Chlorine in PDB 6gh2: Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound

All present enzymatic activity of Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound:
2.4.1.31;

The structure of Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound, PDB code: 6gh2 was solved by S.Kuhaudomlarp, S.Walpole, C.E.M.Stevenson, S.A.Nepogodiev, D.M.Lawson, J.Angulo, R.A.Field, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.69 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	146.405, 146.405, 221.860, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.8

The binding sites of Chlorine atom in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound (pdb code 6gh2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound, PDB code: 6gh2:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1006 b:62.8 occ:1.00 N A:ARG368 3.5 56.6 1.0 CB A:ARG368 3.8 60.1 1.0 N A:GLY370 3.9 62.7 1.0 CA A:ARG368 4.0 58.3 1.0 N A:GLY369 4.1 59.0 1.0 C A:ARG368 4.2 59.0 1.0 CA A:GLY370 4.3 64.0 1.0 CG A:ARG368 4.6 60.8 1.0 C A:GLY367 4.6 54.9 1.0 CA A:GLY367 4.8 53.8 1.0 C A:GLY370 4.8 63.1 1.0 O A:GLY370 4.8 62.4 1.0 O A:ARG368 4.9 60.3 1.0 C A:GLY369 4.9 61.6 1.0

Chlorine binding site 2 out of 4 in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1007 b:70.0 occ:1.00 NH2 A:ARG92 3.4 53.2 1.0 NE A:ARG92 3.4 49.4 1.0 CZ A:ARG92 3.8 51.3 1.0 CG A:ARG92 4.4 44.2 1.0 CD A:ARG92 4.5 46.3 1.0

Chlorine binding site 3 out of 4 in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1007 b:52.3 occ:1.00 O B:HOH1388 3.1 50.7 1.0 N B:ARG368 3.5 42.7 1.0 N B:GLY370 3.7 43.3 1.0 CB B:ARG368 3.9 45.0 1.0 CA B:ARG368 4.0 43.4 1.0 N B:GLY369 4.1 41.5 1.0 CA B:GLY370 4.2 44.2 1.0 C B:ARG368 4.2 42.0 1.0 CG B:ARG368 4.6 46.9 1.0 C B:GLY370 4.6 43.8 1.0 C B:GLY367 4.6 40.7 1.0 O B:GLY370 4.7 45.0 1.0 CA B:GLY367 4.8 41.1 1.0 C B:GLY369 4.8 42.8 1.0 O B:ARG368 4.8 42.9 1.0

Chlorine binding site 4 out of 4 in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Glc-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1008 b:64.0 occ:1.00 NH2 B:ARG92 3.4 48.8 1.0 NE B:ARG92 3.6 46.6 1.0 CE B:LYS122 3.9 60.8 1.0 CZ B:ARG92 4.0 47.6 1.0 NZ B:LYS122 4.1 63.4 1.0 CD B:LYS122 4.7 59.1 1.0 CG B:ARG92 4.7 42.0 1.0 CD B:ARG92 4.8 43.3 1.0

S.Kuhaudomlarp, S.Walpole, C.E.M.Stevenson, S.A.Nepogodiev, D.M.Lawson, J.Angulo, R.A.Field. Unravelling the Specificity of Laminaribiose Phosphorylase From Paenibacillus Sp. Ym-1 Towards Donor Substrates Glucose/Mannose 1-Phosphate By Using X-Ray Crystallography and Saturation Transfer Difference uc(Nmr) Spectroscopy. Chembiochem V. 20 181 2019.
ISSN: ESSN 1439-7633
PubMed: 29856496
DOI: 10.1002/CBIC.201800260