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Calcium in PDB 6wz7: Mn-Bound Structure of A TRICYT3 Variant

Protein crystallography data

The structure of Mn-Bound Structure of A TRICYT3 Variant, PDB code: 6wz7 was solved by F.A.Tezcan, A.Kakkis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.40 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.978, 81.847, 53.385, 90.00, 90.04, 90.00
R / Rfree (%) 18 / 21.9

Other elements in 6wz7:

The structure of Mn-Bound Structure of A TRICYT3 Variant also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Iron (Fe) 3 atoms
Chlorine (Cl) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mn-Bound Structure of A TRICYT3 Variant (pdb code 6wz7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Mn-Bound Structure of A TRICYT3 Variant, PDB code: 6wz7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6wz7

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Calcium binding site 1 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:79.1
occ:1.00
 O A:ALA1 2.7 49.3 1.0
N A:ALA1 2.8 48.6 1.0
OD1 A:ASP39 2.8 38.1 1.0
OD2 A:ASP39 2.9 37.1 1.0
CG A:ASP39 3.2 41.4 1.0
C A:ALA1 3.5 41.5 1.0
CA A:ALA1 3.8 41.6 1.0
O A:HOH342 3.9 43.2 1.0
O A:HOH384 4.3 54.4 1.0
O A:ASP39 4.4 32.1 1.0
CD A:LYS42 4.5 35.3 1.0
CB A:ASP39 4.6 24.5 1.0
N A:ASP2 4.7 41.9 1.0
ND2 A:ASN6 4.7 32.0 1.0
CB A:ALA1 4.9 37.2 1.0
NZ A:LYS42 5.0 37.4 1.0
C A:ASP39 5.0 32.2 1.0

Calcium binding site 2 out of 9 in 6wz7

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Calcium binding site 2 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:44.2
occ:1.00
 OD1 A:ASP21 2.3 51.0 1.0
O A:LYS19 2.4 48.6 1.0
CG A:ASP21 3.1 45.4 1.0
OD2 A:ASP21 3.3 58.8 1.0
C A:LYS19 3.5 44.3 1.0
CA A:LYS19 4.2 42.6 1.0
O A:HOH339 4.2 61.2 1.0
CB A:LYS19 4.3 40.3 1.0
C A:ALA20 4.4 43.6 1.0
O A:ALA20 4.5 44.3 1.0
CB A:ASP21 4.5 46.1 1.0
N A:ALA20 4.5 53.1 1.0
N A:ASP21 4.6 46.1 1.0
CA A:ALA20 4.8 49.3 1.0
CA A:ASP21 4.9 51.8 1.0

Calcium binding site 3 out of 9 in 6wz7

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Calcium binding site 3 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:82.3
occ:1.00
 O C:HOH372 2.5 67.2 1.0
OE2 B:GLU80 4.5 50.8 1.0
ND1 A:HIS77 4.8 29.5 1.0
CE1 A:HIS77 4.9 28.8 1.0

Calcium binding site 4 out of 9 in 6wz7

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Calcium binding site 4 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:82.0
occ:1.00
 N B:ALA1 2.5 49.6 1.0
O B:HOH346 2.6 52.1 1.0
O B:ALA1 2.8 49.6 1.0
OD1 B:ASP39 3.0 38.7 1.0
OD2 B:ASP39 3.1 38.2 1.0
CG B:ASP39 3.4 37.3 1.0
C B:ALA1 3.5 43.3 1.0
CA B:ALA1 3.5 39.9 1.0
O B:HOH318 4.1 48.2 1.0
N B:ASP2 4.7 41.1 1.0
CB B:ALA1 4.7 32.8 1.0
O B:HOH326 4.8 47.4 1.0
O B:ASP39 4.8 33.5 1.0
CD B:LYS42 4.8 34.7 1.0
O B:HOH374 4.8 48.0 1.0
CB B:ASP39 4.9 25.1 1.0

