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Magnesium in PDB 6j4j: Soybean Seed H-2 Ferritin

Enzymatic activity of Soybean Seed H-2 Ferritin

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

Protein crystallography data

The structure of Soybean Seed H-2 Ferritin, PDB code: 6j4j was solved by X.Zhang, J.Zang, H.Chen, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.70 / 2.10
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 130.827, 130.827, 171.256, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Soybean Seed H-2 Ferritin (pdb code 6j4j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Soybean Seed H-2 Ferritin, PDB code: 6j4j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6j4j

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Magnesium binding site 1 out of 10 in the 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 Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:39.1
occ:1.00
 OE2 H:GLU91 2.0 41.6 1.0
OE1 H:GLU56 2.0 36.2 1.0
ND1 H:HIS94 2.2 37.6 1.0
O H:HOH406 2.4 47.0 1.0
O H:HOH431 2.4 43.0 1.0
CD H:GLU56 3.0 36.7 1.0
CD H:GLU91 3.0 42.3 1.0
CE1 H:HIS94 3.2 37.3 1.0
CG H:HIS94 3.2 36.2 1.0
OE2 H:GLU56 3.3 43.4 1.0
OE1 H:GLU91 3.4 50.0 1.0
CB H:HIS94 3.5 29.4 1.0
O H:HOH451 3.7 43.0 1.0
CG2 H:THR143 4.0 30.6 1.0
OE1 H:GLN174 4.1 44.2 1.0
CA H:GLU91 4.3 30.1 1.0
NE2 H:HIS94 4.3 43.9 1.0
CG H:GLU91 4.3 36.8 1.0
CG H:GLU56 4.3 32.7 1.0
CD2 H:HIS94 4.4 34.9 1.0
CB H:GLU91 4.5 31.5 1.0
CB H:GLU56 4.7 27.6 1.0
O H:GLU91 4.8 28.4 1.0

Magnesium binding site 2 out of 10 in 6j4j

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Magnesium binding site 2 out of 10 in the 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 Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:40.8
occ:1.00
 O B:HOH403 2.2 49.5 1.0
O H:HOH433 2.6 49.7 1.0
OD1 B:ASP164 2.7 35.0 1.0
OD1 H:ASP164 2.8 35.9 1.0
OE1 B:GLU167 2.9 39.6 1.0
OE1 H:GLU167 3.0 38.9 1.0
CG B:ASP164 3.9 36.5 1.0
CG H:ASP164 3.9 36.5 1.0
CD B:GLU167 4.2 37.8 1.0
CD H:GLU167 4.2 35.1 1.0
OG H:SER168 4.5 45.8 1.0
CB H:ASP164 4.5 31.6 1.0
CB B:ASP164 4.5 30.8 1.0
CB B:GLU167 4.8 31.0 1.0
CA B:ASP164 4.8 32.0 1.0
CA H:ASP164 4.8 29.9 1.0
OD2 B:ASP164 4.9 36.4 1.0
CB H:GLU167 4.9 33.6 1.0
OD2 H:ASP164 4.9 32.7 1.0
OE2 B:GLU167 5.0 41.5 1.0
OE2 H:GLU167 5.0 39.4 1.0

Magnesium binding site 3 out of 10 in 6j4j

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Magnesium binding site 3 out of 10 in the 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 Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:37.6
occ:1.00
 OE2 A:GLU91 2.0 40.9 1.0
OE1 A:GLU56 2.0 37.9 1.0
ND1 A:HIS94 2.2 39.3 1.0
O A:HOH420 2.3 45.0 1.0
CD A:GLU56 2.9 36.2 1.0
CD A:GLU91 3.0 40.7 1.0
OE2 A:GLU56 3.1 37.5 1.0
CE1 A:HIS94 3.2 38.7 1.0
CG A:HIS94 3.2 36.4 1.0
OE1 A:GLU91 3.5 48.7 1.0
CB A:HIS94 3.5 32.0 1.0
CA A:GLU91 4.2 30.6 1.0
CG A:GLU56 4.2 30.5 1.0
CG A:GLU91 4.2 35.5 1.0
CG2 A:THR143 4.3 34.5 1.0
OE1 A:GLN174 4.3 42.0 1.0
NE2 A:HIS94 4.3 42.0 1.0
CD2 A:HIS94 4.4 35.9 1.0
CB A:GLU91 4.4 30.2 1.0
CB A:GLU56 4.7 26.8 1.0
O A:GLU91 4.7 29.5 1.0
C A:GLU91 5.0 31.3 1.0

