Calcium in PDB 4lin: Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography

The structure of Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography, PDB code: 4lin was solved by A.Bhardwaj, G.Cingolani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.99 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.689, 147.929, 151.011, 87.94, 90.05, 89.95
R / Rfree (%)	22.9 / 26.8

The structure of Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Calcium atom in the Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography (pdb code 4lin). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography, PDB code: 4lin:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1301 b:79.0 occ:1.00 OD1 A:ASN1063 2.3 55.5 1.0 OE1 C:GLN1066 2.4 74.7 1.0 OE1 A:GLN1066 2.4 46.8 1.0 OD1 B:ASN1063 2.5 44.7 1.0 NE2 C:GLN1066 2.5 49.5 1.0 CD C:GLN1066 2.8 74.6 1.0 CA A:ASN1063 2.8 57.9 1.0 CG A:ASN1063 2.9 58.4 1.0 NE2 B:GLN1066 3.1 57.3 1.0 CD A:GLN1066 3.3 48.7 1.0 CB A:ASN1063 3.3 59.8 1.0 CG B:ASN1063 3.4 49.3 1.0 O A:ASN1063 3.7 63.5 1.0 O A:LYS1062 3.7 55.5 1.0 C A:ASN1063 3.7 58.6 1.0 N A:ASN1063 3.7 59.0 1.0 ND2 B:ASN1063 3.8 54.2 1.0 OD1 C:ASN1063 3.8 61.8 1.0 CB A:GLN1066 3.9 43.4 1.0 ND2 A:ASN1063 4.0 58.3 1.0 C A:LYS1062 4.1 61.2 1.0 CG A:GLN1066 4.1 45.8 1.0 NE2 A:GLN1066 4.2 54.5 1.0 CG C:GLN1066 4.3 74.9 1.0 OD1 A:ASP1067 4.3 60.3 1.0 CD B:GLN1066 4.3 53.6 1.0 CB B:ASN1063 4.6 47.7 1.0 OE1 B:GLN1066 4.7 56.5 1.0 CG C:ASN1063 4.8 60.6 1.0 N A:ASP1064 5.0 58.5 1.0

Calcium binding site 2 out of 4 in the Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1301 b:54.6 occ:1.00 OE1 D:GLN1066 2.3 63.7 1.0 OD1 E:ASN1063 2.3 42.1 1.0 ND2 F:ASN1063 2.4 53.2 1.0 OD1 F:ASN1063 2.4 52.2 1.0 OE1 E:GLN1066 2.4 82.0 1.0 CG E:ASN1063 2.5 41.4 1.0 NE2 D:GLN1066 2.6 72.5 1.0 OD1 D:ASN1063 2.7 63.1 1.0 CG F:ASN1063 2.7 58.2 1.0 CD D:GLN1066 2.7 65.1 1.0 ND2 E:ASN1063 2.9 50.1 1.0 NE2 F:GLN1066 3.3 58.3 1.0 CB E:ASN1063 3.3 59.4 1.0 CD E:GLN1066 3.4 76.7 1.0 CA E:ASN1063 3.4 59.8 1.0 CG D:ASN1063 3.6 76.5 1.0 N E:ASN1063 4.0 60.0 1.0 NE2 E:GLN1066 4.1 74.1 1.0 ND2 D:ASN1063 4.2 60.3 1.0 CB F:ASN1063 4.2 57.5 1.0 CG D:GLN1066 4.2 93.9 1.0 CD F:GLN1066 4.4 56.1 1.0 CG E:GLN1066 4.5 71.3 1.0 CB E:GLN1066 4.6 68.5 1.0 C E:LYS1062 4.6 68.4 1.0 CG D:LYS1062 4.6 69.5 1.0 CA D:ASN1063 4.7 82.3 1.0 N D:ASN1063 4.7 79.6 1.0 C E:ASN1063 4.7 69.8 1.0 CB D:ASN1063 4.7 77.2 1.0 OE1 F:GLN1066 4.8 67.8 1.0 O E:LYS1062 4.9 71.6 1.0 O E:ASN1063 5.0 74.4 1.0 CB D:LYS1062 5.0 88.2 1.0 CB D:GLN1066 5.0 65.5 1.0