Calcium binding site 5 out of 9 in 6wz7

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Calcium binding site 5 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:44.9
occ:0.52
 O B:HOH338 2.3 53.3 0.6
OD1 B:ASP21 2.3 49.7 1.0
O B:HOH314 2.3 64.9 0.6
O B:LYS19 2.4 45.1 1.0
CG B:ASP21 3.0 46.6 1.0
OD2 B:ASP21 3.1 45.9 1.0
C B:LYS19 3.5 45.6 1.0
CA B:LYS19 4.1 45.8 1.0
CB B:LYS19 4.3 43.7 1.0
C B:ALA20 4.3 44.8 1.0
O B:ALA20 4.4 47.6 1.0
CB B:ASP21 4.4 46.7 1.0
N B:ALA20 4.5 48.6 1.0
N B:ASP21 4.6 45.9 1.0
CA B:ALA20 4.7 48.3 1.0
CA B:ASP21 4.8 49.2 1.0

Calcium binding site 6 out of 9 in 6wz7

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Calcium binding site 6 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:87.0
occ:1.00
 OE1 B:GLU4 2.4 54.1 1.0
CD B:GLU4 2.5 59.1 1.0
O2A B:HEC201 2.6 59.9 1.0
OE2 B:GLU4 2.6 59.2 1.0
CG B:GLU4 3.6 58.5 1.0
CGA B:HEC201 3.7 61.4 1.0
O1A B:HEC201 4.2 70.8 1.0
O B:HOH321 4.5 53.6 1.0
CB B:GLU4 4.7 41.9 1.0
CBA B:HEC201 5.0 53.8 1.0

Calcium binding site 7 out of 9 in 6wz7

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Calcium binding site 7 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:82.8
occ:1.00
 N C:ALA1 2.7 53.5 1.0
O C:ALA1 2.7 46.6 1.0
O C:HOH359 2.8 57.1 1.0
OD1 C:ASP39 2.8 42.4 1.0
OD2 C:ASP39 2.9 37.2 1.0
CG C:ASP39 3.2 37.0 1.0
C C:ALA1 3.5 42.9 1.0
CA C:ALA1 3.7 42.3 1.0
O C:HOH347 4.3 47.4 1.0
O C:ASP39 4.7 31.0 1.0
CB C:ASP39 4.7 26.8 1.0
CD C:LYS42 4.7 34.9 1.0
N C:ASP2 4.7 40.1 1.0
CB C:ALA1 4.7 35.2 1.0
O B:HOH336 4.8 45.2 1.0
ND2 C:ASN6 4.8 34.3 1.0

Calcium binding site 8 out of 9 in 6wz7

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Calcium binding site 8 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:82.9
occ:1.00
 O C:HOH302 2.1 49.8 1.0
O2A C:HEC201 2.4 66.9 1.0
O1A C:HEC201 2.5 61.3 1.0
CGA C:HEC201 2.8 58.8 1.0
CA C:CA205 3.0 90.0 1.0
OE2 C:GLU4 3.4 68.4 1.0
OE1 C:GLU8 3.6 71.6 1.0
CD C:GLU4 3.7 70.1 1.0
OE1 C:GLU4 3.7 65.3 1.0
O C:HOH339 4.0 65.9 1.0
CBA C:HEC201 4.3 53.4 1.0
CD C:GLU8 4.8 63.0 1.0
CG C:GLU4 4.8 59.6 1.0

Calcium binding site 9 out of 9 in 6wz7

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Calcium binding site 9 out of 9 in the Mn-Bound Structure of A TRICYT3 Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Mn-Bound Structure of A TRICYT3 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca205

b:90.0
occ:1.00
 OE1 C:GLU4 2.6 65.3 1.0
CA C:CA204 3.0 82.9 1.0
OE2 C:GLU4 3.3 68.4 1.0
CD C:GLU4 3.3 70.1 1.0
O2A C:HEC201 3.8 66.9 1.0
O C:HOH339 3.8 65.9 1.0
O C:HOH302 4.7 49.8 1.0
CG C:GLU4 4.8 59.6 1.0
CGA C:HEC201 4.9 58.8 1.0
O C:HOH306 5.0 54.4 1.0

Reference:

F.A.Tezcan, A.Kakkis, D.Gagnon, J.Esselborn, R.D.Britt. Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32830423
DOI: 10.1002/ANIE.202009226
Page generated: Tue Jul 16 17:38:22 2024

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