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Chlorine in PDB 5hml: Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions

Enzymatic activity of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions

All present enzymatic activity of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions:
3.1.11.3;

Protein crystallography data

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hml was solved by C.S.Flemming, M.Feng, S.E.Sedelnikova, J.Zhang, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.60 / 1.48
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.380, 58.380, 59.720, 66.53, 79.48, 73.71
R / Rfree (%) 14.1 / 19.6

Other elements in 5hml:

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Iodine (I) 3 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions (pdb code 5hml). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 13 binding sites of Chlorine where determined in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hml:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 5hml

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Chlorine binding site 1 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:20.1
occ:1.00
 N A:GLU210 3.5 18.4 1.0
CB A:GLU210 3.9 25.9 1.0
NH2 A:ARG207 4.0 38.6 1.0
CB A:ASN245 4.0 18.4 1.0
CA A:VAL209 4.2 14.6 1.0
CG A:ASN245 4.2 22.8 1.0
OG A:SER249 4.3 17.0 1.0
O A:HOH531 4.3 35.6 1.0
CA A:GLU210 4.3 20.9 1.0
C A:VAL209 4.3 13.5 1.0
CG1 A:VAL209 4.4 14.1 1.0
O A:GLY208 4.5 18.6 1.0
ND2 A:ASN245 4.6 23.6 1.0
OD1 A:ASN245 4.6 23.6 1.0
O A:ASN245 4.6 16.3 1.0
CA A:ASN245 4.7 16.0 1.0
CB A:VAL209 4.9 12.9 1.0
C A:ASN245 4.9 14.3 1.0

Chlorine binding site 2 out of 13 in 5hml

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Chlorine binding site 2 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:35.7
occ:1.00
 CA A:GLY213 3.1 20.1 1.0
N A:GLY213 3.2 20.9 1.0
CG A:ARG216 3.5 31.2 1.0
C A:GLY213 3.6 18.4 1.0
N A:ARG216 3.7 24.2 1.0
CD A:ARG216 3.7 30.7 1.0
CB A:ARG216 3.8 26.4 1.0
O A:GLY213 3.9 18.2 1.0
NE A:ARG216 4.2 31.2 1.0
O A:HOH576 4.2 35.5 1.0
CB A:LYS215 4.3 28.4 1.0
N A:ALA214 4.3 15.6 1.0
CA A:ARG216 4.4 25.8 1.0
N A:LYS215 4.4 22.8 1.0
C A:ILE212 4.5 20.2 1.0
CA A:LYS215 4.7 25.7 1.0
C A:LYS215 4.7 23.8 1.0
O A:GLY211 4.8 22.1 1.0
CG A:LYS215 4.8 37.9 1.0
CZ A:ARG216 4.9 40.1 1.0
CA A:ILE212 5.0 17.2 1.0

Chlorine binding site 3 out of 13 in 5hml

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Chlorine binding site 3 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:14.7
occ:1.00
 O A:HOH451 3.4 37.1 1.0
O A:HOH653 3.5 37.3 1.0
NH2 A:ARG93 3.5 19.0 1.0
NH1 A:ARG93 3.8 19.1 1.0
CG A:GLU102 4.1 19.3 1.0
CZ A:ARG93 4.2 14.4 1.0
CD2 A:PHE105 4.2 25.5 1.0
CE2 A:TYR90 4.3 37.6 1.0
CE2 A:PHE105 4.3 28.1 1.0
CB A:ASP101 4.5 17.7 1.0
CD2 A:TYR90 4.6 36.5 1.0
N A:GLU102 4.7 18.8 1.0
CE A:LYS98 4.7 17.6 1.0
CA A:GLU102 4.8 17.4 1.0
C A:ASP101 4.9 16.5 1.0
O A:HOH648 4.9 50.5 1.0
CG A:LYS98 4.9 19.3 1.0

