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Calcium in PDB 7s5k: M. Xanthus Ferritin-Like Protein Encb

Protein crystallography data

The structure of M. Xanthus Ferritin-Like Protein Encb, PDB code: 7s5k was solved by E.Eren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.44 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.49, 44.37, 127.96, 90, 114.08, 90
R / Rfree (%) 20.5 / 25.5

Other elements in 7s5k:

The structure of M. Xanthus Ferritin-Like Protein Encb also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the M. Xanthus Ferritin-Like Protein Encb (pdb code 7s5k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the M. Xanthus Ferritin-Like Protein Encb, PDB code: 7s5k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7s5k

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Calcium binding site 1 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:28.4
occ:0.32
 O B:HOH311 2.6 36.3 1.0
OE2 A:GLU58 2.9 35.2 1.0
OG1 A:THR31 2.9 24.5 1.0
CA B:CA203 3.2 68.7 1.0
CA A:GLU28 3.5 20.6 1.0
CB A:THR31 3.6 27.2 1.0
CG A:ARG27 3.7 26.3 1.0
N A:GLU28 3.7 21.3 1.0
FE A:FE101 3.7 77.6 1.0
O A:ARG27 3.8 21.3 1.0
CG A:GLU28 3.8 23.7 1.0
C A:ARG27 3.8 22.2 1.0
OH B:TYR35 3.9 30.1 1.0
CD A:GLU58 3.9 35.8 1.0
CG2 B:THR31 3.9 28.0 1.0
OG1 B:THR31 4.0 25.9 1.0
CG2 A:THR31 4.1 27.4 1.0
CB A:GLU28 4.2 20.5 1.0
CD A:ARG27 4.4 31.7 1.0
NE A:ARG27 4.4 28.8 1.0
CB A:ARG27 4.5 23.7 1.0
OE1 A:GLU58 4.6 31.6 1.0
CB B:THR31 4.6 26.5 1.0
C A:GLU28 4.7 22.1 1.0
OE1 B:GLU58 4.8 31.7 1.0
CA A:ARG27 4.8 23.7 1.0
O A:GLU28 4.8 19.1 1.0
CG A:GLU58 4.9 27.7 1.0
CZ B:TYR35 4.9 28.2 1.0

Calcium binding site 2 out of 9 in 7s5k

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Calcium binding site 2 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:68.7
occ:1.00
 OG1 B:THR31 2.7 25.9 1.0
OE1 B:GLU58 3.0 31.7 1.0
O A:HOH305 3.0 37.0 1.0
CA A:CA102 3.2 28.4 0.3
CB B:THR31 3.4 26.5 1.0
OG1 A:THR31 3.7 24.5 1.0
CG2 B:THR31 3.8 28.0 1.0
CG2 A:THR31 3.8 27.4 1.0
CG B:ARG27 3.9 29.8 1.0
CA B:GLU28 3.9 25.3 1.0
O B:ARG27 3.9 21.5 1.0
CD B:GLU58 4.0 35.7 1.0
FE B:FE202 4.0 80.9 1.0
N B:GLU28 4.1 22.3 1.0
C B:ARG27 4.1 26.6 1.0
CG B:GLU28 4.2 26.1 1.0
NE B:ARG27 4.2 29.3 1.0
OH A:TYR35 4.3 30.1 1.0
CD B:ARG27 4.3 30.6 1.0
CB A:THR31 4.4 27.2 1.0
CB B:GLU28 4.6 27.7 1.0
NE A:ARG27 4.6 28.8 1.0
CB B:ARG27 4.6 25.9 1.0
OE2 B:GLU58 4.7 33.6 1.0
NH2 A:ARG27 4.8 22.2 1.0
OE2 A:GLU58 4.8 35.2 1.0
CA B:THR31 4.8 24.6 1.0
CG B:GLU58 4.9 29.7 1.0
C B:GLU28 5.0 25.5 1.0
FE A:FE101 5.0 77.6 1.0

