7 54.9 1.0
NE2 C:GLN239 2.8 66.9 1.0
NE2 E:GLN71 2.8 75.5 1.0
ND2 C:ASN276 2.8 48.7 1.0
OD1 E:ASN108 3.3 49.5 1.0
CG E:ASN108 3.4 61.5 1.0
CB C:GLU235 3.6 46.7 1.0
OD1 C:ASN276 3.6 44.6 1.0
CG C:ASN276 3.7 57.6 1.0
CG C:GLU235 3.7 56.2 1.0
CD E:GLN71 4.0 86.6 1.0
CB E:GLN110 4.0 44.4 1.0
CD C:GLN239 4.0 79.4 1.0
CG E:GLU67 4.2 67.5 1.0
CB E:GLU67 4.2 55.5 1.0
CG E:GLN110 4.6 57.7 1.0
OE1 E:GLN71 4.6 84.4 1.0
OE1 C:GLN239 4.6 75.2 1.0
O C:HOH502 4.6 60.1 1.0
CB C:GLN278 4.8 48.1 1.0
CA C:GLU235 4.9 45.1 1.0
CG1 C:ILE279 4.9 52.3 1.0
CB E:ASN108 4.9 47.8 1.0
O C:GLU235 4.9 46.4 1.0
CD1 C:ILE279 5.0 58.5 1.0
CD C:GLU235 5.0 67.1 1.0

Magnesium binding site 9 out of 10 in 5mfm

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Magnesium binding site 9 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:56.0
occ:1.00
 O C:HOH511 2.8 39.6 1.0
ND2 C:ASN234 3.0 39.2 1.0
O E:HOH511 3.1 53.6 1.0
ND2 E:ASN150 3.1 65.2 1.0
OD1 E:ASN150 3.2 66.0 1.0
CG E:ASN150 3.6 73.1 1.0
OD1 C:ASN234 3.6 35.2 1.0
CG C:ASN234 3.7 50.2 1.0
CB E:GLN152 3.7 52.6 1.0
CB C:GLU193 3.9 46.6 1.0
CG E:GLN152 4.1 64.9 1.0
CB E:GLU109 4.1 49.2 1.0
OE1 C:GLN236 4.2 81.4 1.0
CB C:GLN236 4.3 44.6 1.0
CG C:GLU193 4.3 55.8 1.0
CG E:GLU109 4.4 59.6 1.0
CD C:GLN236 4.5 83.4 1.0
CG1 E:ILE153 4.7 54.6 1.0
CG C:GLN236 4.8 61.3 1.0
O C:GLU193 4.8 47.0 1.0
CD1 E:ILE153 4.9 59.5 1.0
CG1 C:ILE237 4.9 49.9 1.0
CD1 C:ILE237 4.9 59.8 1.0

Magnesium binding site 10 out of 10 in 5mfm

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Magnesium binding site 10 out of 10 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg405

b:68.9
occ:1.00
 O F:HOH525 2.8 63.6 1.0
ND2 D:ASN150 2.8 60.1 1.0
ND2 F:ASN234 3.0 62.0 1.0
O F:HOH534 3.1 57.0 1.0
OD1 F:ASN234 3.4 58.0 1.0
OD1 D:ASN150 3.5 62.7 1.0
CG D:ASN150 3.6 70.0 1.0
CG F:ASN234 3.7 68.8 1.0
CB F:GLU193 3.9 55.7 1.0
CB D:GLU109 4.0 54.7 1.0
CB F:GLN236 4.2 48.8 1.0
CG D:GLU109 4.2 65.4 1.0
CB D:GLN152 4.2 49.8 1.0
CG F:GLU193 4.2 67.0 1.0
CG F:GLN236 4.5 66.0 1.0
CG D:GLN152 4.6 63.6 1.0
O D:HOH506 4.7 57.1 1.0
CD1 F:ILE237 4.7 54.7 1.0
CG1 F:ILE237 4.8 52.4 1.0
O F:GLU193 4.9 54.3 1.0

Reference:

S.Hansen, P.Ernst, S.L.B.Konig, C.Reichen, C.Ewald, D.Nettels, P.R.E.Mittl, B.Schuler, A.Pluckthun. Curvature of Designed Armadillo Repeat Proteins Allows Modular Peptide Binding. J. Struct. Biol. V. 201 108 2018.
ISSN: ESSN 1095-8657
PubMed: 28864298
DOI: 10.1016/J.JSB.2017.08.009
Page generated: Sun Sep 29 21:21:41 2024

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