Chlorine binding site 4 out of 13 in 5hml

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Chlorine binding site 4 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:17.1
occ:1.00
 O B:HOH656 3.0 23.7 1.0
O A:HOH614 3.0 23.7 1.0
N B:GLY213 3.3 12.9 1.0
N B:ARG216 3.3 12.5 1.0
CA B:GLY213 3.4 14.1 1.0
O B:HOH576 3.4 22.6 1.0
C B:GLY213 3.5 11.9 1.0
CG B:ARG216 3.6 13.9 1.0
CB B:ARG216 3.7 12.4 1.0
CD B:ARG216 3.7 12.1 1.0
N B:LYS215 3.8 14.2 1.0
O B:GLY213 3.8 13.6 1.0
N B:ALA214 3.9 13.9 1.0
CB B:LYS215 4.0 13.8 1.0
CA B:ARG216 4.1 12.7 1.0
CA B:LYS215 4.2 12.2 1.0
O A:HOH615 4.2 18.2 1.0
C B:LYS215 4.3 11.6 1.0
NE B:ARG216 4.4 13.7 1.0
C B:ILE212 4.5 12.9 1.0
C B:ALA214 4.6 12.9 1.0
CZ A:PHE254 4.7 11.1 1.0
O B:GLY211 4.8 14.7 1.0
CA B:ALA214 4.9 14.9 1.0
CA B:ILE212 4.9 11.8 1.0
O B:HOH650 5.0 20.4 1.0
N B:GLY217 5.0 11.6 1.0

Chlorine binding site 5 out of 13 in 5hml

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Chlorine binding site 5 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:14.6
occ:0.50
 CE1 B:PHE169 0.9 18.9 0.4
CZ B:PHE169 1.2 18.8 0.4
CD1 B:PHE169 2.2 20.0 0.4
CE2 B:PHE169 2.6 17.2 0.4
CG B:PHE169 3.2 18.4 0.4
CD2 B:PHE169 3.3 17.9 0.4
CG2 B:THR50 4.1 13.8 1.0
CE2 B:PHE167 4.2 16.0 1.0
CB B:PHE169 4.2 20.3 0.6
CZ B:ARG33 4.3 47.5 1.0
NH2 B:ARG33 4.3 55.8 1.0
NE B:ARG33 4.3 40.7 1.0
CD2 B:LEU54 4.4 18.7 1.0
CB B:PHE169 4.6 16.1 0.4
CZ B:PHE167 4.7 15.8 1.0
CG B:LEU54 4.7 15.1 1.0
CD1 B:LEU54 4.8 18.6 1.0
O B:HOH445 4.8 32.9 1.0
NH1 B:ARG33 4.9 38.0 1.0
CD B:ARG33 5.0 30.4 1.0

Chlorine binding site 6 out of 13 in 5hml

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Chlorine binding site 6 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl306

b:20.8
occ:1.00
 O B:HOH664 2.8 29.2 1.0
O B:HOH584 2.9 42.1 1.0
N B:LYS239 3.4 13.3 1.0
CG B:LYS239 3.7 16.9 1.0
CB B:LYS239 3.8 17.3 1.0
CA B:GLY238 3.9 16.9 1.0
CD B:LYS239 4.1 23.3 1.0
C B:GLY238 4.1 14.9 1.0
CA B:LYS239 4.2 13.9 1.0
CE B:LYS239 4.7 29.2 1.0
N B:GLY238 4.8 16.1 1.0

Chlorine binding site 7 out of 13 in 5hml

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Chlorine binding site 7 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl307

b:25.9
occ:1.00
 ND1 B:HIS36 3.1 23.9 1.0
O A:HOH521 3.8 26.1 1.0
CE1 B:PHE169 3.9 16.7 0.6
CB B:HIS36 3.9 26.3 1.0
CG B:HIS36 3.9 27.0 1.0
CE1 B:HIS36 4.1 23.3 1.0
CD A:LYS283 4.2 27.2 1.0
CB A:ASP279 4.3 17.2 1.0
CG2 B:THR170 4.3 16.5 1.0
O A:ASP279 4.4 15.8 1.0
O B:PHE32 4.4 20.3 1.0
CA B:ARG33 4.5 18.9 1.0
C A:ASP279 4.5 13.3 1.0
CB A:LYS283 4.6 16.8 1.0
CZ B:PHE169 4.7 18.0 0.6
CD1 B:PHE169 4.8 19.9 0.6
CG A:LYS283 4.9 23.6 1.0
N A:LYS280 4.9 14.3 1.0
C B:PHE32 4.9 15.9 1.0
N B:ARG33 4.9 16.6 1.0

