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Chlorine in PDB 7lkc: Crystal Structure of Keratinimicin A

Protein crystallography data

The structure of Crystal Structure of Keratinimicin A, PDB code: 7lkc was solved by K.M.Davis, P.D.Jeffrey, M.R.Seyedsayamdost, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.97 / 0.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 20.72, 32.251, 37.941, 90, 90, 90
R / Rfree (%) 15.4 / 16.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Keratinimicin A (pdb code 7lkc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Keratinimicin A, PDB code: 7lkc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7lkc

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Chlorine binding site 1 out of 6 in the Crystal Structure of Keratinimicin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:10.9
occ:0.64
CL3 A:0UZ1 0.0 10.9 0.6
O4 A:0UZ1 0.7 12.1 0.4
C4 A:0UZ1 1.5 11.8 0.4
H7 A:0UZ1 1.5 14.5 0.4
C3 A:0UZ1 1.7 9.8 0.6
H8 A:0UZ1 1.9 14.4 0.4
C5 A:0UZ1 2.0 12.0 0.4
H7 A:0UZ1 2.6 12.5 0.6
C2 A:0UZ1 2.7 9.3 0.6
C4 A:0UZ1 2.7 9.8 0.6
C3 A:0UZ1 2.8 11.4 0.4
H6 A:0UZ1 2.8 11.2 0.6
O4 A:0UZ1 3.1 10.4 0.6
O A:HOH202 3.3 18.2 1.0
C6 A:0UZ1 3.4 11.9 0.4
CL3 A:0UZ1 3.6 11.2 0.4
O A:HOH209 3.7 15.2 1.0
C2 A:0UZ1 3.9 11.3 0.4
H9 A:0UZ1 4.0 14.3 0.4
C1 A:0UZ1 4.0 9.6 0.6
C5 A:0UZ1 4.0 9.8 0.6
C1 A:0UZ1 4.1 11.6 0.4
HO2 A:MAN101 4.2 22.4 1.0
H2 A:MAN101 4.3 20.9 1.0
H1 A:MAN101 4.4 18.5 1.0
O2 A:MAN101 4.5 18.7 1.0
C6 A:0UZ1 4.5 9.5 0.6
H6 A:0UZ1 4.7 13.6 0.4
H8 A:0UZ1 4.7 11.8 0.6
C2 A:MAN101 4.8 17.4 1.0
O2 A:FMT103 4.8 11.1 1.0
H A:FMT103 5.0 13.2 1.0

Chlorine binding site 2 out of 6 in 7lkc

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Chlorine binding site 2 out of 6 in the Crystal Structure of Keratinimicin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:11.2
occ:0.36
CL3 A:0UZ1 0.0 11.2 0.4
C4 A:0UZ1 1.1 9.8 0.6
C5 A:0UZ1 1.1 9.8 0.6
H8 A:0UZ1 1.3 11.8 0.6
O4 A:0UZ1 1.6 10.4 0.6
C3 A:0UZ1 1.7 11.4 0.4
H7 A:0UZ1 2.3 12.5 0.6
C6 A:0UZ1 2.3 9.5 0.6
C3 A:0UZ1 2.3 9.8 0.6
H7 A:0UZ1 2.6 14.5 0.4
C2 A:0UZ1 2.7 11.3 0.4
C4 A:0UZ1 2.7 11.8 0.4
H6 A:0UZ1 2.8 13.6 0.4
H9 A:0UZ1 3.0 11.4 0.6
O4 A:0UZ1 3.1 12.1 0.4
C2 A:0UZ1 3.1 9.3 0.6
C1 A:0UZ1 3.1 9.6 0.6
HE2 A:PHE3 3.1 13.3 1.0
HD2 A:PHE3 3.1 12.5 1.0
CL3 A:0UZ1 3.6 10.9 0.6
CE2 A:PHE3 3.7 11.1 1.0
CD2 A:PHE3 3.7 10.4 1.0
C1 A:0UZ1 4.0 11.6 0.4
H6 A:0UZ1 4.0 11.2 0.6
C5 A:0UZ1 4.0 12.0 0.4
O A:HOH202 4.0 18.2 1.0
O2 A:MAN101 4.1 18.7 1.0
O A:HOH209 4.3 15.2 1.0
HO2 A:MAN101 4.3 22.4 1.0
HO3 A:MAN101 4.5 23.4 1.0
C6 A:0UZ1 4.5 11.9 0.4
CA A:0UZ1 4.6 10.6 0.6
H8 A:0UZ1 4.7 14.4 0.4
H2 A:MAN101 4.8 20.9 1.0
CZ A:PHE3 5.0 10.8 1.0

