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Magnesium in PDB 1sof: Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution

Protein crystallography data

The structure of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution, PDB code: 1sof was solved by H.L.Liu, J.F.Huang, R.C.Bi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.32 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 124.965, 124.965, 287.406, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 24.6

Other elements in 1sof:

The structure of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution also contains other interesting chemical elements:

Barium (Ba) 2 atoms
Iron (Fe) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution (pdb code 1sof). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution, PDB code: 1sof:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1sof

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Magnesium binding site 1 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:42.4
occ:1.00
 O A:HOH409 2.2 35.0 1.0
O A:HOH423 2.6 26.3 1.0
O A:HOH411 2.7 29.4 1.0
O A:HOH419 2.8 28.6 1.0
OE1 A:GLU135 3.2 39.3 1.0
OD1 A:ASP132 3.7 37.9 1.0
CB A:GLU135 3.8 34.5 1.0
CD A:GLU135 3.9 38.0 1.0
CG A:GLU135 4.5 37.6 1.0
OG1 A:THR136 4.7 34.2 1.0
OE2 A:GLU135 4.7 39.0 1.0
O A:ASP132 4.8 28.4 1.0
N A:THR136 4.8 32.0 1.0
OD2 A:ASP139 4.9 37.8 1.0
C A:GLU135 4.9 32.7 1.0
CG A:ASP132 4.9 35.3 1.0
CA A:GLU135 5.0 33.0 1.0

Magnesium binding site 2 out of 10 in 1sof

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Magnesium binding site 2 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:40.4
occ:1.00
 O B:HOH1201 2.3 31.2 1.0
OD2 B:ASP34 3.7 28.1 1.0
OD1 B:ASP34 4.3 29.0 1.0
CG B:ASP34 4.4 27.4 1.0
O B:ASP34 4.5 25.0 1.0
O A:PHE64 4.7 30.5 1.0
N A:MET1 4.8 40.2 1.0
O A:LEU63 4.8 26.8 1.0

Magnesium binding site 3 out of 10 in 1sof

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Magnesium binding site 3 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:34.0
occ:1.00
 O C:HOH2229 2.4 45.3 1.0
O C:HOH2203 2.5 24.7 1.0
OD2 E:ASP34 3.6 25.8 1.0
OD1 E:ASP34 3.6 25.0 1.0
OD1 C:ASP132 3.9 28.9 1.0
CG E:ASP34 3.9 24.8 1.0
O E:ASP34 4.0 24.5 1.0
OG1 C:THR136 4.2 20.8 1.0
OE1 C:GLU135 4.2 25.8 1.0
CG C:ASP132 4.5 27.2 1.0
OD2 C:ASP132 4.7 26.8 1.0
OD2 C:ASP139 4.7 32.1 1.0
OE2 F:GLU66 4.9 34.5 1.0
C E:ASP34 4.9 24.3 1.0
O F:PHE64 5.0 19.4 1.0

Magnesium binding site 4 out of 10 in 1sof

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Magnesium binding site 4 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:35.6
occ:1.00
 O D:HOH524 1.9 25.1 1.0
OE1 D:GLU85 2.3 28.4 1.0
OE2 D:GLU85 2.6 26.8 1.0
CD D:GLU85 2.7 25.5 1.0
OE2 D:GLU81 3.2 36.7 1.0
CD D:GLU81 4.1 35.0 1.0
CB D:GLU81 4.1 25.9 1.0
CG D:GLU85 4.2 23.1 1.0
NE2 D:HIS82 4.3 23.3 1.0
CD2 D:HIS82 4.3 20.6 1.0
CG D:GLU81 4.4 31.5 1.0
N D:GLU81 4.6 23.0 1.0
CB D:GLU85 4.6 21.1 1.0

Magnesium binding site 5 out of 10 in 1sof

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Magnesium binding site 5 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:50.3
occ:1.00
 O B:HOH1218 1.8 45.3 1.0
O B:HOH1220 1.9 32.1 1.0
O B:HOH1217 2.0 42.1 1.0
OD2 D:ASP34 3.4 26.1 1.0
OD1 D:ASP34 3.4 27.1 1.0
CG D:ASP34 3.8 25.6 1.0
OD1 B:ASP132 4.0 35.2 1.0
O D:ASP34 4.1 26.8 1.0
O C:LEU63 4.3 21.3 1.0
OE1 B:GLU135 4.4 34.2 1.0
OG1 B:THR136 4.6 30.6 1.0
CA C:PHE64 4.8 24.1 1.0
O C:PHE64 4.9 23.5 1.0
C D:ASP34 5.0 26.2 1.0

