Magnesium in PDB 6lpe: Phascolosoma Esculenta Ferritin

Enzymatic activity of Phascolosoma Esculenta Ferritin

All present enzymatic activity of Phascolosoma Esculenta Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Phascolosoma Esculenta Ferritin, PDB code: 6lpe was solved by X.R.Su, T.H.Ming, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.18 / 1.99
Space group I 4 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 232.76, 232.76, 232.76, 90, 90, 90
R / Rfree (%) 24.9 / 30.2

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Phascolosoma Esculenta Ferritin (pdb code 6lpe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Phascolosoma Esculenta Ferritin, PDB code: 6lpe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6lpe

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Magnesium binding site 1 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:57.5
occ:1.00
 O A:HOH327 2.2 47.1 1.0
O A:HOH417 2.2 33.5 0.9
O A:HOH415 2.3 63.7 1.0
O A:HOH302 2.3 44.4 1.0
OD2 A:ASP125 2.3 37.8 0.8
CG A:ASP125 3.1 39.5 1.0
OD1 A:ASP125 3.2 43.6 1.0
O A:GLY123 3.9 34.2 1.0
O1 A:SO4208 4.2 101.0 0.8
CB A:ASP125 4.5 41.2 1.0
O2 A:SO4208 4.7 89.6 0.8
C A:GLY123 4.7 36.0 1.0
CA A:GLY123 4.8 36.4 1.0
S A:SO4208 4.9 114.9 0.8

Magnesium binding site 2 out of 12 in 6lpe

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Magnesium binding site 2 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:31.7
occ:1.00
 OE1 A:GLU60 1.9 37.3 1.0
O A:HOH363 1.9 42.8 1.0
OE1 A:GLU25 2.0 36.6 1.0
O A:HOH303 2.2 51.4 1.0
CD2 A:HIS63 2.3 35.8 0.9
CD A:GLU60 2.9 41.1 1.0
ND1 A:HIS63 2.9 46.0 0.1
CD A:GLU25 2.9 37.4 1.0
OE2 A:GLU60 3.2 51.9 1.0
CG A:HIS63 3.2 38.7 0.9
OE2 A:GLU25 3.3 42.9 1.0
NE2 A:HIS63 3.3 39.4 0.9
CB A:HIS63 3.6 39.4 0.1
CB A:HIS63 3.6 32.5 0.9
CG A:HIS63 3.6 43.2 0.1
CE1 A:HIS63 3.9 46.6 0.1
OE1 A:GLN139 4.0 53.5 1.0
CG1 A:VAL108 4.1 40.3 1.0
CG A:GLU60 4.2 36.7 1.0
CG A:GLU25 4.3 36.2 1.0
O A:HOH411 4.4 69.2 1.0
ND1 A:HIS63 4.4 44.2 0.9
CA A:GLU60 4.4 35.7 1.0
CE1 A:HIS63 4.5 39.6 0.9
CB A:GLU60 4.6 36.4 1.0
CB A:GLU25 4.7 35.0 1.0
CE1 A:PHE135 4.8 55.5 1.0
CD2 A:HIS63 4.8 42.8 0.1
CA A:GLU25 4.9 32.1 1.0
O A:GLU60 4.9 34.2 1.0
OE1 A:GLU105 5.0 58.9 1.0
NE2 A:HIS63 5.0 42.6 0.1

Magnesium binding site 3 out of 12 in 6lpe

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Magnesium binding site 3 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:75.8
occ:0.80
 O A:HOH321 2.6 63.0 1.0
O A:HOH444 3.2 62.0 1.0
OG A:SER133 4.0 62.1 1.0
OD1 A:ASP129 4.6 44.6 1.0

