Magnesium in PDB 6j4m: Thermal Treated Soybean Seed H-2 Ferritin

Enzymatic activity of Thermal Treated Soybean Seed H-2 Ferritin

All present enzymatic activity of Thermal Treated Soybean Seed H-2 Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Thermal Treated Soybean Seed H-2 Ferritin, PDB code: 6j4m was solved by X.Zhang, J.Zang, H.Chen, K.Zhou, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.06 / 2.60
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 149.902, 149.902, 149.902, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermal Treated Soybean Seed H-2 Ferritin (pdb code 6j4m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Thermal Treated Soybean Seed H-2 Ferritin, PDB code: 6j4m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6j4m

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Magnesium binding site 1 out of 7 in the Thermal Treated Soybean Seed H-2 Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermal Treated Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:34.7
occ:0.33
 OE2 H:GLU167 2.7 46.5 1.0
OD1 H:ASP164 2.7 46.2 1.0
CG H:ASP164 3.8 42.8 1.0
O H:HOH424 3.8 53.4 0.3
O H:HOH431 3.8 57.6 0.3
CD H:GLU167 3.9 45.1 1.0
CB H:ASP164 4.1 37.5 1.0
OE1 H:GLU167 4.4 51.8 1.0
CA H:ASP164 4.5 41.1 1.0
OG H:SER168 4.8 54.7 1.0
OD2 H:ASP164 4.8 45.8 1.0
CB H:GLU167 4.9 41.2 1.0

Magnesium binding site 2 out of 7 in 6j4m

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Magnesium binding site 2 out of 7 in the Thermal Treated Soybean Seed H-2 Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermal Treated Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:44.3
occ:1.00
 OD2 H:ASP44 1.9 41.5 1.0
O H:HOH409 2.3 39.9 1.0
O H:HOH404 2.5 49.4 1.0
CG H:ASP44 2.7 42.0 1.0
OD1 H:ASP44 2.9 47.4 1.0
CB H:ASP44 4.1 43.1 1.0
OD1 H:ASN157 4.4 49.4 1.0
O H:HOH430 4.5 33.2 1.0
ND2 H:ASN157 4.9 45.3 1.0

Magnesium binding site 3 out of 7 in 6j4m

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Magnesium binding site 3 out of 7 in the Thermal Treated Soybean Seed H-2 Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermal Treated Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg303

b:44.3
occ:1.00
 O H:HOH411 2.1 51.0 1.0
OE1 H:GLU56 2.1 42.5 1.0
OE2 H:GLU91 2.3 46.7 1.0
O H:HOH420 2.3 44.5 1.0
ND1 H:HIS94 2.4 48.7 1.0
CD H:GLU56 3.0 40.4 1.0
CE1 H:HIS94 3.1 42.3 1.0
OE2 H:GLU56 3.2 43.7 1.0
CD H:GLU91 3.3 51.9 1.0
CG H:HIS94 3.5 41.0 1.0
OE1 H:GLU91 3.7 48.2 1.0
OE1 H:GLN174 3.8 50.8 1.0
CG2 H:THR143 3.9 39.7 1.0
CB H:HIS94 3.9 38.7 1.0
MG H:MG304 4.3 64.0 1.0
NE2 H:HIS94 4.3 41.4 1.0
CG H:GLU56 4.4 36.0 1.0
CD2 H:HIS94 4.5 44.1 1.0
CG H:GLU91 4.6 40.6 1.0
CA H:GLU91 4.7 41.1 1.0
CB H:GLU91 4.9 41.4 1.0
CD H:GLN174 4.9 46.0 1.0
CB H:GLU56 4.9 34.8 1.0

Magnesium binding site 4 out of 7 in 6j4m

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Magnesium binding site 4 out of 7 in the Thermal Treated Soybean Seed H-2 Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermal Treated Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg304

b:64.0
occ:1.00
 O H:HOH420 2.3 44.5 1.0
O H:HOH423 2.4 54.1 1.0
OE2 H:GLU140 2.5 51.5 1.0
OE1 H:GLU91 2.6 48.2 1.0
OE1 H:GLU140 2.9 48.8 1.0
CD H:GLU140 3.0 45.6 1.0
CD H:GLU91 3.7 51.9 1.0
OG H:SER177 3.8 55.2 1.0
CB H:SER177 3.9 42.5 1.0
OE2 H:GLU91 4.1 46.7 1.0
MG H:MG303 4.3 44.3 1.0
CE1 H:HIS94 4.3 42.3 1.0
OE1 H:GLN174 4.3 50.8 1.0
CG H:GLU140 4.4 42.2 1.0
NE2 H:GLN174 4.4 46.2 1.0
CD H:GLN174 4.7 46.0 1.0
ND1 H:HIS94 4.9 48.7 1.0
CG H:GLU91 5.0 40.6 1.0