Magnesium binding site 6 out of 10 in 1sof

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Magnesium binding site 6 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:37.2
occ:1.00
 O D:HOH523 2.0 15.4 1.0
O D:HOH507 2.2 24.4 1.0
O D:HOH516 2.4 19.6 1.0
O D:HOH528 2.5 28.8 1.0
OD1 D:ASP132 3.9 31.8 1.0
OE1 D:GLU135 4.2 26.4 1.0
CG D:ASP132 5.0 28.2 1.0

Magnesium binding site 7 out of 10 in 1sof

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Magnesium binding site 7 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg306

b:44.8
occ:1.00
 O B:HOH1216 1.9 34.6 1.0
O A:HOH424 2.3 46.4 1.0
O F:HOH316 2.4 41.4 1.0
OE1 F:GLU135 3.8 40.6 1.0
OD1 F:ASP132 4.1 29.5 1.0
OD2 A:ASP34 4.2 31.5 1.0
OD1 A:ASP34 4.4 28.3 1.0
CB F:GLU135 4.5 32.9 1.0
OD1 F:ASP139 4.5 37.6 1.0
CG A:ASP34 4.6 28.2 1.0
CD F:GLU135 4.7 38.3 1.0
OE2 B:GLU66 4.7 36.6 1.0
N B:MET1 4.8 39.0 1.0
O A:ASP34 4.8 29.6 1.0
OG1 F:THR136 4.8 35.3 1.0
O B:PHE64 4.9 28.4 1.0
CD1 B:PHE64 5.0 30.9 1.0

Magnesium binding site 8 out of 10 in 1sof

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Magnesium binding site 8 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg307

b:38.4
occ:1.00
 O F:HOH308 1.9 20.1 1.0
O G:HOH4204 2.3 38.0 1.0
O G:HOH4214 2.4 36.0 1.0
OD2 F:ASP34 3.3 26.9 1.0
OD1 F:ASP34 3.6 25.2 1.0
OD1 G:ASP132 3.7 26.7 1.0
CG F:ASP34 3.8 26.0 1.0
O F:ASP34 4.0 26.7 1.0
OG1 G:THR136 4.2 17.8 1.0
OE1 G:GLU135 4.7 27.8 1.0
O E:LEU63 4.7 23.1 1.0
CG G:ASP132 4.9 26.4 1.0
CD1 E:PHE64 5.0 26.8 1.0
O E:PHE64 5.0 24.8 1.0
CA E:PHE64 5.0 25.2 1.0
C F:ASP34 5.0 26.7 1.0

Magnesium binding site 9 out of 10 in 1sof

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Magnesium binding site 9 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:44.8
occ:1.00
 O G:HOH4233 1.8 31.2 1.0
OE2 G:GLU85 2.4 29.8 1.0
CD G:GLU85 3.1 28.9 1.0
OE1 G:GLU85 3.1 30.0 1.0
OE1 G:GLU81 3.2 29.0 1.0
CD G:GLU81 4.3 25.8 1.0
CG G:GLU85 4.6 26.9 1.0
CG G:GLU81 4.8 24.3 1.0

Magnesium binding site 10 out of 10 in 1sof

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Magnesium binding site 10 out of 10 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg308

b:34.7
occ:1.00
 O G:HOH4216 1.8 39.5 1.0
O G:HOH4232 2.2 28.6 1.0
O G:HOH4206 2.3 35.5 1.0
O G:HOH4226 2.4 40.9 1.0
O G:HOH4210 2.5 24.8 1.0
OD2 G:ASP34 3.8 32.7 1.0
OD1 G:ASP34 4.1 31.2 1.0
CG G:ASP34 4.3 30.5 1.0
OE2 H:GLU66 4.5 39.3 1.0
O G:ASP34 4.6 26.5 1.0
O H:LEU63 4.6 19.2 1.0
N H:MET1 4.6 39.1 1.0
O H:PHE64 4.6 21.5 1.0
CG H:GLU66 4.8 33.3 1.0
CA H:PHE64 4.8 21.4 1.0
CD1 H:PHE64 5.0 23.8 1.0

Reference:

H.L.Liu, H.N.Zhou, W.M.Xing, J.F.Zhao, S.X.Li, J.F.Huang, R.C.Bi. 2.6 A Resolution Crystal Structure of the Bacterioferritin From Azotobacter Vinelandii Febs Lett. V. 573 93 2004.
ISSN: ISSN 0014-5793
PubMed: 15327981
DOI: 10.1016/J.FEBSLET.2004.07.054
Page generated: Tue Aug 13 14:18:12 2024

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