Magnesium binding site 4 out of 12 in 6lpe

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Magnesium binding site 4 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:85.4
occ:0.80
 O A:HOH326 1.9 41.7 0.3
OE1 A:GLU132 2.6 43.6 1.0
CD A:GLU132 3.5 34.0 1.0
OE2 A:GLU132 3.7 37.5 1.0
OD1 A:ASP129 4.1 44.6 1.0
O A:HOH395 4.6 45.6 1.0
O2 A:SO4207 4.6 40.4 0.3
CG A:GLU132 4.9 35.2 1.0
CB A:ASP129 4.9 35.5 1.0
CA A:ASP129 5.0 36.7 1.0

Magnesium binding site 5 out of 12 in 6lpe

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Magnesium binding site 5 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:48.4
occ:0.80
 OD2 B:ASP125 2.1 44.7 1.0
O B:HOH315 2.2 44.3 1.0
O B:HOH302 2.2 43.9 1.0
O B:HOH415 2.2 36.6 1.0
O B:HOH337 2.3 64.6 1.0
CG B:ASP125 2.9 40.6 1.0
OD1 B:ASP125 3.1 43.3 1.0
O B:GLY123 3.8 33.8 1.0
O3 B:SO4205 4.2 104.0 0.8
CB B:ASP125 4.4 40.8 1.0
C B:GLY123 4.6 37.0 1.0
O4 B:SO4205 4.6 83.8 0.8
CA B:GLY123 4.7 36.5 1.0
S B:SO4205 4.9 113.1 0.8
O B:HOH363 5.0 53.4 1.0

Magnesium binding site 6 out of 12 in 6lpe

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Magnesium binding site 6 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:31.8
occ:1.00
 OE1 B:GLU60 1.9 37.8 1.0
O B:HOH345 1.9 41.9 1.0
OE2 B:GLU25 2.0 37.7 1.0
CD2 B:HIS63 2.1 33.6 0.6
O B:HOH306 2.2 52.4 1.0
CD B:GLU60 2.9 41.7 1.0
CD2 B:HIS63 2.9 47.0 0.4
CD B:GLU25 2.9 36.8 1.0
CG B:HIS63 3.1 37.2 0.6
NE2 B:HIS63 3.1 37.9 0.6
OE2 B:GLU60 3.2 51.9 1.0
OE1 B:GLU25 3.3 43.1 1.0
CG B:HIS63 3.5 44.2 0.4
CB B:HIS63 3.6 31.7 0.6
CB B:HIS63 3.6 37.3 0.4
OE1 B:GLN139 3.9 51.3 1.0
NE2 B:HIS63 4.0 53.7 0.4
CG1 B:VAL108 4.0 40.4 1.0
CG B:GLU60 4.2 37.1 1.0
O B:HOH414 4.3 66.3 1.0
ND1 B:HIS63 4.3 43.9 0.6
CE1 B:HIS63 4.3 36.2 0.6
CG B:GLU25 4.3 37.5 1.0
CA B:GLU60 4.5 35.0 1.0
CB B:GLU60 4.6 36.8 1.0
CB B:GLU25 4.7 35.2 1.0
ND1 B:HIS63 4.7 47.2 0.4
CE1 B:PHE135 4.7 53.6 1.0
OE1 B:GLU105 5.0 59.1 1.0
CA B:GLU25 5.0 32.2 1.0
O B:GLU60 5.0 34.9 1.0
CE1 B:HIS63 5.0 49.6 0.4

Magnesium binding site 7 out of 12 in 6lpe

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Magnesium binding site 7 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:64.4
occ:0.80
 O B:HOH396 2.5 48.6 1.0
O B:HOH402 2.5 51.4 1.0
O B:HOH451 2.9 70.6 1.0
O B:HOH332 2.9 71.4 1.0
OD1 B:ASP129 4.3 44.4 1.0
CB B:SER133 4.7 40.5 1.0