Magnesium binding site 4 out of 10 in 6j4j

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Magnesium binding site 4 out of 10 in the 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 Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.3
occ:1.00
 OE1 A:GLU46 2.3 36.7 1.0
OD1 A:ASP43 2.7 40.7 1.0
O A:HOH414 3.2 38.7 1.0
CD A:GLU46 3.2 36.6 1.0
CG A:ASP43 3.5 41.0 1.0
OE2 A:GLU46 3.6 31.4 1.0
NH1 A:ARG38 4.0 30.0 1.0
OD2 A:ASP43 4.1 51.4 1.0
O A:HOH458 4.3 38.7 1.0
CB A:ASP43 4.3 35.5 1.0
NH2 A:ARG38 4.4 32.9 1.0
CG A:GLU46 4.6 29.2 1.0
CZ A:ARG38 4.7 34.0 1.0
CA A:ASP43 4.7 29.2 1.0
CB A:GLU46 5.0 27.1 1.0

Magnesium binding site 5 out of 10 in 6j4j

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Magnesium binding site 5 out of 10 in the 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 Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:39.8
occ:1.00
 OE1 B:GLU56 2.0 39.0 1.0
OE2 B:GLU91 2.0 45.4 1.0
O B:HOH438 2.2 45.9 1.0
O B:HOH431 2.2 44.7 1.0
ND1 B:HIS94 2.3 37.2 1.0
CD B:GLU56 2.9 37.5 1.0
CD B:GLU91 3.0 40.5 1.0
CE1 B:HIS94 3.2 40.1 1.0
OE2 B:GLU56 3.2 41.1 1.0
CG B:HIS94 3.3 34.7 1.0
OE1 B:GLU91 3.4 48.9 1.0
CB B:HIS94 3.6 31.3 1.0
CG2 B:THR143 4.0 32.8 1.0
OE1 B:GLN174 4.1 44.5 1.0
CG B:GLU91 4.3 37.1 1.0
CG B:GLU56 4.3 32.7 1.0
NE2 B:HIS94 4.3 44.6 1.0
CA B:GLU91 4.4 32.7 1.0
CD2 B:HIS94 4.4 34.8 1.0
CB B:GLU91 4.5 32.5 1.0
CB B:GLU56 4.7 28.7 1.0
O B:GLU91 4.9 30.0 1.0

Magnesium binding site 6 out of 10 in 6j4j

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Magnesium binding site 6 out of 10 in the 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 Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:57.9
occ:1.00
 OE1 B:GLU96 2.5 62.2 1.0
CD B:ARG92 3.3 46.5 1.0
NH1 B:ARG92 3.3 56.5 1.0
CD B:GLU96 3.6 58.0 1.0
NE C:ARG92 3.7 49.7 1.0
CA C:GLU89 3.8 35.4 1.0
OG C:SER88 3.9 31.6 1.0
CE1 C:HIS64 3.9 51.4 1.0
NE B:ARG92 4.0 52.5 1.0
N C:GLU89 4.0 31.9 1.0
CZ B:ARG92 4.0 52.0 1.0
CB C:GLU89 4.2 39.0 1.0
C C:SER88 4.2 31.8 1.0
OE2 B:GLU96 4.2 55.5 1.0
O C:SER88 4.2 30.6 1.0
NE2 C:HIS64 4.3 45.8 1.0
CG B:ARG92 4.3 42.0 1.0
CD C:ARG92 4.4 45.2 1.0
ND1 C:HIS64 4.5 48.8 1.0
NH2 C:ARG92 4.6 55.1 1.0
CZ C:ARG92 4.6 48.8 1.0
CB C:SER88 4.6 32.5 1.0
CG B:GLU96 4.8 44.3 1.0
CB C:ARG92 4.9 35.5 1.0
OG C:SER60 4.9 32.1 1.0
CG C:GLU89 4.9 51.2 1.0

Magnesium binding site 7 out of 10 in 6j4j

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Magnesium binding site 7 out of 10 in the 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 Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:45.3
occ:1.00
 O C:HOH421 2.7 46.3 1.0
OD1 C:ASP164 2.8 36.2 1.0
OD1 D:ASP164 2.9 33.8 1.0
OE1 D:GLU167 2.9 38.4 1.0
OE1 C:GLU167 3.0 38.9 1.0
CG C:ASP164 4.0 33.5 1.0
CG D:ASP164 4.0 33.1 1.0
CD D:GLU167 4.2 32.4 1.0
CD C:GLU167 4.2 36.9 1.0
CB C:ASP164 4.5 33.2 1.0
CB D:ASP164 4.6 28.6 1.0
CB D:GLU167 4.8 31.4 1.0
CA D:ASP164 4.8 30.8 1.0
CA C:ASP164 4.9 31.7 1.0
CB C:GLU167 4.9 32.4 1.0
OE2 D:GLU167 4.9 40.7 1.0
OE2 C:GLU167 4.9 40.0 1.0
OD2 C:ASP164 5.0 34.5 1.0