Calcium binding site 3 out of 9 in 7s5k

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Calcium binding site 3 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:37.7
occ:0.37
 OG1 E:THR31 2.7 30.8 1.0
O F:HOH301 2.8 35.6 1.0
OE1 E:GLU58 2.9 48.9 1.0
CA F:CA202 3.1 35.7 0.4
CB E:THR31 3.5 29.8 1.0
CA E:GLU28 3.7 30.4 1.0
O E:ARG27 3.7 28.8 1.0
FE E:FE201 3.8 95.2 1.0
CG E:ARG27 3.8 34.6 1.0
N E:GLU28 3.8 28.0 1.0
CG2 E:THR31 3.9 32.3 1.0
C E:ARG27 3.9 29.6 1.0
CG2 F:THR31 3.9 33.3 1.0
OG1 F:THR31 3.9 22.9 1.0
CG E:GLU28 4.0 34.2 1.0
CD E:GLU58 4.0 49.5 1.0
OH F:TYR35 4.0 32.1 1.0
CD E:ARG27 4.3 31.3 1.0
NE E:ARG27 4.3 31.5 1.0
CB E:GLU28 4.4 31.9 1.0
CB E:ARG27 4.4 30.1 1.0
CB F:THR31 4.5 28.3 1.0
OE2 E:GLU58 4.7 51.7 1.0
OE1 F:GLU58 4.8 48.3 1.0
C E:GLU28 4.8 31.2 1.0
CA E:ARG27 4.8 31.2 1.0
NE F:ARG27 4.8 28.5 1.0
CG E:GLU58 4.8 42.1 1.0
FE F:FE201 4.8 106.2 1.0
CA E:THR31 4.9 27.2 1.0
O E:GLU28 4.9 26.0 1.0

Calcium binding site 4 out of 9 in 7s5k

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Calcium binding site 4 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca202

b:35.7
occ:0.41
 OE1 F:GLU58 2.7 48.3 1.0
OG1 F:THR31 2.9 22.9 1.0
CA E:CA203 3.1 37.7 0.4
CB F:THR31 3.5 28.3 1.0
FE F:FE201 3.5 106.2 1.0
CD F:GLU58 3.7 44.6 1.0
CG2 F:THR31 3.7 33.3 1.0
CA F:GLU28 3.8 27.8 1.0
CG2 E:THR31 3.9 32.3 1.0
OG1 E:THR31 3.9 30.8 1.0
N F:GLU28 4.0 28.1 1.0
OH E:TYR35 4.0 28.9 1.0
CG F:GLU28 4.0 32.4 1.0
O F:ARG27 4.1 24.5 1.0
CG F:ARG27 4.2 26.8 1.0
C F:ARG27 4.2 25.6 1.0
OE2 F:GLU58 4.3 48.5 1.0
OE1 E:GLU58 4.4 48.9 1.0
CD F:ARG27 4.5 30.1 1.0
CB F:GLU28 4.5 29.6 1.0
NE F:ARG27 4.5 28.5 1.0
CB E:THR31 4.5 29.8 1.0
FE E:FE201 4.6 95.2 1.0
CG F:GLU58 4.6 38.4 1.0
C F:GLU28 4.8 28.2 1.0
O F:GLU28 4.9 27.0 1.0
NE E:ARG27 4.9 31.5 1.0
CB F:ARG27 4.9 27.2 1.0
CA F:THR31 4.9 27.7 1.0
CD E:GLU58 5.0 49.5 1.0

Calcium binding site 5 out of 9 in 7s5k

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Calcium binding site 5 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca203

