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Calcium in PDB 5gn8: Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign

Enzymatic activity of Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign

All present enzymatic activity of Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign:
1.16.3.1;

Protein crystallography data

The structure of Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign, PDB code: 5gn8 was solved by S.Zhang, J.Zang, G.Zhao, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.74 / 2.81
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 236.120, 236.120, 236.120, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign (pdb code 5gn8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign, PDB code: 5gn8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5gn8

Go back to Calcium Binding Sites List in 5gn8
Calcium binding site 1 out of 2 in the Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:75.8
occ:1.00
OE1 A:GLU27 2.2 70.8 1.0
OE1 A:GLU62 2.2 64.4 1.0
OE2 A:GLU62 2.9 64.8 1.0
CD A:GLU62 2.9 64.2 1.0
CD A:GLU27 2.9 68.1 1.0
OE2 A:GLU27 3.0 72.0 1.0
OE1 A:GLU107 3.7 73.0 1.0
O A:HOH302 3.7 53.4 1.0
OE2 A:GLU107 3.8 69.1 1.0
CD2 A:HIS65 3.8 78.5 1.0
CG1 A:VAL110 4.1 76.0 1.0
CD A:GLU107 4.2 69.0 1.0
CG2 A:THR135 4.2 89.8 1.0
CG A:GLU62 4.4 63.4 1.0
CG A:GLU27 4.4 68.4 1.0
NE2 A:HIS65 4.7 82.7 1.0
CG A:HIS65 4.7 79.0 1.0
CB A:GLU62 4.9 63.5 1.0
CB A:GLU27 4.9 66.7 1.0

Calcium binding site 2 out of 2 in 5gn8

Go back to Calcium Binding Sites List in 5gn8
Calcium binding site 2 out of 2 in the Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A 48-Mer Protein Nanocage Fabricated From Its 24-Mer Analogue By Subunit Interface Redesign within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:0.3
occ:1.00
OE1 B:GLU61 2.7 0.8 1.0
OE1 B:GLN58 3.1 0.5 1.0
OD1 B:ASP144 3.4 0.9 1.0
NE2 B:GLN58 3.6 93.2 1.0
CD B:GLN58 3.7 87.4 1.0
CD B:GLU61 3.9 0.0 1.0
O B:LYS140 3.9 98.9 1.0
OE2 B:GLU61 4.5 0.9 1.0
CG B:ASP144 4.5 0.5 1.0
CE1 B:HIS65 4.7 97.0 1.0
CA B:LYS140 4.8 82.3 1.0
C B:LYS140 4.8 83.0 1.0
OD2 B:ASP144 4.8 0.1 1.0
CB B:GLU61 4.8 81.6 1.0
O B:ILE139 4.9 78.2 1.0
OE2 B:GLU62 4.9 72.6 1.0
CG B:GLU61 5.0 96.3 1.0

Reference:

S.Zhang, J.Zang, X.Zhang, H.Chen, B.Mikami, G.Zhao. "Silent" Amino Acid Residues at Key Subunit Interfaces Regulate the Geometry of Protein Nanocages Acs Nano V. 10 10382 2016.
ISSN: ESSN 1936-086X
PubMed: 27934076
DOI: 10.1021/ACSNANO.6B06235
Page generated: Sun Jul 14 19:39:15 2024

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