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Calcium in PDB 7ong: Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein

Protein crystallography data

The structure of Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein, PDB code: 7ong was solved by S.M.L.Wouters, H.Noguchi, G.Velpula, D.E.Clarke, A.R.D.Voet, S.De Feyter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.91 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 43.784, 75.799, 72.228, 90, 90, 90
R / Rfree (%) 19.2 / 21.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein (pdb code 7ong). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein, PDB code: 7ong:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7ong

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Calcium binding site 1 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:33.8
occ:0.50
 O A:GLY116 2.2 26.8 1.0
OD1 A:ASN120 2.4 36.1 1.0
C A:GLY116 3.2 26.1 1.0
CG A:ASN120 3.6 30.6 1.0
CA A:GLY116 4.0 23.7 1.0
N A:THR117 4.2 26.8 1.0
ND2 A:ASN120 4.3 32.2 1.0
O A:HOH505 4.4 32.2 1.0
CA A:THR117 4.4 28.3 1.0
CB A:ASN120 4.7 31.9 1.0
OH A:TYR114 4.8 27.0 1.0
O A:THR117 5.0 31.1 1.0

Calcium binding site 2 out of 10 in 7ong

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Calcium binding site 2 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:32.8
occ:1.00
 O A:GLY166 2.2 25.1 1.0
ND2 A:ASN170 2.3 33.1 1.0
C A:GLY166 3.2 26.1 1.0
CG A:ASN170 3.6 31.1 1.0
CA A:GLY166 4.0 25.4 1.0
N A:THR167 4.2 28.1 1.0
OD1 A:ASN170 4.3 37.6 1.0
CA A:THR167 4.4 27.8 1.0
CB A:ASN170 4.7 31.0 1.0
OH A:TYR164 4.8 30.4 1.0
O A:HOH578 5.0 32.0 1.0

Calcium binding site 3 out of 10 in 7ong

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Calcium binding site 3 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:34.1
occ:1.00
 O A:GLY216 2.2 25.6 1.0
ND2 A:ASN220 2.3 28.7 1.0
C A:GLY216 3.2 26.3 1.0
CG A:ASN220 3.5 30.5 1.0
OD1 A:ASN220 3.8 32.7 1.0
CA A:GLY216 3.9 24.2 1.0
N A:THR217 4.2 26.3 1.0
O A:HOH520 4.4 31.4 1.0
CA A:THR217 4.5 27.7 1.0
CB A:ASN220 4.7 30.6 1.0
OH A:TYR214 4.8 27.2 1.0
O A:THR217 5.0 27.9 1.0

Calcium binding site 4 out of 10 in 7ong

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Calcium binding site 4 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:35.1
occ:0.50
 O A:GLY266 2.2 25.6 1.0
C A:GLY266 3.3 24.6 1.0
CA A:GLY266 4.0 24.0 1.0
N A:THR267 4.2 26.3 1.0
CA A:THR267 4.5 25.1 1.0
O A:HOH523 4.6 33.2 1.0
CB A:ASN270 4.7 28.6 1.0
OH A:TYR264 4.9 26.0 1.0

Calcium binding site 5 out of 10 in 7ong

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Calcium binding site 5 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:21.4
occ:1.00
 O A:HOH608 2.3 25.8 1.0
O A:TRP286 2.3 19.4 1.0
OE1 A:GLU285 2.5 21.8 1.0
O A:HOH563 2.7 20.0 1.0
O A:HOH613 2.7 18.5 1.0
C A:TRP286 3.5 18.5 1.0
CD A:GLU285 3.7 22.8 1.0
N A:TRP286 3.9 19.3 1.0
CB A:GLU285 4.1 20.9 1.0
CA A:TRP286 4.3 16.1 1.0
CG A:GLU285 4.4 19.5 1.0
O A:HOH586 4.5 18.9 1.0
N A:SER287 4.5 16.4 1.0
CA A:GLU285 4.5 19.5 1.0
C A:GLU285 4.5 17.6 1.0
CA A:SER287 4.6 20.8 1.0
OE2 A:GLU285 4.6 20.4 1.0
O A:HOH567 4.7 25.3 1.0
O A:HOH607 4.7 18.8 1.0
CB A:SER287 4.8 16.2 1.0
O A:HOH568 4.9 17.7 1.0

Calcium binding site 6 out of 10 in 7ong

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Calcium binding site 6 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:21.8
occ:1.00
 O A:HOH598 2.3 25.1 1.0
O A:TRP136 2.3 17.3 1.0
OE1 A:GLU135 2.4 22.1 1.0
O A:HOH579 2.6 18.5 1.0
C A:TRP136 3.5 16.5 1.0
CD A:GLU135 3.6 21.7 1.0
N A:TRP136 3.9 16.5 1.0
CB A:GLU135 4.1 19.6 1.0
CA A:TRP136 4.3 15.7 1.0
CG A:GLU135 4.4 18.6 1.0
CA A:GLU135 4.5 17.0 1.0
O A:HOH596 4.5 20.4 1.0
C A:GLU135 4.5 16.5 1.0
N A:SER137 4.5 17.2 1.0
OE2 A:GLU135 4.6 19.1 1.0
CA A:SER137 4.6 19.2 1.0
O A:HOH576 4.7 24.2 1.0
O A:HOH606 4.7 17.4 1.0
CB A:SER137 4.8 17.7 1.0
O A:HOH573 4.9 17.0 1.0