Magnesium binding site 8 out of 12 in 6lpe

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Magnesium binding site 8 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:56.7
occ:0.95
 O C:HOH390 2.1 42.1 1.0
O C:HOH314 2.2 45.4 1.0
O C:HOH313 2.2 45.1 1.0
OD2 C:ASP125 2.2 45.0 1.0
O C:HOH445 2.3 60.2 1.0
CG C:ASP125 3.0 41.3 1.0
OD1 C:ASP125 3.2 43.4 1.0
O C:GLY123 3.9 33.8 1.0
CB C:ASP125 4.5 41.6 1.0
C C:GLY123 4.7 37.5 1.0
CA C:GLY123 4.8 36.5 1.0

Magnesium binding site 9 out of 12 in 6lpe

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Magnesium binding site 9 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:31.5
occ:1.00
 OE2 C:GLU60 1.8 28.1 0.7
OE2 C:GLU25 1.9 37.3 1.0
O C:HOH335 2.0 41.9 1.0
O C:HOH302 2.2 50.2 1.0
ND1 C:HIS63 2.2 43.8 0.9
CD C:GLU60 2.8 36.0 1.0
CD C:GLU25 2.9 38.1 1.0
CE1 C:HIS63 3.1 43.4 0.9
OE1 C:GLU60 3.1 38.1 0.7
CD2 C:HIS63 3.2 45.0 0.1
CG C:HIS63 3.3 41.5 0.9
OE1 C:GLU25 3.3 42.8 1.0
CG C:HIS63 3.6 42.6 0.1
CB C:HIS63 3.6 39.6 0.1
CB C:HIS63 3.7 33.0 0.9
NE2 C:GLN139 3.8 38.9 0.4
CG1 C:VAL108 4.1 40.7 1.0
CG C:GLU60 4.1 35.3 1.0
OE1 C:GLN139 4.2 41.7 0.5
NE2 C:HIS63 4.2 46.9 0.1
CG C:GLU25 4.3 37.1 1.0
NE2 C:HIS63 4.3 44.9 0.9
O C:HOH343 4.3 66.0 1.0
CA C:GLU60 4.4 35.0 1.0
CD2 C:HIS63 4.4 46.6 0.9
CB C:GLU60 4.5 37.1 1.0
CB C:GLU25 4.7 35.6 1.0
ND1 C:HIS63 4.7 44.2 0.1
CE1 C:PHE135 4.8 53.4 1.0
OE2 C:GLU105 4.9 61.3 1.0
O C:GLU60 4.9 34.5 1.0
CA C:GLU25 5.0 31.6 1.0

Magnesium binding site 10 out of 12 in 6lpe

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Magnesium binding site 10 out of 12 in the Phascolosoma Esculenta Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Phascolosoma Esculenta Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:47.8
occ:0.80
 O D:HOH407 2.1 63.1 1.0
O D:HOH317 2.2 44.2 1.0
O D:HOH322 2.2 43.7 1.0
O D:HOH411 2.2 37.2 1.0
OD2 D:ASP125 2.3 44.8 1.0
CG D:ASP125 3.1 40.9 1.0
OD1 D:ASP125 3.3 44.4 1.0
O D:GLY123 4.0 34.4 1.0
O4 D:SO4206 4.3 96.2 0.8
CB D:ASP125 4.6 42.4 1.0
O1 D:SO4206 4.7 77.9 0.8
C D:GLY123 4.7 36.8 1.0
CA D:GLY123 4.8 36.8 1.0
S D:SO4206 4.9 116.4 0.8
O2 D:SO4206 5.0 110.2 0.8

Reference:

T.Ming, H.Huan, C.Su, C.Huo, Y.Wu, Q.Jiang, X.Qiu, C.Lu, J.Zhou, Y.Li, X.Su. Structural Comparison of Two Ferritins From the Marine Invertebrate Phascolosoma Esculenta. Febs Open Bio 2021.
ISSN: ESSN 2211-5463
PubMed: 33448656
DOI: 10.1002/2211-5463.13080
Page generated: Wed Mar 3 14:50:38 2021

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