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Iodine in PDB 4e27: Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing

Protein crystallography data

The structure of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing, PDB code: 4e27 was solved by T.K.Craig, J.Abendroth, D.Lorimer, A.B.Burgin Jr, A.Segall, F.Rohwer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.51 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.710, 68.360, 107.830, 90.00, 93.69, 90.00
R / Rfree (%) 20.2 / 25.6

Other elements in 4e27:

The structure of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing (pdb code 4e27). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 28 binding sites of Iodine where determined in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing, PDB code: 4e27:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 28 in 4e27

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Iodine binding site 1 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:37.4
occ:1.00
N A:ALA144 3.6 21.7 1.0
CG2 A:VAL169 4.0 16.8 1.0
CB A:VAL143 4.0 14.4 1.0
CA A:VAL143 4.1 21.4 1.0
CG A:PRO82 4.1 20.8 1.0
CB A:ALA144 4.2 18.8 1.0
CB A:PRO82 4.2 21.2 1.0
CG1 A:VAL169 4.3 9.8 1.0
CG1 A:VAL143 4.4 15.2 1.0
C A:VAL143 4.4 21.5 1.0
CA A:ALA144 4.5 19.9 1.0
CB A:VAL169 4.6 14.9 1.0

Iodine binding site 2 out of 28 in 4e27

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Iodine binding site 2 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:31.4
occ:1.00
O E:HOH301 3.2 6.1 1.0
O B:HOH382 3.3 27.1 1.0
O D:HOH315 3.3 14.5 1.0
O A:HOH334 3.3 10.7 1.0
O C:HOH352 3.4 21.3 1.0
O D:HOH391 3.8 22.2 1.0
NE2 C:GLN130 4.0 10.7 1.0
CG D:GLN130 4.0 8.5 1.0
CG B:GLN130 4.1 4.4 1.0
CG C:GLN130 4.1 9.5 1.0
CG E:GLN130 4.2 9.0 1.0
NE2 B:GLN130 4.2 10.7 1.0
CG A:GLN130 4.2 12.3 1.0
NE2 D:GLN130 4.2 14.0 1.0
NE2 A:GLN130 4.3 13.2 1.0
CD C:GLN130 4.4 11.3 1.0
CD D:GLN130 4.4 13.1 1.0
NE2 E:GLN130 4.5 6.5 1.0
CD B:GLN130 4.5 8.9 1.0
CD A:GLN130 4.6 15.8 1.0
CD E:GLN130 4.6 11.5 1.0

Iodine binding site 3 out of 28 in 4e27

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Iodine binding site 3 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:47.5
occ:1.00
O A:GLN53 3.2 38.4 1.0
N A:GLU55 3.6 17.8 1.0
C A:GLN53 3.7 33.9 1.0
NH1 E:ARG54 3.7 18.5 1.0
C A:ARG54 3.7 18.0 1.0
CA A:ARG54 4.0 20.3 1.0
O A:HOH342 4.0 24.0 1.0
CA A:GLU55 4.0 20.3 1.0
N A:ARG54 4.0 25.7 1.0
O A:ARG54 4.2 19.2 1.0
CD1 A:LEU173 4.2 21.5 1.0
CA A:GLN53 4.5 38.6 1.0
CB A:GLN58 4.5 12.7 1.0
O A:ALA52 4.6 51.0 1.0
CD E:ARG54 4.7 17.1 1.0
CB A:GLU55 4.7 22.3 1.0
CZ E:ARG54 4.9 19.9 1.0
CG A:GLN58 4.9 13.5 1.0

Iodine binding site 4 out of 28 in 4e27

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Iodine binding site 4 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:75.5
occ:1.00
O A:LEU63 3.7 10.7 1.0
CG2 C:THR111 3.8 11.0 1.0
OG1 C:THR111 4.0 21.4 1.0
CB C:THR111 4.0 15.4 1.0
NZ C:LYS113 4.1 6.5 1.0
O A:HOH384 4.1 24.2 1.0
O C:HOH379 4.1 34.6 1.0
CA A:ILE64 4.2 15.7 1.0
CG A:LEU63 4.2 15.1 1.0
CG1 A:ILE64 4.2 13.6 1.0
C A:LEU63 4.3 12.8 1.0
CE C:LYS113 4.3 7.5 1.0
O C:HOH370 4.5 16.9 1.0
N A:ILE64 4.6 14.4 1.0
CD1 A:LEU63 4.7 17.0 1.0
CB A:ILE64 4.8 15.4 1.0
CD2 A:LEU63 4.9 16.1 1.0

Iodine binding site 5 out of 28 in 4e27

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Iodine binding site 5 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:83.5
occ:1.00
O E:HOH356 2.8 3.9 1.0
CA A:GLY125 3.9 8.2 1.0
O A:HOH405 4.3 30.0 1.0
C A:GLY125 4.3 9.3 1.0
O A:GLY125 4.5 6.0 1.0
O E:HOH328 4.7 11.5 1.0
N A:GLY125 4.8 9.7 1.0
N A:THR126 5.0 10.9 1.0

