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Chlorine in PDB 5i0d: Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan

Protein crystallography data

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan, PDB code: 5i0d was solved by S.H.Light, G.Minasov, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.77
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.753, 101.233, 166.391, 90.00, 101.02, 90.00
R / Rfree (%) 14.4 / 17.1

Other elements in 5i0d:

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan (pdb code 5i0d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan, PDB code: 5i0d:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5i0d

Go back to Chlorine Binding Sites List in 5i0d
Chlorine binding site 1 out of 7 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1107

b:35.8
occ:1.00
 O A:HOH2080 3.0 26.7 1.0
O A:HOH2158 3.0 21.1 1.0
OE1 A:GLN527 3.2 25.8 1.0
O A:HOH2420 3.3 46.4 1.0
N A:TRP528 3.3 20.2 1.0
ND2 A:ASN301 3.5 17.7 1.0
CB A:TRP528 3.7 19.4 1.0
CB A:GLN527 3.8 23.1 1.0
O A:HOH1895 3.8 31.5 1.0
CA A:GLN527 4.1 22.6 1.0
CA A:TRP528 4.1 19.9 1.0
CD A:GLN527 4.1 25.6 1.0
CH2 A:TRP571 4.2 15.5 1.0
CB A:ASN301 4.2 15.8 1.0
C A:GLN527 4.2 21.3 1.0
CG A:ASN301 4.3 16.5 1.0
O A:HOH1842 4.4 12.7 1.0
CG A:GLN527 4.4 24.2 1.0
O A:HOH1213 4.6 36.7 1.0
O A:ASN301 4.8 15.7 1.0
O A:TRP528 4.8 18.6 1.0
CZ3 A:TRP571 4.9 15.6 1.0

Chlorine binding site 2 out of 7 in 5i0d

Go back to Chlorine Binding Sites List in 5i0d
Chlorine binding site 2 out of 7 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1108

b:40.0
occ:1.00
 O A:HOH1293 3.1 24.0 1.0
N A:TYR142 3.2 18.9 1.0
O A:HOH2042 3.2 29.2 1.0
O A:HOH2217 3.3 29.6 1.0
O A:TYR142 3.6 18.7 1.0
O A:HOH1750 3.7 20.3 1.0
CD2 A:TYR142 3.8 23.1 1.0
CA A:PHE141 3.9 18.2 1.0
ND2 A:ASN264 4.0 18.8 1.0
CA A:TYR142 4.0 19.8 1.0
C A:PHE141 4.0 18.7 1.0
CB A:TYR142 4.0 21.0 1.0
O A:HOH2162 4.0 35.0 1.0
CB A:PHE141 4.1 17.8 1.0
C A:TYR142 4.2 19.1 1.0
CG A:TYR142 4.4 22.4 1.0
OD1 A:ASP57 4.5 19.5 1.0
O A:HOH1215 4.5 17.5 1.0
CG2 A:VAL262 4.6 24.6 1.0
CG1 A:VAL262 4.7 25.5 1.0
CE2 A:TYR142 4.8 23.9 1.0
OH A:TYR40 4.9 19.5 1.0
O A:THR140 4.9 19.0 1.0

Chlorine binding site 3 out of 7 in 5i0d

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Chlorine binding site 3 out of 7 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1105

b:26.1
occ:1.00
 OG1 B:THR1056 3.1 18.4 1.0
O B:HOH2237 3.2 45.0 1.0
NE B:ARG1022 3.2 15.1 1.0
O B:HOH2140 3.2 23.5 0.5
O B:HOH2090 3.3 40.3 1.0
C B:ASN1055 3.6 15.2 1.0
O B:HOH2140 3.7 19.3 0.5
CA B:ASN1055 3.7 15.1 1.0
N B:THR1056 3.8 16.6 1.0
CD B:ARG1022 3.8 14.3 1.0
O B:TRP1054 3.8 14.9 1.0
N B:ASN1055 3.9 14.2 1.0
C B:TRP1054 3.9 14.3 1.0
CG B:ARG1022 4.0 13.9 1.0
CB B:THR1056 4.0 18.2 1.0
O B:ASN1055 4.1 14.3 1.0
CZ B:ARG1022 4.1 15.5 1.0
NH2 B:ARG1022 4.2 16.0 1.0
CB B:TRP1054 4.2 13.7 1.0
CA B:THR1056 4.5 17.3 1.0
CA B:TRP1054 4.7 13.9 1.0

Chlorine binding site 4 out of 7 in 5i0d

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Chlorine binding site 4 out of 7 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1106

b:29.9
occ:1.00
 O B:HOH1707 2.9 24.8 1.0
NZ B:LYS228 3.1 23.6 1.0
O B:THR153 3.5 21.3 1.0
CA B:SER154 3.5 19.6 1.0
C B:THR153 3.5 20.6 1.0
N B:SER154 3.7 19.6 1.0
CE B:LYS228 3.9 23.0 1.0
CD B:LYS228 3.9 23.2 1.0
C B:SER154 4.1 18.8 1.0
N B:VAL155 4.2 18.7 1.0
CG2 B:VAL155 4.3 18.4 1.0
CA B:THR153 4.3 20.7 1.0
O B:VAL152 4.5 20.5 1.0
O B:HOH1987 4.6 35.2 1.0
CG1 B:VAL152 4.7 19.1 1.0
CB B:SER154 4.7 20.1 1.0
O B:SER154 4.8 17.7 1.0
N B:THR153 4.8 19.9 1.0
C B:VAL152 4.8 19.9 1.0
OD1 B:ASP210 5.0 25.1 1.0

Chlorine binding site 5 out of 7 in 5i0d

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Chlorine binding site 5 out of 7 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1107

b:33.5
occ:1.00
 O B:HOH1207 3.2 27.7 1.0
O B:HOH2025 3.2 30.1 1.0
N B:TYR142 3.3 17.9 1.0
O B:TYR142 3.7 18.5 1.0
O B:HOH1607 3.7 38.7 1.0
O B:HOH1558 3.7 16.6 1.0
ND2 B:ASN264 3.8 17.8 1.0
CD2 B:TYR142 3.8 21.9 1.0
CA B:PHE141 3.9 16.9 1.0
CB B:PHE141 4.1 16.4 1.0
C B:PHE141 4.1 17.4 1.0
CA B:TYR142 4.1 18.9 1.0
CB B:TYR142 4.2 20.1 1.0
C B:TYR142 4.3 18.4 1.0
OD1 B:ASP57 4.4 18.1 1.0
CG B:TYR142 4.5 21.2 1.0
O B:HOH1205 4.5 24.9 1.0
CG2 B:VAL262 4.6 21.1 1.0
CG1 B:VAL262 4.7 22.0 1.0
CG B:ASN264 4.7 17.6 1.0
OD1 B:ASN264 4.8 17.8 1.0
CE2 B:TYR142 4.8 22.6 1.0
OH B:TYR40 4.9 20.0 1.0
O B:THR140 4.9 17.1 1.0

Chlorine binding site 6 out of 7 in 5i0d

Go back to Chlorine Binding Sites List in 5i0d
Chlorine binding site 6 out of 7 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1108

b:34.4
occ:1.00
 O B:HOH2420 2.9 42.0 1.0
N B:GLU757 3.0 17.4 1.0
N B:PRO756 3.4 15.1 1.0
C B:TYR755 3.4 14.9 1.0
CD B:PRO756 3.4 15.4 1.0
CA B:TYR755 3.4 14.8 1.0
CB B:GLU757 3.5 21.1 1.0
CA B:GLU757 3.7 19.1 1.0
CG B:GLU757 3.9 23.7 1.0
O B:TYR755 3.9 14.6 1.0
CG B:PRO756 3.9 15.8 1.0
N B:ASP758 4.0 16.7 1.0
C B:PRO756 4.0 16.5 1.0
CB B:TYR755 4.2 14.6 1.0
CA B:PRO756 4.2 15.6 1.0
C B:GLU757 4.3 18.1 1.0
CD B:GLU757 4.6 26.7 1.0
O B:ASP754 4.6 14.5 1.0
N B:TYR755 4.6 14.5 1.0
O B:HOH2357 4.7 36.5 1.0
O B:HOH2558 4.7 45.6 1.0
CB B:PRO756 4.8 15.8 1.0
OE1 B:GLU757 4.8 30.0 1.0
CD1 B:TYR755 4.8 15.5 1.0
O B:HOH2451 4.8 45.2 1.0
O B:HOH2394 4.9 37.3 1.0
CG B:TYR755 5.0 14.8 1.0
CB B:ASP758 5.0 15.9 1.0

Chlorine binding site 7 out of 7 in 5i0d

Go back to Chlorine Binding Sites List in 5i0d
Chlorine binding site 7 out of 7 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1109

b:24.8
occ:1.00
 O B:HOH1847 2.9 20.3 1.0
O B:HOH2187 3.0 40.2 1.0
N B:THR1062 3.3 17.3 1.0
CB B:ILE1036 3.6 14.2 1.0
CG1 B:ILE1036 3.7 14.1 1.0
CA B:VAL1061 3.8 17.1 1.0
CG2 B:ILE1036 3.9 13.9 1.0
O B:HOH2204 4.0 41.1 1.0
CB B:THR1062 4.0 18.1 1.0
C B:VAL1061 4.0 17.4 1.0
O B:THR1062 4.1 16.9 1.0
CA B:THR1062 4.2 17.3 1.0
CD B:LYS1039 4.2 19.6 1.0
O B:HOH2354 4.2 25.9 1.0
NE2 B:GLN1041 4.2 20.9 1.0
CB B:VAL1061 4.2 16.1 1.0
OG1 B:THR1062 4.3 18.5 1.0
O B:HOH2174 4.5 39.9 1.0
C B:THR1062 4.6 17.0 1.0
O B:PRO1060 4.7 19.4 1.0
CB B:LYS1039 4.7 17.7 1.0
CG B:LYS1039 4.7 19.1 1.0
CG1 B:VAL1061 4.8 15.8 1.0
NZ B:LYS1039 4.9 22.0 1.0
CE B:LYS1039 4.9 21.3 1.0
O B:ILE1036 4.9 14.2 1.0
CA B:ILE1036 5.0 13.9 1.0

Reference:

S.H.Light, L.A.Cahoon, K.V.Mahasenan, M.Lee, B.Boggess, A.S.Halavaty, S.Mobashery, N.E.Freitag, W.F.Anderson. Transferase Versus Hydrolase: the Role of Conformational Flexibility in Reaction Specificity. Structure V. 25 295 2017.
ISSN: ISSN 1878-4186
PubMed: 28089449
DOI: 10.1016/J.STR.2016.12.007
Page generated: Fri Jul 26 09:04:43 2024

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