Calcium in PDB 9r2v: De Novo Designed M16 Protein Fold

The structure of De Novo Designed M16 Protein Fold, PDB code: 9r2v was solved by M.Pacesa, Y.Miao, S.Georgeon, J.Schmidt, B.E.Correia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.19 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.25, 82.11, 111.42, 90, 92.45, 90
R / Rfree (%)	23.5 / 29

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the De Novo Designed M16 Protein Fold (pdb code 9r2v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the De Novo Designed M16 Protein Fold, PDB code: 9r2v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:91.1 occ:1.00 OE2 A:GLU131 2.5 65.8 1.0 OE1 A:GLU131 2.7 69.0 1.0 CD A:GLU131 3.0 74.3 1.0 CA A:CA206 3.0 107.8 1.0 OE2 A:GLU150 4.2 80.8 1.0 OE1 C:GLU135 4.3 97.6 1.0 CG A:GLU131 4.5 63.8 1.0

Calcium binding site 2 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:107.8 occ:1.00 O A:HOH303 3.0 90.2 1.0 CA A:CA205 3.0 91.1 1.0 OE1 A:GLU131 3.3 69.0 1.0 NZ A:LYS152 3.8 118.5 1.0 CE A:LYS152 4.0 111.9 1.0 CD A:GLU131 4.4 74.3 1.0 OE2 A:GLU150 4.6 80.8 1.0 OE2 A:GLU131 4.8 65.8 1.0

Calcium binding site 3 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:102.2 occ:1.00 O A:GLY153 2.7 102.4 1.0 OD1 A:ASP129 3.0 66.6 1.0 O A:ASN127 3.1 76.5 1.0 C A:GLY153 3.6 89.6 1.0 CG A:ASP129 3.8 70.8 1.0 C A:ASN127 3.9 82.6 1.0 CA A:LYS128 4.0 74.2 1.0 CA A:GLY153 4.1 83.3 1.0 OD2 A:ASP129 4.1 76.5 1.0 N A:GLY153 4.2 70.9 1.0 C A:LYS128 4.2 63.5 1.0 N A:ASP129 4.3 64.8 1.0 N A:LYS128 4.3 77.1 1.0 N A:GLY154 4.8 95.5 1.0 O A:LYS128 4.8 64.7 1.0 C A:GLY154 4.9 99.8 1.0 CB A:ASP129 4.9 55.5 1.0

Calcium binding site 4 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:87.1 occ:1.00 OE1 C:GLU131 2.5 81.8 1.0 OE2 C:GLU131 2.6 79.5 1.0 CD C:GLU131 2.9 73.8 1.0 OE2 C:GLU150 4.3 87.7 1.0 CG C:GLU131 4.4 70.5 1.0 CD C:GLU150 5.0 81.1 1.0

Calcium binding site 5 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca202 b:125.0 occ:1.00 OE1 E:GLU150 2.7 111.2 1.0 CA E:CA203 3.0 125.2 1.0 CD E:GLU150 3.6 106.0 1.0 OE2 E:GLU150 3.8 105.4 1.0 NZ E:LYS87 4.6 101.8 1.0 CE E:LYS148 4.8 89.5 1.0 OE1 E:GLU131 5.0 99.3 1.0 CG E:GLU150 5.0 87.5 1.0

Calcium binding site 6 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca203 b:125.2 occ:1.00 OE1 E:GLU131 2.4 99.3 1.0 OE2 E:GLU150 2.5 105.4 1.0 CA E:CA204 2.7 132.8 1.0 CD E:GLU150 2.7 106.0 1.0 OE1 E:GLU150 2.8 111.2 1.0 CA E:CA202 3.0 125.0 1.0 CD E:GLU131 3.4 100.4 1.0 OE2 E:GLU131 3.8 108.7 1.0 CG E:GLU150 3.8 87.5 1.0 CB E:GLU150 4.7 79.6 1.0 CG E:GLU131 4.8 77.3 1.0 CB E:GLU131 5.0 75.8 1.0

Calcium binding site 7 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca204 b:132.8 occ:1.00 OE2 E:GLU131 2.4 108.7 1.0 CA E:CA203 2.7 125.2 1.0 OE1 E:GLU131 3.0 99.3 1.0 CD E:GLU131 3.0 100.4 1.0 CG E:GLU131 4.5 77.3 1.0 OE2 E:GLU150 4.5 105.4 1.0

Calcium binding site 8 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca205 b:118.8 occ:1.00 OE1 E:GLU135 2.9 98.6 1.0 CA E:CA206 3.6 116.3 1.0 CD E:GLU135 4.0 89.7 1.0 OE2 E:GLU135 4.5 95.9 1.0

Calcium binding site 9 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca206 b:116.3 occ:1.00 CA E:CA205 3.6 118.8 1.0 OE2 E:GLU133 4.8 103.8 1.0 OE1 E:GLU135 5.0 98.6 1.0

Calcium binding site 10 out of 14 in the De Novo Designed M16 Protein Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of De Novo Designed M16 Protein Fold within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca207 b:105.3 occ:1.00 OE1 E:GLU29 2.7 103.3 1.0 CD E:GLU29 3.9 99.2 1.0 CB E:GLU29 4.2 89.0 1.0 CG E:GLU29 4.7 87.9 1.0 OE2 E:GLU29 4.8 103.6 1.0

Y.Miao, M.Pacesa, S.Georgeon, J.Schmidt, T.Lu, P.Huang, B.E.Correia. Reimagine Accessibility of Protein Space with Generative Model To Be Published.