b:37.4
occ:0.33
 OG1 G:THR31 2.5 29.4 1.0
O H:HOH206 2.8 38.3 1.0
OE2 G:GLU58 3.0 48.3 1.0
CA H:CA103 3.1 81.7 1.0
CB G:THR31 3.3 36.0 1.0
O G:ARG27 3.6 31.5 1.0
CA G:GLU28 3.7 31.4 1.0
CG G:ARG27 3.7 34.1 1.0
CG2 G:THR31 3.8 33.5 1.0
C G:ARG27 3.8 31.3 1.0
N G:GLU28 3.8 30.4 1.0
FE G:FE201 3.8 42.1 0.3
OG1 H:THR31 4.0 27.6 1.0
CD G:GLU58 4.0 42.7 1.0
CG G:GLU28 4.1 33.9 1.0
OH H:TYR35 4.2 37.5 1.0
CG2 H:THR31 4.2 34.9 1.0
CD G:ARG27 4.4 38.1 1.0
NE G:ARG27 4.4 36.4 1.0
CB G:ARG27 4.4 31.9 1.0
CB G:GLU28 4.4 32.1 1.0
NH2 H:ARG27 4.7 30.8 1.0
CB H:THR31 4.7 30.2 1.0
CA G:THR31 4.7 32.4 1.0
NE H:ARG27 4.7 40.4 1.0
OE1 G:GLU58 4.7 44.8 1.0
C G:GLU28 4.7 31.4 1.0
CA G:ARG27 4.8 29.9 1.0
O G:GLU28 4.9 26.5 1.0
FE H:FE102 4.9 104.9 1.0
CG G:GLU58 4.9 36.6 1.0
OE1 H:GLU58 5.0 43.4 1.0

Calcium binding site 6 out of 9 in 7s5k

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Calcium binding site 6 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca103

b:81.7
occ:1.00
 OE1 H:GLU58 2.8 43.4 1.0
OG1 H:THR31 2.9 27.6 1.0
CA G:CA203 3.1 37.4 0.3
FE H:FE102 3.5 104.9 1.0
CB H:THR31 3.5 30.2 1.0
OG1 G:THR31 3.7 29.4 1.0
CD H:GLU58 3.8 40.8 1.0
CG2 H:THR31 3.8 34.9 1.0
CA H:GLU28 3.9 26.7 1.0
CG H:GLU28 4.0 31.4 1.0
CG2 G:THR31 4.0 33.5 1.0
CG H:ARG27 4.1 31.9 1.0
OH G:TYR35 4.1 39.5 1.0
O H:ARG27 4.1 29.2 1.0
N H:GLU28 4.2 25.9 1.0
C H:ARG27 4.3 28.4 1.0
NE H:ARG27 4.4 40.4 1.0
OE2 H:GLU58 4.4 42.7 1.0
CB H:GLU28 4.5 28.0 1.0
CB G:THR31 4.5 36.0 1.0
CD H:ARG27 4.5 37.0 1.0
OE2 G:GLU58 4.6 48.3 1.0
FE G:FE201 4.7 42.1 0.3
CG H:GLU58 4.8 36.1 1.0
CB H:ARG27 4.9 30.2 1.0
NE G:ARG27 4.9 36.4 1.0
C H:GLU28 4.9 26.6 1.0
CA H:THR31 5.0 30.8 1.0

Calcium binding site 7 out of 9 in 7s5k

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Calcium binding site 7 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca202

b:71.0
occ:1.00
 OG1 I:THR31 2.6 26.9 1.0
OE1 I:GLU58 3.1 55.5 1.0
CA J:CA102 3.2 33.0 0.4
FE I:FE201 3.3 118.8 1.0
CB I:THR31 3.3 27.8 1.0
O J:HOH202 3.4 37.0 1.0
CG2 I:THR31 3.7 30.2 1.0
O I:ARG27 3.7 27.0 1.0
OG1 J:THR31 3.8 24.7 1.0
CA I:GLU28 3.8 30.0 1.0
C I:ARG27 4.0 26.6 1.0
N I:GLU28 4.0 28.3 1.0
CG2 J:THR31 4.0 30.3 1.0
OH J:TYR35 4.0 32.8 1.0
CG I:ARG27 4.1 32.1 1.0
CG I:GLU28 4.2 34.1 1.0
CD I:GLU58 4.3 46.0 1.0
NE I:ARG27 4.3 32.0 1.0
CD I:ARG27 4.4 33.3 1.0
OE2 J:GLU58 4.5 44.0 1.0
CB J:THR31 4.5 28.9 1.0
CB I:GLU28 4.6 34.2 1.0
CB I:ARG27 4.6 28.6 1.0
CA I:THR31 4.7 26.0 1.0
NE J:ARG27 4.7 33.2 1.0
C I:GLU28 4.8 27.5 1.0
NH2 J:ARG27 4.9 24.4 1.0
CA I:ARG27 4.9 28.2 1.0
O I:GLU28 4.9 25.1 1.0
FE I:FE203 5.0 40.4 0.4

