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Chlorine in PDB 5hmm: 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: 5hmm was solved by C.S.Flemming, S.E.Sedelnikova, 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) 38.35 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.831, 58.591, 59.729, 66.88, 79.40, 73.78
R / Rfree (%) 14.8 / 19.7

Other elements in 5hmm:

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

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions (pdb code 5hmm). 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 T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hmm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5hmm

Go back to Chlorine Binding Sites List in 5hmm
Chlorine binding site 1 out of 6 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 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:Cl305

b:17.5
occ:1.00
 O B:HOH459 3.0 31.8 1.0
O B:HOH538 3.1 25.9 1.0
O A:HOH537 3.3 12.3 1.0
CA B:GLY211 3.7 14.5 1.0
CA A:GLU251 3.9 12.7 1.0
OE1 A:GLU250 4.1 24.4 1.0
ND2 B:ASN245 4.3 11.4 1.0
N B:GLY211 4.3 11.3 1.0
CB A:PHE254 4.3 9.3 1.0
NH1 B:ARG216 4.4 17.5 1.0
CB A:GLU251 4.4 16.1 1.0
O B:GLU210 4.4 12.4 1.0
CB B:TYR242 4.5 11.7 1.0
N B:TYR242 4.6 9.1 1.0
C B:GLU210 4.6 12.2 1.0
CG A:GLU250 4.6 22.3 1.0
N A:GLU251 4.6 12.2 1.0
O A:GLU250 4.6 12.6 1.0
CG A:PHE254 4.6 9.7 1.0
CG A:GLU251 4.7 20.3 1.0
CD2 A:PHE254 4.7 9.9 1.0
CA B:TYR242 4.7 13.7 1.0
CD A:GLU250 4.7 25.3 1.0
CG B:GLU210 4.8 23.2 1.0
O A:GLU251 4.8 11.3 1.0
C A:GLU250 4.8 12.6 1.0
O A:HOH593 4.8 41.5 1.0
C B:GLY211 4.9 13.9 1.0
C A:GLU251 4.9 11.5 1.0

Chlorine binding site 2 out of 6 in 5hmm

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Chlorine binding site 2 out of 6 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 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:Cl306

b:22.9
occ:1.00
 O A:HOH640 3.1 38.8 1.0
O A:HOH609 3.2 30.8 1.0
N A:ARG178 3.3 16.6 1.0
NH1 A:ARG178 3.5 21.7 1.0
CB A:ARG178 3.7 17.8 1.0
CG A:ARG178 3.7 17.7 1.0
O A:HOH417 3.7 15.7 1.0
CB A:LEU177 3.8 14.3 1.0
N A:LEU177 3.8 10.9 1.0
CA A:ARG178 4.1 15.9 1.0
CD A:ARG178 4.1 18.7 1.0
CA A:ASP162 4.1 17.8 1.0
CA A:LEU177 4.1 14.3 1.0
C A:LEU177 4.1 14.7 1.0
CB A:HIS176 4.3 11.2 1.0
O A:THR161 4.3 18.5 1.0
CZ A:ARG178 4.5 23.9 1.0
C A:HIS176 4.6 12.5 1.0
O A:ASP162 4.7 21.5 1.0
NE A:ARG178 4.7 21.4 1.0
CB A:ASP162 4.7 23.4 1.0
N A:ASP162 4.8 17.7 1.0
CG A:LEU177 4.8 15.2 1.0
C A:ASP162 4.8 18.3 1.0
C A:THR161 4.8 14.1 1.0
CA A:HIS176 4.9 11.4 1.0