Calcium binding site 7 out of 10 in 7ong

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Calcium binding site 7 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:20.7
occ:1.00
 O A:TRP86 2.3 17.4 1.0
OE1 A:GLU85 2.4 20.4 1.0
O A:HOH609 2.7 16.4 1.0
C A:TRP86 3.5 17.2 1.0
CD A:GLU85 3.7 21.3 1.0
N A:TRP86 3.9 18.5 1.0
CB A:GLU85 4.0 19.0 1.0
CA A:TRP86 4.3 16.6 1.0
O A:HOH591 4.3 19.2 1.0
CG A:GLU85 4.3 20.0 1.0
CA A:GLU85 4.4 16.5 1.0
C A:GLU85 4.4 17.8 1.0
N A:SER87 4.5 17.5 1.0
CA A:SER87 4.6 18.6 1.0
OE2 A:GLU85 4.6 20.9 1.0
O A:HOH554 4.7 24.5 1.0
CB A:SER87 4.7 18.5 1.0
O A:HOH610 4.8 18.3 1.0
O A:HOH572 4.9 17.3 1.0

Calcium binding site 8 out of 10 in 7ong

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Calcium binding site 8 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:20.9
occ:1.00
 O A:HOH615 2.3 25.8 1.0
O A:TRP36 2.3 16.4 1.0
OE1 A:GLU35 2.5 23.6 1.0
O A:HOH574 2.6 17.6 1.0
O A:HOH614 2.8 18.5 1.0
C A:TRP36 3.5 17.5 1.0
CD A:GLU35 3.7 22.5 1.0
N A:TRP36 3.9 18.4 1.0
CB A:GLU35 4.1 19.0 1.0
CA A:TRP36 4.3 16.4 1.0
CG A:GLU35 4.4 17.5 1.0
O A:HOH602 4.4 18.5 1.0
O A:HOH604 4.4 23.2 1.0
CA A:GLU35 4.5 18.0 1.0
C A:GLU35 4.5 17.5 1.0
N A:SER37 4.5 18.4 1.0
O A:HOH605 4.6 17.1 1.0
OE2 A:GLU35 4.6 20.6 1.0
CA A:SER37 4.6 21.5 1.0
CB A:SER37 4.8 17.8 1.0
O A:HOH580 4.9 16.3 1.0

Calcium binding site 9 out of 10 in 7ong

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Calcium binding site 9 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


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 the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:20.3
occ:1.00
 O A:HOH616 2.3 23.5 1.0
O A:TRP236 2.3 15.9 1.0
OE1 A:GLU235 2.5 20.0 1.0
O A:HOH595 2.6 19.0 1.0
C A:TRP236 3.5 18.1 1.0
CD A:GLU235 3.7 21.1 1.0
N A:TRP236 3.9 16.8 1.0
CB A:GLU235 4.0 19.0 1.0
CA A:TRP236 4.3 16.9 1.0
CG A:GLU235 4.4 18.7 1.0
O A:HOH570 4.4 18.6 1.0
CA A:GLU235 4.5 16.1 1.0
C A:GLU235 4.5 16.5 1.0
N A:SER237 4.5 16.6 1.0
OE2 A:GLU235 4.6 19.9 1.0
O A:HOH611 4.6 17.9 1.0
CA A:SER237 4.6 19.2 1.0
O A:HOH565 4.7 24.0 1.0
CB A:SER237 4.8 16.5 1.0
O A:HOH561 4.8 16.2 1.0

Calcium binding site 10 out of 10 in 7ong

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Calcium binding site 10 out of 10 in the Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Computationally Designed SAKE6BE-L1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:21.1
occ:1.00
 O A:TRP186 2.3 16.4 1.0
OE1 A:GLU185 2.5 21.4 1.0
O A:HOH599 2.6 20.0 1.0
C A:TRP186 3.5 16.6 1.0
CD A:GLU185 3.7 21.3 1.0
N A:TRP186 3.9 17.6 1.0
CB A:GLU185 4.1 19.4 1.0
CA A:TRP186 4.3 15.8 1.0
O A:HOH584 4.4 19.6 1.0
CG A:GLU185 4.4 20.0 1.0
CA A:GLU185 4.5 18.1 1.0
C A:GLU185 4.5 17.5 1.0
N A:SER187 4.5 16.8 1.0
O A:HOH581 4.5 26.7 1.0
CA A:SER187 4.6 19.5 1.0
OE2 A:GLU185 4.6 20.9 1.0
O A:HOH603 4.7 18.2 1.0
O A:HOH585 4.8 19.4 1.0
CB A:SER187 4.8 16.4 1.0

Reference:

S.M.L.Wouters, D.E.Clarke, H.Noguchi, G.Velpula, A.R.D.Voet, S.De Feyter. Sake: Computationally Designed Modular Protein Building Blocks For Macromolecular Assemblies To Be Published.
Page generated: Wed Jul 9 23:53:31 2025

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