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Chlorine in PDB 3rul: New Strategy to Analyze Structures of Glycopeptide-Target Complexes

Protein crystallography data

The structure of New Strategy to Analyze Structures of Glycopeptide-Target Complexes, PDB code: 3rul was solved by N.J.Economou, V.Nahoum, S.D.Weeks, K.C.Grasty, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.60 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.300, 86.250, 107.190, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 27.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes (pdb code 3rul). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes, PDB code: 3rul:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 3rul

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Chlorine binding site 1 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl3

b:55.0
occ:1.00
 CL E:HCL3 0.0 55.0 1.0
C2 E:HCL3 1.7 50.7 1.0
C3 E:HCL3 2.7 65.0 1.0
C1 E:HCL3 2.7 48.3 1.0
O3 E:HCL3 2.8 50.5 1.0
CA E:HCL3 3.1 55.0 1.0
O E:HCL3 3.6 46.6 1.0
C E:HCL3 3.9 56.7 1.0
C4 E:HCL3 4.0 57.1 1.0
C5 E:HCL3 4.0 49.0 1.0
O E:DTY2 4.1 53.6 1.0
N E:HCL3 4.3 54.6 1.0
C6 E:HCL3 4.5 57.5 1.0
C E:DTY2 4.6 43.2 1.0

Chlorine binding site 2 out of 9 in 3rul

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Chlorine binding site 2 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl6

b:67.4
occ:1.00
 CL E:OMY6 0.0 67.4 1.0
CE1 E:OMY6 1.7 65.8 1.0
CZ E:OMY6 2.7 55.5 1.0
CD1 E:OMY6 2.7 61.0 1.0
OCZ E:OMY6 2.9 60.6 1.0
O6B E:N1L8 3.1 75.4 1.0
C5 E:GHP4 3.2 59.6 1.0
O5 E:N1L8 3.2 67.4 1.0
C6 E:N1L8 3.3 71.0 1.0
CB A:DAL79 3.5 42.9 1.0
C6 E:GHP4 3.5 53.1 1.0
C A:DAL78 3.7 46.9 1.0
O6A E:N1L8 3.7 69.2 1.0
C5 E:N1L8 3.8 73.4 1.0
N A:DAL79 3.9 54.0 1.0
O A:DAL78 3.9 53.6 1.0
CE2 E:OMY6 4.0 50.9 1.0
CG E:OMY6 4.0 62.4 1.0
C4 E:GHP4 4.0 61.8 1.0
CA A:DAL78 4.1 49.9 1.0
N A:DAL78 4.3 55.4 1.0
CA A:DAL79 4.3 52.1 1.0
C1 E:N1L8 4.4 62.8 1.0
O4 E:GHP4 4.5 69.2 1.0
CD2 E:OMY6 4.5 62.9 1.0
C1 E:GHP4 4.5 43.9 1.0
O A:CCS76 4.6 66.1 1.0
C A:CCS76 4.6 72.0 1.0
O A:GLY75 4.6 69.8 1.0
O E:GHP4 4.6 66.8 1.0
C A:LYS77 4.7 61.2 1.0
CA A:CCS76 4.8 71.2 1.0
O A:LYS77 4.9 53.3 1.0
C3 E:GHP4 4.9 67.7 1.0

Chlorine binding site 3 out of 9 in 3rul

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Chlorine binding site 3 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl3

b:54.2
occ:1.00
 CL F:HCL3 0.0 54.2 1.0
C2 F:HCL3 1.7 58.6 1.0
C3 F:HCL3 2.7 55.7 1.0
C1 F:HCL3 2.8 50.5 1.0
O3 F:HCL3 2.9 56.0 1.0
CA F:HCL3 3.1 45.8 1.0
O F:HCL3 3.7 39.8 1.0
C F:HCL3 3.9 54.3 1.0
C4 F:HCL3 4.0 53.1 1.0
C5 F:HCL3 4.0 50.5 1.0
O F:DTY2 4.1 58.8 1.0
N F:HCL3 4.3 50.2 1.0
C F:DTY2 4.5 53.1 1.0
C6 F:HCL3 4.5 50.5 1.0

