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Chlorine in PDB 6m5e: Human Serum Albumin with Cyclic Peptide Dalbavancin

Protein crystallography data

The structure of Human Serum Albumin with Cyclic Peptide Dalbavancin, PDB code: 6m5e was solved by S.Ito, A.Senoo, S.Nagatoishi, M.Ohue, M.Yamamoto, K.Tsumoto, N.Wakui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.78 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.050, 125.680, 125.740, 90.00, 90.32, 90.00
R / Rfree (%) 18 / 22.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Serum Albumin with Cyclic Peptide Dalbavancin (pdb code 6m5e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Human Serum Albumin with Cyclic Peptide Dalbavancin, PDB code: 6m5e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6m5e

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Chlorine binding site 1 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl3

b:0.0
occ:1.00
 CL F:HCL3 0.0 0.0 1.0
C2 F:HCL3 1.7 0.5 1.0
C3 F:HCL3 2.7 0.6 1.0
C1 F:HCL3 2.7 0.7 1.0
O3 F:HCL3 3.0 0.4 1.0
CA F:HCL3 3.0 0.0 1.0
C F:HCL3 3.2 97.6 1.0
O F:HCL3 3.5 0.0 1.0
N F:D4P4 3.9 92.2 1.0
C4 F:HCL3 4.0 1.0 1.0
C5 F:HCL3 4.0 0.1 1.0
N F:HCL3 4.3 92.2 1.0
C6 F:HCL3 4.5 0.3 1.0
N F:D4P5 4.7 85.4 1.0
CA F:D4P4 4.7 81.9 1.0

Chlorine binding site 2 out of 10 in 6m5e

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Chlorine binding site 2 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl6

b:0.6
occ:1.00
 CL F:OMZ6 0.0 0.6 1.0
CE1 F:OMZ6 1.7 96.1 1.0
CD1 F:OMZ6 2.7 83.7 1.0
CZ F:OMZ6 2.7 84.5 1.0
OH F:OMZ6 3.0 83.9 1.0
O A:GLU60 3.4 71.2 1.0
C5 F:D4P4 3.4 75.3 1.0
CD1 A:PHE49 3.6 45.6 1.0
CB A:GLU60 3.7 73.0 1.0
CE1 A:PHE49 3.7 41.7 1.0
C6 F:D4P4 3.7 71.1 1.0
O F:D4P4 3.8 95.3 1.0
CE2 F:OMZ6 4.0 80.7 1.0
CG F:OMZ6 4.0 82.1 1.0
C A:GLU60 4.0 68.8 1.0
CG A:GLU60 4.1 80.7 1.0
C4 F:D4P4 4.2 77.6 1.0
C2 F:M12102 4.3 83.4 1.0
CB A:ASN61 4.4 65.6 1.0
CA A:GLU60 4.4 67.3 1.0
CD2 F:OMZ6 4.5 83.4 1.0
C1 F:D4P4 4.6 73.3 1.0
O4 F:D4P4 4.6 93.7 1.0
C F:D4P4 4.8 84.0 1.0
CG A:PHE49 4.8 45.0 1.0
CG A:ASN61 4.8 71.4 1.0
ND2 A:ASN61 4.8 68.0 1.0
C1 F:M12102 4.9 88.0 1.0
N A:ASN61 5.0 70.0 1.0
CZ A:PHE49 5.0 44.2 1.0
N A:GLU60 5.0 68.7 1.0

Chlorine binding site 3 out of 10 in 6m5e

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Chlorine binding site 3 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl3

b:0.6
occ:1.00
 CL G:HCL3 0.0 0.6 1.0
C2 G:HCL3 1.7 0.1 1.0
C3 G:HCL3 2.7 0.7 1.0
C1 G:HCL3 2.7 0.9 1.0
O3 G:HCL3 2.9 0.0 1.0
CA G:HCL3 3.1 0.4 1.0
C G:HCL3 3.3 0.4 1.0
O G:HCL3 3.5 0.4 1.0
C4 G:HCL3 4.0 0.1 1.0
C5 G:HCL3 4.0 98.7 1.0
N G:D4P4 4.1 0.9 1.0
N G:HCL3 4.3 0.8 1.0
C6 G:HCL3 4.5 0.9 1.0
N G:D4P5 4.9 0.0 1.0
CA G:D4P4 5.0 0.1 1.0

