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Calcium in PDB 7dya: Crystal Structure of Tmftn with Calcium Ions

Enzymatic activity of Crystal Structure of Tmftn with Calcium Ions

All present enzymatic activity of Crystal Structure of Tmftn with Calcium Ions:
1.16.3.2;

Protein crystallography data

The structure of Crystal Structure of Tmftn with Calcium Ions, PDB code: 7dya was solved by X.Zhang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.58 / 2.20
Space group H 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.434, 175.434, 357.421, 90, 90, 120
R / Rfree (%) 17.5 / 20

Other elements in 7dya:

The structure of Crystal Structure of Tmftn with Calcium Ions also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Tmftn with Calcium Ions (pdb code 7dya). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Tmftn with Calcium Ions, PDB code: 7dya:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7dya

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Calcium binding site 1 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca203

b:37.5
occ:1.00
 OE2 H:GLU132 2.2 32.0 1.0
O H:HOH409 2.3 31.7 1.0
OE2 H:GLU51 2.4 40.1 1.0
O H:HOH331 2.5 34.1 1.0
O H:HOH345 2.5 34.9 1.0
OE1 H:GLN135 2.5 38.0 1.0
OE1 H:GLU51 2.6 35.0 1.0
CD H:GLU51 2.8 35.6 1.0
CD H:GLU132 3.4 32.7 1.0
CD H:GLN135 3.5 38.8 1.0
NE2 H:GLN135 3.9 38.3 1.0
CG H:GLU132 4.1 32.9 1.0
O H:HOH403 4.2 38.6 1.0
OE1 H:GLN48 4.2 32.7 1.0
NH2 H:ARG163 4.3 29.1 1.0
CG H:GLU51 4.4 32.9 1.0
OE1 H:GLU132 4.4 32.8 1.0
NE2 H:GLN48 4.4 32.8 1.0
OE1 H:GLU131 4.6 43.2 1.0
CA H:GLU132 4.7 33.7 1.0
CD H:GLN48 4.8 34.6 1.0
O H:HOH318 4.8 30.0 1.0
OE2 H:GLU128 4.8 40.5 1.0
CG H:GLN135 4.9 37.5 1.0
CB H:GLU132 4.9 31.4 1.0

Calcium binding site 2 out of 9 in 7dya

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Calcium binding site 2 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:36.5
occ:1.00
 OE2 A:GLU132 2.3 37.7 1.0
O A:HOH315 2.3 35.2 1.0
OE2 A:GLU51 2.3 38.6 1.0
OE1 A:GLN135 2.5 35.5 1.0
O A:HOH414 2.5 35.9 1.0
OE1 A:GLU51 2.6 36.2 1.0
O A:HOH320 2.7 34.9 1.0
CD A:GLU51 2.8 34.4 1.0
CD A:GLU132 3.5 33.9 1.0
CD A:GLN135 3.5 39.2 1.0
NE2 A:GLN135 4.0 37.5 1.0
O A:HOH405 4.0 29.9 1.0
CG A:GLU132 4.2 36.8 1.0
OE1 A:GLN48 4.2 30.8 1.0
O A:HOH419 4.2 39.5 1.0
NH2 A:ARG163 4.3 28.8 1.0
CG A:GLU51 4.3 29.0 1.0
NE2 A:GLN48 4.4 29.5 1.0
OE1 A:GLU132 4.4 35.9 1.0
OE2 A:GLU131 4.5 37.5 1.0
O A:HOH412 4.7 43.6 1.0
CA A:GLU132 4.7 36.6 1.0
CD A:GLN48 4.8 33.5 1.0
O A:HOH307 4.8 29.0 1.0
CG A:GLN135 4.9 32.5 1.0
OE2 A:GLU128 4.9 40.3 1.0
CB A:GLU132 5.0 33.1 1.0

Calcium binding site 3 out of 9 in 7dya

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Calcium binding site 3 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:41.7
occ:1.00
 O B:HOH389 2.0 35.8 1.0
OE2 B:GLU132 2.3 39.6 1.0
OE2 B:GLU51 2.4 37.5 1.0
O B:HOH327 2.5 41.3 1.0
OE1 B:GLN135 2.5 45.1 1.0
OE1 B:GLU51 2.6 39.5 1.0
O B:HOH328 2.6 40.5 1.0
CD B:GLU51 2.8 40.9 1.0
CD B:GLN135 3.5 40.8 1.0
CD B:GLU132 3.6 38.8 1.0
NE2 B:GLN135 3.8 42.5 1.0
O B:HOH400 4.0 39.8 1.0
NH2 B:ARG163 4.1 35.0 1.0
OE1 B:GLN48 4.2 33.9 1.0
O B:HOH401 4.2 42.9 1.0
CG B:GLU132 4.3 35.3 1.0
CG B:GLU51 4.3 35.2 1.0
NE2 B:GLN48 4.4 32.5 1.0
OE1 B:GLU132 4.5 36.4 1.0
OE2 B:GLU131 4.7 48.8 1.0
OE2 B:GLU128 4.7 43.2 1.0
CD B:GLN48 4.7 35.5 1.0
O B:HOH320 4.8 41.1 1.0
CA B:GLU132 4.8 38.5 1.0
O B:HOH392 4.9 53.0 1.0
CG B:GLN135 4.9 39.1 1.0
CZ B:ARG163 5.0 36.1 1.0