Magnesium binding site 5 out of 7 in 6j4m

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Magnesium binding site 5 out of 7 in the Thermal Treated Soybean Seed H-2 Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermal Treated Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:36.9
occ:0.33
 OE1 A:GLU167 2.0 48.7 1.0
OD1 A:ASP164 2.3 51.6 1.0
O A:HOH416 3.0 52.7 0.3
CD A:GLU167 3.2 50.6 1.0
CG A:ASP164 3.5 44.5 1.0
CG A:GLU167 3.9 46.8 1.0
CB A:ASP164 4.1 40.8 1.0
O A:HOH404 4.1 48.2 1.0
OE2 A:GLU167 4.2 42.9 1.0
OD2 A:ASP164 4.5 44.1 1.0
O A:HOH432 4.5 50.0 1.0
CA A:ASP164 4.5 42.0 1.0
OG A:SER168 4.7 55.7 1.0

Magnesium binding site 6 out of 7 in 6j4m

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Magnesium binding site 6 out of 7 in the Thermal Treated Soybean Seed H-2 Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermal Treated Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:46.3
occ:1.00
 O A:HOH410 2.0 49.8 1.0
OE1 A:GLU56 2.0 44.5 1.0
OE2 A:GLU91 2.2 45.9 1.0
O A:HOH417 2.3 44.3 1.0
ND1 A:HIS94 2.4 49.9 1.0
CD A:GLU56 3.0 42.9 1.0
CD A:GLU91 3.2 48.1 1.0
OE2 A:GLU56 3.2 44.1 1.0
CE1 A:HIS94 3.2 45.5 1.0
CG A:HIS94 3.5 43.7 1.0
OE1 A:GLU91 3.6 51.6 1.0
CG2 A:THR143 3.8 47.0 1.0
OE1 A:GLN174 3.9 51.3 1.0
CB A:HIS94 3.9 40.2 1.0
CG A:GLU56 4.4 36.8 1.0
NE2 A:HIS94 4.4 45.9 1.0
MG A:MG303 4.5 62.6 1.0
CG A:GLU91 4.5 39.1 1.0
CD2 A:HIS94 4.6 45.1 1.0
CA A:GLU91 4.6 41.1 1.0
CB A:GLU91 4.8 41.0 1.0
CB A:GLU56 4.8 36.3 1.0
CB A:THR143 4.9 43.6 1.0
CD A:GLN174 5.0 43.9 1.0
OG1 A:THR143 5.0 45.8 1.0

Magnesium binding site 7 out of 7 in 6j4m

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Magnesium binding site 7 out of 7 in the Thermal Treated Soybean Seed H-2 Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermal Treated Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:62.6
occ:1.00
 O A:HOH417 2.5 44.3 1.0
OE2 A:GLU140 2.5 44.7 1.0
OE1 A:GLU91 2.8 51.6 1.0
CD A:GLU140 3.2 46.0 1.0
OE1 A:GLU140 3.3 46.8 1.0
OG A:SER177 3.4 53.2 1.0
CB A:SER177 3.7 38.5 1.0
CD A:GLU91 3.9 48.1 1.0
CE1 A:HIS94 4.3 45.5 1.0
OE1 A:GLN174 4.3 51.3 1.0
OE2 A:GLU91 4.4 45.9 1.0
NE2 A:GLN174 4.4 45.0 1.0
MG A:MG302 4.5 46.3 1.0
CG A:GLU140 4.6 42.5 1.0
CD A:GLN174 4.8 43.9 1.0
ND1 A:HIS94 4.9 49.9 1.0

Reference:

X.Zhang, J.Zang, H.Chen, K.Zhou, T.Zhang, C.Lv, G.Zhao. Thermostability of Protein Nanocages: the Effect of Natural Extra Peptide on the Exterior Surface. Rsc Adv V. 9 24777 2019.
ISSN: ESSN 2046-2069
DOI: 10.1039/C9RA04785
Page generated: Mon Dec 14 22:59:31 2020

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