Chlorine binding site 3 out of 6 in 5hmm

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Chlorine binding site 3 out of 6 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
B:Cl304

b:14.8
occ:1.00
 O B:HOH686 3.0 19.9 1.0
O A:HOH624 3.1 25.1 1.0
N B:ARG216 3.3 14.2 1.0
N B:GLY213 3.3 14.4 1.0
CA B:GLY213 3.5 15.8 1.0
C B:GLY213 3.5 15.8 1.0
CG B:ARG216 3.5 18.0 1.0
CB B:ARG216 3.6 16.9 1.0
O B:HOH625 3.6 31.3 1.0
CD B:ARG216 3.7 15.9 1.0
O B:GLY213 3.7 13.6 1.0
N B:LYS215 3.7 14.3 1.0
N B:ALA214 3.9 14.5 1.0
CB B:LYS215 4.0 17.9 1.0
CA B:ARG216 4.0 15.1 1.0
CA B:LYS215 4.2 15.3 1.0
C B:LYS215 4.2 16.0 1.0
CZ A:PHE254 4.3 11.0 1.0
O A:HOH634 4.3 18.4 1.0
NE B:ARG216 4.5 17.1 1.0
C B:ILE212 4.5 14.2 1.0
C B:ALA214 4.6 12.9 1.0
CE1 A:PHE254 4.7 13.3 1.0
O B:GLY211 4.8 13.4 1.0
CA B:ALA214 4.9 14.1 1.0
O B:HOH665 4.9 28.1 1.0
CA B:ILE212 4.9 13.8 1.0
N B:GLY217 5.0 11.1 1.0

Chlorine binding site 4 out of 6 in 5hmm

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Chlorine binding site 4 out of 6 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:Cl305

b:20.1
occ:1.00
 O B:HOH712 3.2 32.2 1.0
N B:SER45 3.3 10.4 1.0
O B:HOH605 3.4 18.9 1.0
N B:ALA44 3.6 9.9 1.0
CB B:SER45 3.8 13.9 1.0
CB B:ALA44 3.9 11.8 1.0
CB B:PRO42 4.0 22.0 1.0
CA B:ALA44 4.1 10.6 1.0
CA B:SER45 4.2 11.1 1.0
C B:PRO42 4.2 15.8 1.0
C B:ALA44 4.2 10.2 1.0
C B:PHE43 4.2 10.4 1.0
N B:PHE43 4.3 11.6 1.0
O B:PRO42 4.3 18.4 1.0
CA B:PHE43 4.5 11.3 1.0
O B:HOH518 4.6 42.7 1.0
CA B:PRO42 4.7 19.3 1.0
CG B:PRO42 4.9 26.6 1.0
O B:HOH548 4.9 12.5 1.0

Chlorine binding site 5 out of 6 in 5hmm

Go back to Chlorine Binding Sites List in 5hmm
Chlorine binding site 5 out of 6 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:Cl306

b:24.9
occ:1.00
 O B:HOH654 3.1 21.0 1.0
CG2 B:VAL73 3.8 11.4 1.0
CG B:ARG125 4.0 10.0 1.0
CA B:GLY126 4.0 6.6 1.0
O B:ARG125 4.1 9.6 1.0
C B:ARG125 4.2 9.8 1.0
N B:GLY126 4.3 8.0 1.0
CD B:ARG125 4.4 13.4 1.0
O B:HOH642 4.6 29.8 1.0
O B:HOH615 4.7 33.0 1.0
CB B:ARG125 4.7 8.4 1.0
CG1 B:VAL273 5.0 9.8 1.0

Chlorine binding site 6 out of 6 in 5hmm

Go back to Chlorine Binding Sites List in 5hmm
Chlorine binding site 6 out of 6 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:Cl307

b:22.3
occ:1.00
 O B:HOH633 2.9 24.9 1.0
CD B:LYS56 3.8 21.1 1.0
CA B:SER53 4.1 10.1 1.0
O B:HOH457 4.2 33.1 1.0
O B:GLN52 4.2 10.2 1.0
CB B:LYS56 4.2 12.5 1.0
N B:SER53 4.4 9.7 1.0
C B:GLN52 4.4 8.1 1.0
CG B:LYS56 4.7 15.8 1.0
CB B:SER53 4.8 13.4 1.0
O B:HOH530 4.9 24.5 1.0
OG B:SER53 5.0 20.5 1.0
CB B:GLN52 5.0 9.1 1.0
CE B:LYS56 5.0 31.3 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: Fri Jul 26 08:55:47 2024

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