Chlorine in PDB 6gh3: Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Man-1- Phosphate Bound

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

The structure of Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Man-1- Phosphate Bound, PDB code: 6gh3 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)	73.29 / 1.82
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	146.570, 146.570, 222.227, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.9

The binding sites of Chlorine atom in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Man-1- Phosphate Bound (pdb code 6gh3). 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-Man-1- Phosphate Bound, PDB code: 6gh3:
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-Man-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-Man-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1008 b:59.8 occ:1.00 N A:GLY370 3.4 54.8 1.0 N A:ARG368 3.5 42.5 1.0 CB A:ARG368 3.9 46.2 1.0 CA A:GLY370 3.9 56.6 1.0 CA A:ARG368 3.9 44.4 1.0 N A:GLY369 3.9 47.7 1.0 C A:ARG368 4.0 47.1 1.0 C A:GLY369 4.6 54.2 1.0 O A:ARG368 4.6 50.4 1.0 C A:GLY367 4.6 38.4 1.0 C A:GLY370 4.6 55.1 1.0 CG A:ARG368 4.7 45.9 1.0 CA A:GLY367 4.7 37.6 1.0 CA A:GLY369 4.8 51.0 1.0 O A:GLY370 4.8 53.9 1.0

Chlorine binding site 2 out of 4 in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Man-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-Man-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1009 b:65.1 occ:1.00 NH2 A:ARG92 3.3 42.3 1.0 NE A:ARG92 3.5 37.4 1.0 NZ A:LYS122 3.5 74.7 1.0 CZ A:ARG92 3.9 41.4 1.0 CG A:ARG92 4.5 32.8 1.0 CD A:ARG92 4.6 35.4 1.0 CE A:LYS122 5.0 73.6 1.0

Chlorine binding site 3 out of 4 in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Man-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-Man-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1009 b:53.1 occ:1.00 N B:ARG368 3.5 28.9 1.0 O B:HOH1392 3.5 43.7 1.0 N B:GLY370 3.7 33.0 1.0 CB B:ARG368 4.1 32.7 1.0 CA B:ARG368 4.1 30.2 1.0 CA B:GLY370 4.1 36.0 1.0 N B:GLY369 4.1 27.9 1.0 C B:ARG368 4.2 29.1 1.0 C B:GLY367 4.6 27.2 1.0 CA B:GLY367 4.6 26.9 1.0 C B:GLY370 4.7 35.5 1.0 C B:GLY369 4.8 32.2 1.0 CG B:ARG368 4.8 33.9 1.0 O B:ARG368 4.8 31.8 1.0 O B:GLY370 4.9 34.9 1.0

Chlorine binding site 4 out of 4 in the Paenibacillus Sp. YM1 Laminaribiose Phosphorylase with Alpha-Man-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-Man-1- Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1010 b:66.0 occ:1.00 O B:HOH1304 3.2 39.7 1.0 NH2 B:ARG92 3.6 37.8 1.0 NE B:ARG92 3.6 35.1 1.0 NZ B:LYS122 4.0 74.9 1.0 CZ B:ARG92 4.1 37.0 1.0 CG B:ARG92 4.6 29.6 1.0 CD B:ARG92 4.7 31.1 1.0 CE B:LYS122 4.7 74.8 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