Calcium binding site 4 out of 9 in 7dya

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Calcium binding site 4 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:73.1
occ:1.00
 O B:HOH398 2.3 68.1 1.0
OE2 B:GLU131 2.6 48.8 1.0
O B:HOH434 2.7 59.2 1.0
O B:HOH325 2.8 51.5 1.0
OE1 B:GLU131 3.0 56.5 1.0
CD B:GLU131 3.2 43.9 1.0
OE2 B:GLU128 4.3 43.2 1.0
OE1 B:GLU128 4.5 43.1 1.0
CG B:GLU131 4.6 42.7 1.0
O B:HOH327 4.8 41.3 1.0
CD B:GLU128 4.8 40.0 1.0

Calcium binding site 5 out of 9 in 7dya

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Calcium binding site 5 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:38.2
occ:1.00
 O C:HOH375 2.0 39.2 1.0
O C:HOH346 2.2 32.4 1.0
OE2 C:GLU132 2.2 41.1 1.0
OE2 C:GLU51 2.4 41.4 1.0
OE1 C:GLU51 2.5 35.5 1.0
O C:HOH317 2.5 32.5 1.0
OE1 C:GLN135 2.5 34.7 1.0
CD C:GLU51 2.8 37.9 1.0
CD C:GLU132 3.5 35.3 1.0
CD C:GLN135 3.5 40.2 1.0
NE2 C:GLN135 3.9 37.7 1.0
O C:HOH380 4.0 37.1 1.0
O C:HOH406 4.1 41.0 1.0
OE1 C:GLN48 4.2 31.4 1.0
NH2 C:ARG163 4.2 32.9 1.0
CG C:GLU132 4.3 33.4 1.0
CG C:GLU51 4.3 34.0 1.0
OE1 C:GLU132 4.4 37.7 1.0
OE2 C:GLU131 4.4 43.0 1.0
NE2 C:GLN48 4.4 28.1 1.0
CA C:GLU132 4.7 34.5 1.0
CD C:GLN48 4.7 35.5 1.0
O C:HOH308 4.8 39.8 1.0
OE2 C:GLU128 4.8 44.9 1.0
CG C:GLN135 4.9 36.9 1.0

Calcium binding site 6 out of 9 in 7dya

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Calcium binding site 6 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:30.8
occ:0.72
 O D:HOH377 2.1 42.5 1.0
OE2 D:GLU132 2.3 38.3 1.0
NE2 D:GLN135 2.3 35.9 1.0
OE2 D:GLU51 2.4 38.4 1.0
O D:HOH315 2.5 38.9 1.0
OE1 D:GLU51 2.6 40.8 1.0
O D:HOH322 2.6 39.8 1.0
CD D:GLU51 2.9 38.5 1.0
CD D:GLN135 3.3 43.8 1.0
CD D:GLU132 3.5 37.4 1.0
OE1 D:GLN135 3.6 45.8 1.0
O D:HOH360 4.0 37.3 1.0
O D:HOH395 4.3 43.5 1.0
NH2 D:ARG163 4.3 33.0 1.0
OE1 D:GLN48 4.3 34.4 1.0
NE2 D:GLN48 4.3 31.8 1.0
CG D:GLU132 4.4 37.7 1.0
CG D:GLU51 4.4 33.9 1.0
OE1 D:GLU132 4.4 40.7 1.0
OE1 D:GLU131 4.5 46.1 1.0
CG D:GLN135 4.7 39.0 1.0
CA D:GLU132 4.7 34.5 1.0
O D:HOH372 4.7 48.5 1.0
CD D:GLN48 4.8 36.1 1.0
O D:HOH320 4.8 37.2 1.0