Chlorine binding site 4 out of 9 in 3rul

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Chlorine binding site 4 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl6

b:69.0
occ:1.00
 CL F:OMY6 0.0 69.0 1.0
CE1 F:OMY6 1.7 61.3 1.0
CD1 F:OMY6 2.7 61.5 1.0
CZ F:OMY6 2.7 56.2 1.0
OCZ F:OMY6 3.0 67.3 1.0
O6B F:N1L8 3.0 64.1 1.0
C5 F:GHP4 3.5 52.7 1.0
C6 F:N1L8 3.5 76.6 1.0
O5 F:N1L8 3.5 55.9 1.0
CB B:DAL79 3.5 48.4 1.0
N B:DAL79 3.7 56.3 1.0
C B:DAL78 3.8 56.5 1.0
C6 F:GHP4 3.8 46.4 1.0
N B:DAL78 4.0 58.1 1.0
CG F:OMY6 4.0 68.9 1.0
CA B:DAL78 4.0 57.8 1.0
CE2 F:OMY6 4.0 49.8 1.0
O B:CCS76 4.1 77.5 1.0
C5 F:N1L8 4.1 60.4 1.0
O6A F:N1L8 4.1 69.3 1.0
C B:LYS77 4.2 65.7 1.0
C B:CCS76 4.2 78.6 1.0
CA B:DAL79 4.2 63.1 1.0
O B:DAL78 4.3 49.2 1.0
C4 F:GHP4 4.3 66.1 1.0
O B:LYS77 4.3 60.0 1.0
CD2 F:OMY6 4.5 59.6 1.0
CA B:CCS76 4.6 74.1 1.0
N B:LYS77 4.6 65.2 1.0
O4 F:GHP4 4.7 71.6 1.0
O F:GHP4 4.7 52.6 1.0
C1 F:N1L8 4.7 68.4 1.0
O B:GLY75 4.7 73.1 1.0
C1 F:GHP4 4.8 60.5 1.0
CA B:LYS77 5.0 71.8 1.0

Chlorine binding site 5 out of 9 in 3rul

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Chlorine binding site 5 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl3

b:42.9
occ:1.00
 CL G:HCL3 0.0 42.9 1.0
C2 G:HCL3 1.7 55.7 1.0
C3 G:HCL3 2.7 57.2 1.0
C1 G:HCL3 2.7 52.0 1.0
O3 G:HCL3 2.9 51.0 1.0
CA G:HCL3 3.1 48.0 1.0
O G:HCL3 3.7 43.5 1.0
C G:HCL3 3.9 48.6 1.0
C4 G:HCL3 4.0 45.3 1.0
C5 G:HCL3 4.0 54.2 1.0
O G:DTY2 4.1 47.5 1.0
N G:HCL3 4.3 48.3 1.0
C6 G:HCL3 4.5 52.1 1.0
C G:DTY2 4.6 39.9 1.0

Chlorine binding site 6 out of 9 in 3rul

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Chlorine binding site 6 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl6

b:74.6
occ:1.00
 CL G:OMY6 0.0 74.6 1.0
CE1 G:OMY6 1.7 75.2 1.0
CZ G:OMY6 2.7 64.8 1.0
CD1 G:OMY6 2.7 62.2 1.0
OCZ G:OMY6 3.0 66.6 1.0
O6B G:N1L8 3.0 68.1 1.0
O5 G:N1L8 3.5 64.5 1.0
C5 G:GHP4 3.5 52.6 1.0
C6 G:N1L8 3.7 83.5 1.0
C6 G:GHP4 3.8 54.6 1.0
CB C:DAL79 3.8 45.9 1.0
C C:DAL78 3.9 62.3 1.0
CA C:DAL78 4.0 54.0 1.0
CE2 G:OMY6 4.0 58.1 1.0
CG G:OMY6 4.0 70.4 1.0
N C:DAL78 4.1 54.4 1.0
N C:DAL79 4.1 50.2 1.0
C5 G:N1L8 4.2 68.8 1.0
C4 G:GHP4 4.2 50.7 1.0
O C:CCS76 4.3 75.0 1.0
O C:DAL78 4.3 64.5 1.0
C C:CCS76 4.3 78.9 1.0
C C:LYS77 4.4 72.4 1.0
O6A G:N1L8 4.4 77.9 1.0
CD2 G:OMY6 4.5 61.9 1.0
O C:LYS77 4.5 64.9 1.0
O4 G:GHP4 4.6 58.8 1.0
C1 G:N1L8 4.6 70.9 1.0
CA C:DAL79 4.6 52.3 1.0
CA C:CCS76 4.6 78.2 1.0
O C:GLY75 4.7 73.7 1.0
O G:GHP4 4.8 45.1 1.0
N C:LYS77 4.8 69.2 1.0
C1 G:GHP4 4.8 48.8 1.0