Calcium binding site 8 out of 9 in 7s5k

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Calcium binding site 8 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca102

b:33.0
occ:0.41
 O I:HOH304 2.6 31.2 1.0
OG1 J:THR31 2.8 24.7 1.0
OE2 J:GLU58 2.8 44.0 1.0
CA I:CA202 3.2 71.0 1.0
CB J:THR31 3.5 28.9 1.0
CA J:GLU28 3.7 27.2 1.0
OG1 I:THR31 3.7 26.9 1.0
O J:ARG27 3.8 21.5 1.0
CG J:ARG27 3.8 27.2 1.0
CG2 I:THR31 3.8 30.2 1.0
FE I:FE203 3.9 40.4 0.4
N J:GLU28 3.9 24.0 1.0
CG J:GLU28 3.9 26.2 1.0
CD J:GLU58 3.9 43.4 1.0
C J:ARG27 3.9 22.4 1.0
CG2 J:THR31 4.0 30.3 1.0
OH I:TYR35 4.0 32.6 1.0
NE J:ARG27 4.3 33.2 1.0
CD J:ARG27 4.3 33.0 1.0
CB J:GLU28 4.4 25.5 1.0
CB I:THR31 4.4 27.8 1.0
CB J:ARG27 4.5 28.8 1.0
OE1 I:GLU58 4.5 55.5 1.0
OE1 J:GLU58 4.7 37.0 1.0
FE I:FE201 4.7 118.8 1.0
C J:GLU28 4.8 26.5 1.0
NE I:ARG27 4.8 32.0 1.0
CA J:ARG27 4.9 27.5 1.0
CG J:GLU58 4.9 33.1 1.0
NH2 I:ARG27 4.9 29.4 1.0
O J:GLU28 4.9 25.4 1.0
CA J:THR31 4.9 25.9 1.0
CZ I:TYR35 5.0 29.5 1.0

Calcium binding site 9 out of 9 in 7s5k

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Calcium binding site 9 out of 9 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca103

b:39.2
occ:0.45
 OG1 D:THR31 2.6 23.1 1.0
O C:HOH306 3.0 33.7 1.0
O C:HOH307 3.0 34.7 1.0
OE2 D:GLU58 3.1 42.1 1.0
CB D:THR31 3.3 22.8 1.0
CG2 D:THR31 3.7 25.9 1.0
OG1 C:THR31 3.8 23.7 1.0
O D:ARG27 3.8 24.6 1.0
CG D:ARG27 3.8 29.0 1.0
CA D:GLU28 3.8 27.9 1.0
CG2 C:THR31 3.9 25.4 1.0
OH C:TYR35 4.0 34.5 1.0
N D:GLU28 4.0 24.9 1.0
CD D:GLU58 4.0 43.8 1.0
C D:ARG27 4.0 24.9 1.0
CG D:GLU28 4.3 31.9 1.0
NE D:ARG27 4.4 32.4 1.0
CB C:THR31 4.4 23.1 1.0
FE D:FE102 4.5 118.9 1.0
CD D:ARG27 4.5 31.1 1.0
OE1 D:GLU58 4.6 44.5 1.0
CB D:GLU28 4.6 28.3 1.0
CB D:ARG27 4.7 30.1 1.0
NE C:ARG27 4.7 30.5 1.0
CA D:THR31 4.7 23.9 1.0
NH2 C:ARG27 4.8 29.8 1.0
C D:GLU28 4.9 24.7 1.0
CG D:GLU58 5.0 34.8 1.0
CZ C:TYR35 5.0 30.2 1.0
O D:GLU28 5.0 21.6 1.0
CA D:ARG27 5.0 26.4 1.0

Reference:

E.Eren, B.Wang, D.C.Winkler, N.R.Watts, A.C.Steven, P.T.Wingfield. Structural Characterization of the Myxococcus Xanthus Encapsulin and Ferritin-Like Cargo System Gives Insight Into Its Iron Storage Mechanism. Structure V. 30 551 2022.
ISSN: ISSN 0969-2126
PubMed: 35150605
DOI: 10.1016/J.STR.2022.01.008
Page generated: Fri Jul 19 03:54:47 2024

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