Chlorine binding site 3 out of 6 in 7lkc

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Chlorine binding site 3 out of 6 in the Crystal Structure of Keratinimicin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl6

b:10.2
occ:1.00
CL A:OMY6 0.0 10.2 1.0
CE1 A:OMY6 1.7 8.2 1.0
HO4 G:RAM2 2.4 15.9 1.0
CD1 A:OMY6 2.7 7.8 1.0
CZ A:OMY6 2.7 7.8 1.0
HD1 A:OMY6 2.8 9.4 1.0
H62 G:RAM2 3.0 15.4 1.0
OCZ A:OMY6 3.0 7.9 1.0
C5 A:GHP4 3.2 7.8 1.0
H5 G:RAM2 3.2 14.9 1.0
O4 G:RAM2 3.4 13.3 1.0
C6 A:GHP4 3.5 7.3 1.0
H6 A:GHP4 3.6 8.8 1.0
O A:HOH207 3.7 17.1 1.0
C6 G:RAM2 3.7 12.9 1.0
C5 G:RAM2 3.9 12.4 1.0
C4 A:GHP4 4.0 8.3 1.0
H61 G:RAM2 4.0 15.4 1.0
CG A:OMY6 4.0 7.7 1.0
CE2 A:OMY6 4.0 7.8 1.0
C4 G:RAM2 4.2 13.0 1.0
O A:GHP4 4.2 7.9 1.0
H A:FMT103 4.2 13.2 1.0
H62 K:RAM2 4.3 12.7 1.0
H3 G:RAM2 4.3 16.3 1.0
C1 A:GHP4 4.3 7.5 1.0
HA A:GHP5 4.4 8.6 1.0
O4 A:GHP4 4.4 8.8 1.0
CD2 A:OMY6 4.5 7.8 1.0
H63 G:RAM2 4.7 15.4 1.0
C A:GHP4 4.7 7.4 1.0
C3 A:GHP4 4.7 8.4 1.0
HE2 A:OMY6 4.8 9.4 1.0
C3 G:RAM2 4.9 13.6 1.0
C2 A:GHP4 4.9 8.1 1.0
H61 K:RAM2 4.9 12.7 1.0
HA A:OMY6 5.0 9.1 1.0
CL A:CL104 5.0 15.0 0.7

Chlorine binding site 4 out of 6 in 7lkc

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Chlorine binding site 4 out of 6 in the Crystal Structure of Keratinimicin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1

b:18.1
occ:1.00
CL3 B:0UZ1 0.0 18.1 1.0
C3 B:0UZ1 1.7 15.7 1.0
C2 B:0UZ1 2.6 14.7 1.0
H7 B:0UZ1 2.6 19.6 1.0
C4 B:0UZ1 2.7 15.5 1.0
H6 B:0UZ1 2.7 17.6 1.0
O B:HOH211 2.8 15.9 0.7
O4 B:0UZ1 3.1 16.3 1.0
HB2 B:PHE3 3.2 15.2 1.0
C1 B:0UZ1 3.9 13.6 1.0
HB3 B:PHE3 3.9 15.2 1.0
C5 B:0UZ1 4.0 14.8 1.0
CB B:PHE3 4.0 12.7 1.0
C6 B:0UZ1 4.5 13.8 1.0
H8 B:0UZ1 4.7 17.7 1.0
H B:PHE3 4.9 12.6 1.0
N B:PHE3 4.9 10.5 1.0
CG B:PHE3 4.9 14.3 1.0
HD2 B:PHE3 4.9 19.0 1.0
CA B:PHE3 5.0 10.5 1.0