Chlorine binding site 4 out of 10 in 6m5e

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Chlorine binding site 4 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl6

b:0.1
occ:1.00
 CL G:OMZ6 0.0 0.1 1.0
CE1 G:OMZ6 1.7 0.8 1.0
CD1 G:OMZ6 2.7 98.8 1.0
CZ G:OMZ6 2.7 0.9 1.0
OH G:OMZ6 3.0 0.9 1.0
C5 G:D4P4 3.2 0.8 1.0
C6 G:D4P4 3.4 0.4 1.0
CB B:GLU60 3.5 73.4 1.0
O B:GLU60 3.7 76.1 1.0
CG B:GLU60 3.7 94.0 1.0
O G:D4P4 3.8 95.5 1.0
C4 G:D4P4 4.0 0.9 1.0
CE2 G:OMZ6 4.0 0.3 1.0
CG G:OMZ6 4.0 98.3 1.0
CD1 B:PHE49 4.0 51.6 1.0
C B:GLU60 4.2 68.6 1.0
C1 G:D4P4 4.2 0.6 1.0
C2 G:M12102 4.2 85.7 1.0
CE1 B:PHE49 4.3 55.9 1.0
O4 G:D4P4 4.4 93.9 1.0
CA B:GLU60 4.5 66.9 1.0
CD2 G:OMZ6 4.5 0.6 1.0
C G:D4P4 4.6 97.5 1.0
CB B:ASN61 4.6 57.8 1.0
C1 G:M12102 4.7 91.9 1.0
CA G:D4P4 4.8 0.1 1.0
C3 G:D4P4 4.8 0.0 1.0
ND2 B:ASN61 4.8 58.7 1.0
C2 G:D4P4 4.9 0.2 1.0
CG B:ASN61 5.0 60.9 1.0
O1 G:M12102 5.0 93.8 1.0

Chlorine binding site 5 out of 10 in 6m5e

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Chlorine binding site 5 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl3

b:0.2
occ:1.00
 CL H:HCL3 0.0 0.2 1.0
C2 H:HCL3 1.7 0.7 1.0
C3 H:HCL3 2.7 0.1 1.0
C1 H:HCL3 2.7 0.6 1.0
O3 H:HCL3 2.9 0.4 1.0
CA H:HCL3 3.0 93.0 1.0
C H:HCL3 3.1 83.4 1.0
O H:HCL3 3.2 87.5 1.0
N H:D4P4 3.8 80.4 1.0
C4 H:HCL3 4.0 0.3 1.0
C5 H:HCL3 4.0 0.9 1.0
N H:HCL3 4.3 95.2 1.0
C6 H:HCL3 4.4 98.7 1.0
N H:D4P5 4.6 78.7 1.0
CA H:D4P4 4.6 74.9 1.0

Chlorine binding site 6 out of 10 in 6m5e

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Chlorine binding site 6 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl6

b:0.8
occ:1.00
 CL H:OMZ6 0.0 0.8 1.0
CE1 H:OMZ6 1.7 86.8 1.0
CD1 H:OMZ6 2.7 77.5 1.0
CZ H:OMZ6 2.7 70.2 1.0
OH H:OMZ6 3.0 74.2 1.0
O C:GLU60 3.4 57.7 1.0
C5 H:D4P4 3.4 72.8 1.0
CD1 C:PHE49 3.6 37.8 1.0
C6 H:D4P4 3.8 69.8 1.0
CE1 C:PHE49 3.8 45.9 1.0
CB C:GLU60 3.9 59.0 1.0
CE2 H:OMZ6 4.0 63.3 1.0
CG H:OMZ6 4.0 66.1 1.0
O H:D4P4 4.0 81.9 1.0
C2 H:M12102 4.1 79.0 1.0
C C:GLU60 4.1 52.5 1.0
C4 H:D4P4 4.2 78.3 1.0
CG C:GLU60 4.4 57.1 1.0
CD2 H:OMZ6 4.5 64.7 1.0
CB C:ASN61 4.5 59.4 1.0
O4 H:D4P4 4.5 89.4 1.0
CA C:GLU60 4.6 54.8 1.0
C1 H:M12102 4.6 84.4 1.0
C1 H:D4P4 4.7 70.6 1.0
CG C:PHE49 4.8 36.2 1.0
ND2 C:ASN61 4.9 64.7 1.0
O1 H:M12102 4.9 89.8 1.0
C H:D4P4 4.9 74.1 1.0
CG C:ASN61 5.0 65.4 1.0

Chlorine binding site 7 out of 10 in 6m5e

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Chlorine binding site 7 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl3

b:0.9
occ:1.00
 CL I:HCL3 0.0 0.9 1.0
C2 I:HCL3 1.7 0.1 1.0
C3 I:HCL3 2.7 97.0 1.0
C1 I:HCL3 2.7 99.4 1.0
O3 I:HCL3 2.9 0.8 1.0
CA I:HCL3 3.1 88.7 1.0
N I:HCL3 3.8 85.5 1.0
C5 I:HCL3 4.0 94.4 1.0
C4 I:HCL3 4.0 84.9 1.0
O I:TYR2 4.2 0.4 1.0
C I:HCL3 4.2 81.3 1.0
N I:D4P4 4.4 62.2 1.0
C I:TYR2 4.4 90.0 1.0
C6 I:HCL3 4.5 85.2 1.0
O I:D4P4 4.9 92.2 1.0