Chlorine binding site 8 out of 13 in 5hml

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Chlorine binding site 8 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl308

b:33.2
occ:1.00
 ND2 B:ASN38 3.4 57.5 1.0
O B:LYS35 4.0 27.2 1.0
CE A:LYS280 4.0 33.8 1.0
CD2 B:HIS36 4.0 21.5 1.0
O A:HOH639 4.1 40.4 1.0
CG A:LYS280 4.3 20.8 1.0
CD A:LYS280 4.3 26.2 1.0
O A:HOH502 4.3 29.3 1.0
CG B:LYS35 4.4 27.4 1.0
CE B:LYS35 4.5 32.9 1.0
C B:LYS35 4.5 22.2 1.0
CG B:ASN38 4.6 0.9 1.0
CD B:LYS35 4.7 25.9 1.0
CA B:HIS36 4.7 18.8 1.0
NE2 B:HIS36 4.8 24.8 1.0
N B:HIS36 4.9 23.3 1.0
OD1 B:ASN38 4.9 0.3 1.0

Chlorine binding site 9 out of 13 in 5hml

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Chlorine binding site 9 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl309

b:24.1
occ:1.00
 O B:HOH682 2.9 32.2 1.0
N B:SER45 3.5 12.6 1.0
O B:HOH669 3.5 31.4 1.0
O B:HOH590 3.6 23.5 1.0
N B:ALA44 3.7 12.6 1.0
CB B:PRO42 3.9 28.4 1.0
CB B:SER45 3.9 15.4 1.0
CB B:ALA44 4.1 13.0 1.0
CA B:ALA44 4.2 12.3 1.0
C B:PRO42 4.3 19.1 1.0
CA B:SER45 4.3 13.9 1.0
C B:ALA44 4.3 12.7 1.0
O B:PRO42 4.3 28.4 1.0
C B:PHE43 4.4 11.4 1.0
N B:PHE43 4.4 15.4 1.0
CA B:PHE43 4.7 13.0 1.0
O B:HOH693 4.7 59.0 1.0
CA B:PRO42 4.7 24.9 1.0
O B:HOH563 4.9 16.9 1.0
CG B:PRO42 5.0 35.7 1.0

Chlorine binding site 10 out of 13 in 5hml

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Chlorine binding site 10 out of 13 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl310

b:35.4
occ:0.80
 CL B:CL310 0.0 35.4 0.8
CL B:CL310 2.4 11.4 0.2
CD1 B:PHE104 3.5 23.6 1.0
CB B:PHE104 3.9 22.9 1.0
CA B:PHE104 4.1 19.8 1.0
CG B:PHE104 4.2 21.7 1.0
CD2 B:TYR107 4.2 35.0 1.0
CA B:LYS35 4.4 23.6 1.0
CE2 B:PHE43 4.5 19.3 1.0
CE1 B:PHE104 4.5 22.9 1.0
CA B:LYS40 4.7 51.5 1.0
CG B:LYS35 4.7 27.4 1.0
CE2 B:TYR107 4.7 42.3 1.0
CD2 B:PHE43 4.8 17.0 1.0
N B:LYS40 4.8 55.7 1.0
O B:LYS35 4.8 27.2 1.0
N B:PHE104 4.9 23.5 1.0
O B:PHE34 4.9 26.6 1.0
O B:LYS41 4.9 41.0 1.0
CD B:LYS40 5.0 56.6 1.0

Reference:

F.A.Almalki, C.S.Flemming, J.Zhang, M.Feng, S.E.Sedelnikova, T.Ceska, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk. Direct Observation of Dna Threading in Flap Endonuclease Complexes. Nat.Struct.Mol.Biol. V. 23 640 2016.
ISSN: ESSN 1545-9985
PubMed: 27273516
DOI: 10.1038/NSMB.3241
Page generated: Sat Dec 12 11:48:58 2020

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