Atomistry » Magnesium » PDB 6iux-6j7n » 6j4j
Atomistry »
  Magnesium »
    PDB 6iux-6j7n »
      6j4j »

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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Go back to Magnesium Binding Sites List in 6j4j
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy