Chlorine in PDB 5xpf: High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme

Enzymatic activity of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme

All present enzymatic activity of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme, PDB code: 5xpf was solved by T.Hiromoto, R.Kuroki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.58 / 1.04
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.839, 59.839, 95.828, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 19.3

Other elements in 5xpf:

The structure of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme (pdb code 5xpf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme, PDB code: 5xpf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5xpf

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Chlorine binding site 1 out of 6 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:12.9
occ:0.74
 O A:HOH510 3.2 21.9 1.0
O A:HOH356 3.3 13.2 1.0
O A:HOH427 3.3 15.3 1.0
O A:HOH346 3.6 23.1 1.0
CE1 A:HIS31 3.6 13.5 1.0
CB A:ALA49 3.7 13.9 0.4
NE2 A:HIS31 4.0 13.9 1.0
CB A:ALA49 4.0 10.8 0.6
CA A:ALA49 4.3 11.4 0.4
CA A:ALA49 4.5 10.8 0.6
NE2 A:GLN69 4.6 12.6 1.0
O A:HOH417 4.7 20.7 1.0
CD2 A:LEU66 4.8 16.4 1.0
ND1 A:HIS31 4.8 12.6 1.0

Chlorine binding site 2 out of 6 in 5xpf

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Chlorine binding site 2 out of 6 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:16.7
occ:0.73
 O A:HOH394 3.0 15.9 1.0
NZ A:LYS135 3.2 24.9 1.0
ND2 A:ASN132 3.3 18.0 1.0
CB A:ASN132 3.6 12.9 1.0
CA A:ASN132 3.7 12.0 1.0
CE A:LYS135 3.9 20.6 1.0
CG A:ASN132 3.9 14.2 1.0
N A:ASN132 4.0 11.9 1.0
CD A:LYS135 4.0 18.8 1.0
CG1 A:VAL131 4.1 16.5 1.0
CE A:MET120 4.4 21.7 1.0
C A:VAL131 4.5 12.1 1.0
O A:HOH438 4.7 32.6 1.0
O A:VAL131 4.8 13.5 1.0
O A:GLU128 4.8 12.9 1.0
CB A:VAL131 4.9 14.7 1.0
O A:HOH532 4.9 22.2 1.0

Chlorine binding site 3 out of 6 in 5xpf

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Chlorine binding site 3 out of 6 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:43.8
occ:1.00
 N A:ALA82 3.0 17.7 1.0
CB A:ALA82 3.6 25.4 1.0
CA A:ASN81 3.7 17.9 1.0
C A:ASN81 3.8 16.7 1.0
CA A:ALA82 3.9 18.0 1.0
ND2 A:ASN81 4.0 21.4 1.0
CG A:ASN81 4.0 18.6 1.0
O A:ARG80 4.1 25.6 0.7
O A:ARG80 4.1 25.2 0.3
OD1 A:ASN81 4.4 18.1 1.0
CB A:ASN81 4.4 18.2 1.0
O A:HOH538 4.5 49.8 1.0
O A:HOH465 4.6 31.3 1.0
N A:LYS83 4.8 17.2 1.0
N A:ASN81 4.8 18.1 1.0
C A:ALA82 4.9 17.3 1.0
C A:ARG80 4.9 20.4 0.7
C A:ARG80 4.9 20.9 0.3
OE2 A:GLU108 5.0 25.7 0.7

Chlorine binding site 4 out of 6 in 5xpf

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Chlorine binding site 4 out of 6 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:13.8
occ:0.71
 CL A:CL207 0.0 13.8 0.7
CL A:CL207 2.4 25.7 0.3
O A:HOH531 3.1 20.5 1.0
O A:HOH476 3.2 35.5 1.0
N A:ARG145 3.2 10.9 1.0
N A:ASN144 3.3 11.0 0.4
N A:ASN144 3.4 11.4 0.6
CB A:ASN144 3.4 14.2 0.4
C A:THR142 3.5 10.6 1.0
CA A:THR142 3.5 10.9 1.0
CB A:THR142 3.7 11.5 1.0
N A:PRO143 3.7 9.6 0.6
CA A:ASN144 3.7 12.2 0.4
O A:THR142 3.8 11.1 1.0
CB A:ASN144 3.8 11.6 0.6
N A:PRO143 3.9 14.1 0.4
CA A:ASN144 3.9 11.2 0.6
CB A:ARG145 3.9 13.5 1.0
C A:ASN144 4.0 11.2 0.4
C A:ASN144 4.0 10.9 0.6
CD A:PRO143 4.1 11.1 0.6
CA A:ARG145 4.2 11.4 1.0
C A:PRO143 4.3 9.5 0.6
C A:PRO143 4.3 12.7 0.4
CG2 A:THR142 4.3 13.2 1.0
CG A:ASN144 4.4 13.0 0.4
CD A:PRO143 4.4 12.4 0.4
CA A:PRO143 4.6 10.3 0.6
CA A:PRO143 4.7 12.5 0.4
O A:HOH372 4.7 19.1 1.0
OD1 A:ASN144 4.8 19.1 0.4
CG A:PRO143 4.8 11.2 0.6
CG A:ASN144 4.8 14.3 0.6
OG1 A:THR142 4.9 12.9 1.0
N A:THR142 4.9 11.2 1.0

Chlorine binding site 5 out of 6 in 5xpf

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Chlorine binding site 5 out of 6 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:25.7
occ:0.29
 CL A:CL207 0.0 25.7 0.3
CL A:CL207 2.4 13.8 0.7
N A:ASN144 3.0 11.0 0.4
CB A:ASN144 3.0 14.2 0.4
N A:ASN144 3.1 11.4 0.6
OD1 A:ASN144 3.1 19.1 0.4
CG A:ASN144 3.2 13.0 0.4
CD A:PRO143 3.3 11.1 0.6
CG A:PRO143 3.4 11.2 0.6
CB A:ASN144 3.4 11.6 0.6
CG A:ASN144 3.6 14.3 0.6
CA A:ASN144 3.6 12.2 0.4
ND2 A:ASN144 3.6 18.0 0.6
N A:PRO143 3.6 9.6 0.6
CD A:PRO143 3.7 12.4 0.4
CG A:PRO143 3.8 13.2 0.4
CA A:ASN144 3.8 11.2 0.6
N A:PRO143 3.8 14.1 0.4
C A:PRO143 4.0 12.7 0.4
ND2 A:ASN144 4.1 18.8 0.4
C A:PRO143 4.1 9.5 0.6
C A:THR142 4.2 10.6 1.0
CA A:PRO143 4.2 10.3 0.6
OD1 A:ASN144 4.3 18.5 0.6
CA A:PRO143 4.4 12.5 0.4
O A:HOH476 4.4 35.5 1.0
CB A:PRO143 4.4 11.1 0.6
CA A:THR142 4.5 10.9 1.0
N A:ARG145 4.6 10.9 1.0
C A:ASN144 4.7 11.2 0.4
CB A:PRO143 4.7 13.7 0.4
C A:ASN144 4.8 10.9 0.6
O A:THR142 4.9 11.1 1.0

Chlorine binding site 6 out of 6 in 5xpf

Go back to Chlorine Binding Sites List in 5xpf
Chlorine binding site 6 out of 6 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:25.8
occ:0.16
 O A:HOH327 2.7 27.4 1.0
O A:HOH359 3.1 44.5 1.0
O A:HOH539 3.3 29.9 0.5
CA A:ARG80 4.0 22.0 0.7
CA A:ARG80 4.0 22.0 0.3
O A:LEU79 4.0 24.2 1.0
CB A:ARG80 4.0 23.8 0.7
N A:ARG80 4.1 19.9 0.7
C A:LEU79 4.1 21.4 1.0
N A:ARG80 4.1 20.2 0.3
CB A:ARG80 4.2 23.7 0.3
CB A:LEU79 4.4 20.8 1.0
O A:ARG76 4.8 14.6 0.5
CA A:LEU79 4.9 18.8 1.0

Reference:

T.Hiromoto, F.Meilleur, R.Shimizu, C.Shibazaki, M.Adachi, T.Tamada, R.Kuroki. Neutron Structure of the T26H Mutant of T4 Phage Lysozyme Provides Insight Into the Catalytic Activity of the Mutant Enzyme and How It Differs From That of Wild Type. Protein Sci. V. 26 1953 2017.
ISSN: ESSN 1469-896X
PubMed: 28707339
DOI: 10.1002/PRO.3230
Page generated: Sat Dec 12 12:39:30 2020

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