Chlorine binding site 5 out of 6 in 7lkc

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Chlorine binding site 5 out of 6 in the Crystal Structure of Keratinimicin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl6

b:11.4
occ:1.00
CL B:OMY6 0.0 11.4 1.0
CE1 B:OMY6 1.7 9.2 1.0
CD1 B:OMY6 2.7 8.9 1.0
CZ B:OMY6 2.7 8.5 1.0
HD1 B:OMY6 2.8 10.7 1.0
H62 K:BGC1 2.9 14.6 1.0
OCZ B:OMY6 3.0 8.6 1.0
C5 B:GHP4 3.2 8.0 1.0
C6 B:GHP4 3.5 8.2 1.0
H6 B:GHP4 3.5 9.9 1.0
O5 K:BGC1 3.6 9.9 1.0
H62 G:BGC1 3.7 15.0 1.0
C6 K:BGC1 3.8 12.1 1.0
C4 B:GHP4 3.9 8.2 1.0
CE2 B:OMY6 4.0 8.4 1.0
CG B:OMY6 4.0 8.5 1.0
H61 G:BGC1 4.0 15.0 1.0
HO6 K:BGC1 4.1 15.7 1.0
O6 K:BGC1 4.1 13.1 1.0
C5 K:BGC1 4.2 10.8 1.0
HA B:GHP5 4.3 9.4 1.0
C1 B:GHP4 4.3 8.0 1.0
O4 B:GHP4 4.4 8.7 1.0
O B:GHP4 4.4 8.7 1.0
C6 G:BGC1 4.4 12.5 1.0
H5 K:BGC1 4.4 13.0 1.0
C1 K:BGC1 4.4 9.3 1.0
CD2 B:OMY6 4.5 8.2 1.0
H5 G:BGC1 4.5 12.9 1.0
H61 K:BGC1 4.6 14.6 1.0
C3 B:GHP4 4.7 8.3 1.0
HE2 B:OMY6 4.7 10.1 1.0
C B:GHP4 4.8 7.9 1.0
HA B:OMY6 4.8 10.1 1.0
C2 B:GHP4 4.9 8.2 1.0

Chlorine binding site 6 out of 6 in 7lkc

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Chlorine binding site 6 out of 6 in the Crystal Structure of Keratinimicin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl104

b:15.0
occ:0.66
HN1 A:3FG7 2.2 10.2 1.0
HC2 A:GHP5 2.5 8.9 1.0
HA A:OMY6 2.6 9.1 1.0
O A:HOH207 2.7 17.1 1.0
HD1 A:OMY6 2.8 9.4 1.0
N A:3FG7 3.0 8.5 1.0
O A:HOH211 3.2 23.4 0.9
HB A:OMY6 3.3 9.1 1.0
CA A:OMY6 3.4 7.6 1.0
HA A:GHP5 3.5 8.6 1.0
C2 A:GHP5 3.6 7.4 1.0
CD1 A:OMY6 3.7 7.8 1.0
C A:OMY6 3.7 8.5 1.0
CB A:OMY6 3.7 7.6 1.0
CB A:3FG7 3.9 9.1 1.0
CA A:3FG7 4.0 9.2 1.0
CG1 A:3FG7 4.1 8.9 1.0
CG A:OMY6 4.2 7.7 1.0
C3 A:GHP5 4.3 8.3 1.0
CG2 A:3FG7 4.3 9.9 1.0
CA A:GHP5 4.5 7.2 1.0
C1 A:GHP5 4.5 7.4 1.0
HG2 A:3FG7 4.7 11.9 1.0
N A:OMY6 4.7 7.2 1.0
H6 A:YBJ102 4.7 12.9 1.0
CE1 A:OMY6 4.7 8.2 1.0
HA A:3FG7 4.7 11.1 1.0
O A:3FG7 4.8 11.7 1.0
CD1 A:3FG7 4.8 10.0 1.0
H A:YBJ102 4.8 11.5 1.0
O A:OMY6 4.9 9.6 1.0
C A:3FG7 4.9 10.7 1.0
ODE A:OMY6 4.9 7.7 1.0
CD2 A:3FG7 5.0 10.6 1.0
CL A:OMY6 5.0 10.2 1.0
O A:GHP4 5.0 7.9 1.0

Reference:

K.L.Mcwhorter, V.T.Chioti, F.Xu, P.D.Jeffrey, K.M.Davis, M.R.Seyedsayamdost. Structural and Functional Analysis of Keratinicyclin Reveals Synergistic Antibiosis with Vancomycin Against Clostridium Difficile To Be Published.
Page generated: Sun Jul 13 03:46:01 2025

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