Chlorine binding site 7 out of 9 in 3rul

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Chlorine binding site 7 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl3

b:38.4
occ:1.00
 CL H:HCL3 0.0 38.4 1.0
C2 H:HCL3 1.7 50.9 1.0
C3 H:HCL3 2.7 56.6 1.0
C1 H:HCL3 2.7 47.5 1.0
O3 H:HCL3 2.9 46.4 1.0
CA H:HCL3 3.1 44.7 1.0
O H:HCL3 3.6 48.6 1.0
C H:HCL3 3.9 47.2 1.0
C4 H:HCL3 4.0 52.1 1.0
C5 H:HCL3 4.0 45.1 1.0
O H:DTY2 4.1 44.1 1.0
N H:HCL3 4.3 45.7 1.0
C6 H:HCL3 4.5 53.9 1.0
C H:DTY2 4.6 40.8 1.0

Chlorine binding site 8 out of 9 in 3rul

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Chlorine binding site 8 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl6

b:68.3
occ:1.00
 CL H:OMY6 0.0 68.3 1.0
CE1 H:OMY6 1.7 54.6 1.0
CD1 H:OMY6 2.7 51.7 1.0
CZ H:OMY6 2.7 45.3 1.0
OCZ H:OMY6 3.0 59.7 1.0
O6B H:N1L8 3.1 69.3 1.0
CB D:DAL79 3.4 48.5 1.0
C5 H:GHP4 3.5 54.4 1.0
C6 H:N1L8 3.5 69.6 1.0
C D:DAL78 3.6 63.9 1.0
O5 H:N1L8 3.6 59.0 1.0
O H:HOH203 3.6 64.0 1.0
N D:DAL79 3.7 58.4 1.0
C6 H:GHP4 3.7 52.4 1.0
O D:DAL78 3.8 66.6 1.0
CG H:OMY6 4.0 52.1 1.0
CE2 H:OMY6 4.0 47.4 1.0
CA D:DAL78 4.1 72.3 1.0
O6A H:N1L8 4.1 66.8 1.0
C5 H:N1L8 4.1 65.4 1.0
O D:CCS76 4.1 68.5 1.0
N D:DAL78 4.2 61.2 1.0
CA D:DAL79 4.2 63.8 1.0
C D:CCS76 4.3 74.2 1.0
C D:LYS77 4.3 64.8 1.0
C4 H:GHP4 4.4 60.9 1.0
O D:LYS77 4.4 58.8 1.0
CD2 H:OMY6 4.5 42.7 1.0
O H:GHP4 4.6 56.5 1.0
CA D:CCS76 4.6 71.7 1.0
O D:GLY75 4.7 70.6 1.0
N D:LYS77 4.7 64.3 1.0
C1 H:N1L8 4.7 62.1 1.0
O4 H:GHP4 4.8 69.5 1.0
C1 H:GHP4 4.8 50.8 1.0

Chlorine binding site 9 out of 9 in 3rul

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Chlorine binding site 9 out of 9 in the New Strategy to Analyze Structures of Glycopeptide-Target Complexes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of New Strategy to Analyze Structures of Glycopeptide-Target Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:65.9
occ:1.00
 NZ B:LYS27 3.2 57.5 1.0
CD B:ARG42 3.4 44.6 1.0
NE2 B:GLN49 3.5 59.7 1.0
NE B:ARG42 3.7 46.0 1.0
O B:GLN41 4.1 57.6 1.0
O B:LEU50 4.1 62.0 1.0
CZ B:ARG42 4.4 54.3 1.0
CD B:GLN49 4.4 60.4 1.0
OD1 B:ASP52 4.5 88.0 1.0
CE B:LYS27 4.6 63.0 1.0
NH1 B:ARG42 4.7 54.4 1.0
CG B:GLN49 4.8 64.4 1.0
CG B:ARG42 4.8 43.6 1.0
CA B:ARG42 4.9 48.7 1.0
OD2 B:ASP52 4.9 80.2 1.0
CG B:ASP52 4.9 82.1 1.0
O41 B:TLA102 4.9 61.7 1.0

Reference:

N.J.Economou, V.Nahoum, S.D.Weeks, K.C.Grasty, I.J.Zentner, T.M.Townsend, M.W.Bhuiya, S.Cocklin, P.J.Loll. A Carrier Protein Strategy Yields the Structure of Dalbavancin. J.Am.Chem.Soc. V. 134 4637 2012.
ISSN: ISSN 0002-7863
PubMed: 22352468
DOI: 10.1021/JA208755J
Page generated: Sun Jul 21 03:57:59 2024

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