Chlorine binding site 8 out of 10 in 6m5e

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Chlorine binding site 8 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl6

b:0.1
occ:1.00
 CL1 I:F936 0.0 0.1 1.0
CE1 I:F936 1.7 85.8 1.0
CD1 I:F936 2.7 76.0 1.0
CZ I:F936 2.7 75.3 1.0
OH I:F936 2.9 66.0 1.0
O6A I:F8X102 3.2 85.0 1.0
C5 I:D4P4 3.5 51.9 1.0
O5 I:F8X102 3.8 63.0 1.0
C6 I:D4P4 4.0 50.2 1.0
CE2 I:F936 4.0 82.9 1.0
CG I:F936 4.0 72.2 1.0
C6 I:F8X102 4.2 83.6 1.0
C4 I:D4P4 4.3 43.1 1.0
C1 I:F8X102 4.4 64.5 1.0
CD2 I:F936 4.5 88.8 1.0
O4 I:D4P4 4.5 51.2 1.0
C5 I:F8X102 4.5 67.1 1.0

Chlorine binding site 9 out of 10 in 6m5e

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Chlorine binding site 9 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl3

b:0.1
occ:1.00
 CL J:HCL3 0.0 0.1 1.0
C2 J:HCL3 1.7 0.7 1.0
C3 J:HCL3 2.7 0.2 1.0
C1 J:HCL3 2.7 95.8 1.0
O3 J:HCL3 3.0 0.3 1.0
CA J:HCL3 3.1 87.6 1.0
N J:HCL3 3.8 95.5 1.0
C5 J:HCL3 4.0 87.3 1.0
C4 J:HCL3 4.0 95.2 1.0
C J:HCL3 4.2 78.7 1.0
N J:D4P4 4.3 60.7 1.0
O J:TYR2 4.4 0.9 1.0
C6 J:HCL3 4.5 84.8 1.0
C J:TYR2 4.5 90.3 1.0
O J:D4P4 4.8 86.2 1.0

Chlorine binding site 10 out of 10 in 6m5e

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Chlorine binding site 10 out of 10 in the Human Serum Albumin with Cyclic Peptide Dalbavancin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Human Serum Albumin with Cyclic Peptide Dalbavancin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl6

b:0.2
occ:1.00
 CL1 J:F936 0.0 0.2 1.0
CE1 J:F936 1.7 77.3 1.0
CD1 J:F936 2.7 60.5 1.0
CZ J:F936 2.7 61.8 1.0
OH J:F936 3.0 61.0 1.0
O6B J:F8X102 3.4 72.5 1.0
C5 J:D4P4 3.5 51.7 1.0
C6 J:D4P4 3.8 51.6 1.0
OE1 B:GLN170 3.9 45.2 1.0
O B:CYS169 3.9 55.0 1.0
O5 J:F8X102 4.0 63.8 1.0
CE2 J:F936 4.0 70.0 1.0
CG J:F936 4.0 62.5 1.0
O B:GLN170 4.0 41.6 1.0
CA B:GLN170 4.1 40.1 1.0
C B:GLN170 4.2 40.2 1.0
C4 J:D4P4 4.2 42.5 1.0
C6 J:F8X102 4.4 75.3 1.0
C1 J:F8X102 4.5 62.5 1.0
CD2 J:F936 4.5 80.5 1.0
NZ B:LYS174 4.5 62.4 1.0
O4 J:D4P4 4.6 52.4 1.0
C5 J:F8X102 4.7 69.2 1.0
O B:ALA171 4.7 42.4 1.0
C1 J:D4P4 4.8 44.2 1.0
CD B:GLN170 4.8 54.0 1.0
C B:CYS169 4.9 45.0 1.0
N J:F936 4.9 57.0 1.0
N B:GLN170 5.0 38.5 1.0

Reference:

S.Ito, A.Senoo, S.Nagatoishi, M.Ohue, M.Yamamoto, K.Tsumoto, N.Wakui. Structural Basis For the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin. J.Med.Chem. V. 63 14045 2020.
ISSN: ISSN 0022-2623
PubMed: 33183011
DOI: 10.1021/ACS.JMEDCHEM.0C01578
Page generated: Sun Jul 28 03:02:44 2024

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