Calcium binding site 7 out of 9 in 7dya

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Calcium binding site 7 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:43.8
occ:1.00
 O E:HOH316 2.2 36.6 1.0
OE2 E:GLU132 2.3 42.6 1.0
O E:HOH333 2.4 39.1 1.0
OE2 E:GLU51 2.4 38.9 1.0
OE1 E:GLN135 2.4 42.1 1.0
O E:HOH390 2.5 42.7 1.0
OE1 E:GLU51 2.5 41.1 1.0
CD E:GLU51 2.8 42.2 1.0
CD E:GLN135 3.5 44.2 1.0
CD E:GLU132 3.5 40.5 1.0
NE2 E:GLN135 3.9 44.9 1.0
OE1 E:GLN48 4.2 38.7 1.0
O E:HOH391 4.2 44.8 1.0
NH2 E:ARG163 4.3 35.1 1.0
CG E:GLU132 4.3 36.0 1.0
O E:HOH388 4.3 48.6 1.0
OE1 E:GLU132 4.3 44.0 1.0
O E:HOH358 4.3 38.0 1.0
CG E:GLU51 4.4 36.2 1.0
NE2 E:GLN48 4.4 38.9 1.0
OE2 E:GLU131 4.6 41.9 1.0
O E:HOH308 4.7 38.2 1.0
CD E:GLN48 4.7 39.2 1.0
CA E:GLU132 4.7 37.9 1.0
OE2 E:GLU128 4.8 41.5 1.0
CG E:GLN135 4.8 40.4 1.0

Calcium binding site 8 out of 9 in 7dya

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Calcium binding site 8 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca203

b:35.8
occ:1.00
 O F:HOH310 2.3 37.9 1.0
O F:HOH322 2.4 35.4 1.0
OE2 F:GLU51 2.4 37.5 1.0
OE2 F:GLU132 2.4 36.0 1.0
O F:HOH394 2.5 34.8 1.0
OE1 F:GLN135 2.5 36.2 1.0
OE1 F:GLU51 2.6 37.7 1.0
CD F:GLU51 2.8 37.2 1.0
CD F:GLN135 3.6 39.8 1.0
CD F:GLU132 3.6 38.3 1.0
NE2 F:GLN135 3.9 38.0 1.0
O F:HOH368 4.1 30.8 1.0
CG F:GLU132 4.2 37.5 1.0
OE1 F:GLN48 4.3 33.2 1.0
O F:HOH396 4.3 43.7 1.0
CG F:GLU51 4.4 35.0 1.0
OE1 F:GLU131 4.4 37.7 1.0
NH2 F:ARG163 4.4 30.3 1.0
NE2 F:GLN48 4.5 33.5 1.0
OE1 F:GLU132 4.5 32.4 1.0
CA F:GLU132 4.7 30.3 1.0
O F:HOH305 4.7 35.5 1.0
OE2 F:GLU128 4.7 43.7 1.0
CD F:GLN48 4.9 32.3 1.0
CG F:GLN135 4.9 34.8 1.0
CB F:GLU132 5.0 31.9 1.0

Calcium binding site 9 out of 9 in 7dya

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Calcium binding site 9 out of 9 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca203

b:48.7
occ:1.00
 O G:HOH306 2.2 52.6 1.0
OE2 G:GLU51 2.4 50.0 1.0
OE2 G:GLU132 2.4 51.5 1.0
O G:HOH321 2.4 48.2 1.0
O G:HOH366 2.4 51.0 1.0
OE1 G:GLU51 2.5 46.6 1.0
OE1 G:GLN135 2.6 46.9 1.0
CD G:GLU51 2.8 47.3 1.0
CD G:GLN135 3.5 49.0 1.0
CD G:GLU132 3.6 46.9 1.0
NE2 G:GLN135 3.7 50.7 1.0
OE1 G:GLN48 4.1 43.4 1.0
NH2 G:ARG163 4.2 43.1 1.0
O G:HOH362 4.2 48.7 1.0
CG G:GLU132 4.3 45.1 1.0
OE2 G:GLU131 4.3 55.8 1.0
CG G:GLU51 4.4 41.2 1.0
NE2 G:GLN48 4.5 39.8 1.0
O G:HOH303 4.5 45.5 1.0
OE1 G:GLU132 4.6 46.9 1.0
OE2 G:GLU128 4.7 46.7 1.0
CD G:GLN48 4.8 44.0 1.0
CA G:GLU132 4.8 44.1 1.0
CG G:GLN135 4.9 45.8 1.0

Reference:

X.Zhang, Y.Liu, B.Zheng, J.Zang, C.Lv, T.Zhang, H.Wang, G.Zhao. Protein Interface Redesign Facilitates the Transformation of Nanocage Building Blocks to 1D and 2D Nanomaterials. Nat Commun V. 12 4849 2021.
ISSN: ESSN 2041-1723
PubMed: 34381032
DOI: 10.1038/S41467-021-25199-X
Page generated: Wed Jul 9 21:43:36 2025

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