Magnesium binding site 8 out of 10 in 6j4j

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Magnesium binding site 8 out of 10 in the 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 8 of Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:37.0
occ:1.00
 OE2 C:GLU91 2.0 40.7 1.0
ND1 C:HIS94 2.2 36.2 1.0
OE1 C:GLU56 2.2 40.8 1.0
O C:HOH430 2.3 43.8 1.0
O C:HOH420 2.3 47.0 1.0
CD C:GLU56 2.9 38.8 1.0
CD C:GLU91 3.0 40.1 1.0
CE1 C:HIS94 3.1 38.8 1.0
OE2 C:GLU56 3.1 45.9 1.0
CG C:HIS94 3.2 36.5 1.0
OE1 C:GLU91 3.4 44.6 1.0
CB C:HIS94 3.5 35.2 1.0
CG2 C:THR143 4.1 35.0 1.0
CA C:GLU91 4.2 31.3 1.0
OE1 C:GLN174 4.2 42.6 1.0
NE2 C:HIS94 4.2 41.8 1.0
CG C:GLU91 4.3 36.0 1.0
CD2 C:HIS94 4.3 36.4 1.0
CG C:GLU56 4.3 32.9 1.0
CB C:GLU91 4.4 30.0 1.0
O C:GLU91 4.7 31.8 1.0
CB C:GLU56 4.8 26.3 1.0
C C:GLU91 5.0 33.6 1.0

Magnesium binding site 9 out of 10 in 6j4j

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Magnesium binding site 9 out of 10 in the 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 9 of Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:47.4
occ:1.00
 OE2 D:GLU91 1.7 46.1 1.0
OE1 D:GLU56 2.2 40.7 1.0
ND1 D:HIS94 2.3 37.9 1.0
CD D:GLU56 2.9 39.5 1.0
OE2 D:GLU56 2.9 42.8 1.0
CD D:GLU91 3.0 42.1 1.0
CE1 D:HIS94 3.2 40.2 1.0
CG D:HIS94 3.3 35.1 1.0
CB D:HIS94 3.6 32.7 1.0
OE1 D:GLU91 3.8 39.8 1.0
CG D:GLU91 3.9 45.7 1.0
CG2 D:THR143 3.9 33.9 1.0
OE1 D:GLN174 3.9 41.4 1.0
O D:HOH451 4.0 42.2 1.0
NE2 D:HIS94 4.3 41.5 1.0
CG D:GLU56 4.3 33.9 1.0
CD2 D:HIS94 4.4 37.3 1.0
CD1 D:PHE170 4.7 40.1 1.0
CA D:GLU91 4.8 30.4 1.0
CB D:GLU56 4.9 32.0 1.0
CB D:GLU91 4.9 32.6 1.0
CD D:GLN174 5.0 39.5 1.0
CE1 D:PHE170 5.0 37.8 1.0

Magnesium binding site 10 out of 10 in 6j4j

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Magnesium binding site 10 out of 10 in the 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 10 of Soybean Seed H-2 Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:39.9
occ:1.00
 OE1 E:GLU91 1.9 40.8 1.0
OE1 E:GLU56 2.1 38.9 1.0
ND1 E:HIS94 2.1 36.3 1.0
O E:HOH422 2.4 45.2 1.0
CD E:GLU91 3.0 41.9 1.0
CD E:GLU56 3.0 37.2 1.0
CE1 E:HIS94 3.0 41.3 1.0
CG E:HIS94 3.2 37.9 1.0
OE2 E:GLU56 3.2 42.1 1.0
OE2 E:GLU91 3.4 45.4 1.0
CB E:HIS94 3.6 31.2 1.0
O E:HOH409 3.6 53.0 1.0
OE1 E:GLN174 4.1 43.3 1.0
NE2 E:HIS94 4.2 45.6 1.0
CG2 E:THR143 4.2 34.4 1.0
CG E:GLU91 4.2 38.1 1.0
CA E:GLU91 4.3 32.3 1.0
CD2 E:HIS94 4.3 40.2 1.0
CG E:GLU56 4.3 33.8 1.0
CB E:GLU91 4.5 30.3 1.0
CB E:GLU56 4.8 28.0 1.0
O E:GLU91 4.8 32.5 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: Tue Oct 1 04:32:52 2024

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