Iodine binding site 6 out of 28 in 4e27

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Iodine binding site 6 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:0.6
occ:1.00
C A:PHE5 3.4 61.0 1.0
O A:PHE5 3.6 61.5 1.0
N A:ARG6 3.7 62.6 1.0
CA A:PHE5 3.8 60.0 1.0
OG A:SER33 3.9 48.7 1.0
CB A:ARG6 4.2 64.9 1.0
N A:PHE5 4.2 59.5 1.0
CA A:ARG6 4.3 64.2 1.0
O A:GLN4 4.4 60.6 1.0
C A:GLN4 4.5 59.1 1.0
CB A:SER33 4.9 47.6 1.0

Iodine binding site 7 out of 28 in 4e27

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Iodine binding site 7 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:90.6
occ:1.00
O A:HOH379 3.4 16.6 1.0
N A:GLY99 3.6 12.2 1.0
N A:ALA100 3.8 12.1 1.0
OG A:SER98 3.8 14.2 1.0
CA A:GLY99 3.9 12.4 1.0
O A:HOH306 3.9 11.4 1.0
C A:GLY99 4.0 13.3 1.0
CB A:ALA100 4.3 9.3 1.0
NH2 A:ARG94 4.3 16.6 1.0
CA A:ALA100 4.5 12.8 1.0
C A:SER98 4.7 12.0 1.0
O C:HOH365 4.7 32.2 1.0
ND2 A:ASN154 4.8 22.6 1.0
O A:GLY99 4.8 12.9 1.0
CA A:SER98 5.0 15.7 1.0
CB A:SER98 5.0 15.1 1.0

Iodine binding site 8 out of 28 in 4e27

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Iodine binding site 8 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I208

b:20.0
occ:1.00
NZ C:LYS141 3.3 21.1 1.0
CB A:ALA52 3.5 46.4 1.0
CZ C:PHE84 4.0 4.7 1.0
CD A:PRO176 4.1 22.9 1.0
CG A:PRO176 4.1 21.8 1.0
N A:ALA52 4.2 52.0 1.0
C A:GLY51 4.2 53.2 1.0
O A:GLY51 4.4 53.7 1.0
CE C:LYS141 4.4 19.1 1.0
CA A:ALA52 4.4 47.6 1.0
CB A:ASN175 4.5 20.0 1.0
O A:PRO176 4.5 23.2 1.0
O C:VAL169 4.6 21.8 1.0
CE1 C:PHE84 4.7 7.7 1.0
CA A:GLY51 4.7 55.1 1.0
CD C:LYS141 4.7 18.3 1.0
N A:PRO176 4.8 23.6 1.0
CE2 C:PHE84 5.0 4.1 1.0

Iodine binding site 9 out of 28 in 4e27

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Iodine binding site 9 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I201

b:40.2
occ:1.00
N B:ALA144 3.4 20.8 1.0
CB B:ALA144 3.9 21.4 1.0
CB B:VAL143 4.1 15.4 1.0
CG2 B:VAL169 4.1 30.3 1.0
CA B:ALA144 4.2 21.6 1.0
CA B:VAL143 4.2 16.3 1.0
CG B:PRO82 4.3 16.2 1.0
C B:VAL143 4.3 20.3 1.0
CB B:PRO82 4.3 16.8 1.0
CG1 B:VAL143 4.5 14.5 1.0
CG1 B:VAL169 4.5 29.4 1.0
CB B:VAL169 4.8 31.3 1.0

Iodine binding site 10 out of 28 in 4e27

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Iodine binding site 10 out of 28 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I202

b:73.0
occ:1.00
CB B:GLN53 3.9 20.0 1.0
CA B:GLN58 4.0 18.4 1.0
CD B:PRO176 4.0 19.6 1.0
N B:GLN58 4.1 18.6 1.0
C B:LEU57 4.4 20.6 1.0
CG B:PRO176 4.4 17.1 1.0
CB B:GLN58 4.4 16.4 1.0
O B:LEU57 4.5 21.8 1.0
CB B:LEU57 4.5 17.7 1.0
CZ E:PHE84 4.5 19.6 1.0
CA B:GLN53 4.5 30.0 1.0
O E:HOH367 4.7 34.2 1.0
OD1 B:ASN175 4.7 32.2 1.0
CG B:GLN58 4.8 17.8 1.0
CE2 E:PHE84 4.9 18.6 1.0

Reference:

T.K.Craig, J.Abendroth, D.Lorimer, A.B.Burgin Jr, A.Segall, F.Rohwer. Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences Solved By Iodide Sad Phasing To Be Published.
Page generated: Sun Dec 13 19:32:26 2020

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