Calcium binding site 3 out of 4 in the Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1301 b:36.0 occ:1.00 OD1 H:ASN1063 2.3 62.8 1.0 OD1 G:ASN1063 2.3 35.5 1.0 OE1 G:GLN1066 2.3 36.5 1.0 OE1 H:GLN1066 2.3 51.6 1.0 OD1 I:ASN1063 2.3 40.4 1.0 NE2 I:GLN1066 2.4 70.3 1.0 CG H:ASN1063 3.3 65.4 1.0 CD G:GLN1066 3.4 77.3 1.0 CG G:ASN1063 3.4 67.7 1.0 CD H:GLN1066 3.5 53.3 1.0 CG I:ASN1063 3.5 48.3 1.0 CD I:GLN1066 3.7 67.2 1.0 NE2 G:GLN1066 4.0 37.5 1.0 ND2 H:ASN1063 4.0 66.7 1.0 NE2 H:GLN1066 4.1 42.6 1.0 CA G:ASN1063 4.2 54.4 1.0 OE1 I:GLN1066 4.3 66.1 1.0 ND2 G:ASN1063 4.3 35.3 1.0 ND2 I:ASN1063 4.3 39.9 1.0 CA H:ASN1063 4.3 63.5 1.0 CB H:ASN1063 4.4 65.7 1.0 CB G:ASN1063 4.4 63.2 1.0 CA I:ASN1063 4.5 41.8 1.0 CB I:ASN1063 4.5 51.5 1.0 O G:LYS1062 4.6 52.9 1.0 CG H:GLN1066 4.6 54.1 1.0 CG G:GLN1066 4.7 69.6 1.0 CB H:GLN1066 4.7 55.6 1.0 N G:ASN1063 4.8 55.9 1.0 CB G:GLN1066 4.8 61.8 1.0 N H:ASN1063 4.8 60.8 1.0 CG I:GLN1066 4.8 63.0 1.0 C G:LYS1062 4.9 51.5 1.0

Calcium binding site 4 out of 4 in the Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca1301 b:99.6 occ:1.00 OD1 J:ASN1063 2.3 77.9 1.0 OE1 J:GLN1066 2.4 59.8 1.0 ND2 K:ASN1063 2.5 48.1 1.0 CA J:ASN1063 2.7 42.9 1.0 CG J:ASN1063 2.9 78.0 1.0 NE2 L:GLN1066 3.0 31.6 1.0 CD J:GLN1066 3.0 59.5 1.0 CG K:ASN1063 3.1 45.6 1.0 OD1 K:ASN1063 3.1 44.5 1.0 OD1 L:ASN1063 3.1 37.3 1.0 N J:ASN1063 3.2 43.9 1.0 CB J:ASN1063 3.3 42.5 1.0 OE1 L:GLN1066 3.4 44.8 1.0 O J:LYS1062 3.5 60.8 1.0 C J:LYS1062 3.5 50.6 1.0 CD L:GLN1066 3.6 39.3 1.0 CG J:GLN1066 3.7 58.2 1.0 CB J:GLN1066 3.7 56.0 1.0 C J:ASN1063 3.8 52.3 1.0 NE2 J:GLN1066 3.8 60.0 1.0 ND2 J:ASN1063 3.9 77.6 1.0 CG L:ASN1063 4.0 39.6 1.0 CG J:LYS1062 4.0 53.8 1.0 ND2 L:ASN1063 4.0 28.8 1.0 O J:ASN1063 4.0 52.7 1.0 OE1 K:GLN1066 4.2 47.7 1.0 CB K:ASN1063 4.3 37.6 1.0 O J:ALA1059 4.5 0.1 1.0 CB J:LYS1062 4.7 49.9 1.0 CA J:LYS1062 4.7 51.0 1.0 CD J:LYS1062 4.9 57.7 1.0 N J:ASP1064 4.9 58.3 1.0 CG L:GLN1066 5.0 46.5 1.0

A.Bhardwaj, S.R.Casjens, G.Cingolani. Exploring the Atomic Structure and Conformational Flexibility of A 320 Angstrom Long Engineered Viral Fiber Using X-Ray Crystallography. Acta Crystallogr.,Sect.D V. 70 342 2014.
ISSN: ISSN 0907-4449
PubMed: 24531468
DOI: 10.1107/S1399004713027685