Chlorine in PDB 6hwj: Glucosamine Kinase (Crystal Form A)

Protein crystallography data

The structure of Glucosamine Kinase (Crystal Form A), PDB code: 6hwj was solved by J.A.Manso, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.74 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.812, 96.070, 80.252, 90.00, 106.69, 90.00
R / Rfree (%) 17.6 / 21.4

Other elements in 6hwj:

The structure of Glucosamine Kinase (Crystal Form A) also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Glucosamine Kinase (Crystal Form A) (pdb code 6hwj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Glucosamine Kinase (Crystal Form A), PDB code: 6hwj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6hwj

Go back to Chlorine Binding Sites List in 6hwj
Chlorine binding site 1 out of 4 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Glucosamine Kinase (Crystal Form A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl511

b:33.5
occ:1.00
HE2 A:HIS419 2.3 34.0 1.0
HE A:ARG356 2.4 45.9 1.0
HH A:TYR422 2.5 34.7 1.0
HH21 A:ARG356 2.5 48.6 1.0
HE1 A:TYR422 3.1 36.0 1.0
NE2 A:HIS419 3.2 28.4 1.0
NE A:ARG356 3.2 38.2 1.0
OH A:TYR422 3.3 28.9 1.0
NH2 A:ARG356 3.3 40.5 1.0
HZ3 A:TRP420 3.3 38.3 1.0
HE3 A:TRP420 3.4 37.1 1.0
HD2 A:PHE355 3.5 38.3 1.0
CZ A:ARG356 3.7 39.3 1.0
HE2 A:PHE355 3.7 31.3 1.0
CE1 A:TYR422 3.9 30.0 1.0
CD2 A:PHE355 3.9 32.0 1.0
HH22 A:ARG356 4.0 48.6 1.0
CZ3 A:TRP420 4.0 31.9 1.0
CE3 A:TRP420 4.0 30.9 1.0
CZ A:TYR422 4.0 29.8 1.0
HG22 A:VAL352 4.0 34.7 1.0
CE2 A:PHE355 4.0 26.1 1.0
CD2 A:HIS419 4.1 24.7 1.0
CE1 A:HIS419 4.1 27.6 1.0
HG3 A:ARG356 4.1 36.4 1.0
HD2 A:HIS419 4.1 29.6 1.0
HG2 A:ARG356 4.1 36.4 1.0
HE1 A:HIS419 4.2 33.2 1.0
HG13 A:VAL352 4.4 39.4 1.0
CD A:ARG356 4.4 33.4 1.0
CG A:ARG356 4.4 30.4 1.0
HD21 A:LEU417 4.6 36.2 1.0
HB3 A:PHE355 4.8 29.2 1.0
HA A:VAL352 4.9 29.5 1.0
CG A:PHE355 4.9 26.5 1.0
HD3 A:ARG356 5.0 40.0 1.0
CG2 A:VAL352 5.0 28.9 1.0

Chlorine binding site 2 out of 4 in 6hwj

Go back to Chlorine Binding Sites List in 6hwj
Chlorine binding site 2 out of 4 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Glucosamine Kinase (Crystal Form A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl512

b:33.7
occ:1.00
HH11 A:ARG351 2.3 33.4 1.0
HD13 A:LEU426 3.0 42.7 1.0
HD3 A:ARG351 3.0 32.9 1.0
NH1 A:ARG351 3.1 27.9 1.0
O A:HOH707 3.2 28.2 1.0
HD2 A:ARG351 3.3 32.9 1.0
HG11 A:VAL354 3.4 31.8 1.0
HG21 A:VAL354 3.4 36.3 1.0
HH12 A:ARG351 3.4 33.4 1.0
HB A:VAL354 3.5 37.3 1.0
HA A:ARG351 3.5 28.4 1.0
CD A:ARG351 3.6 27.4 1.0
HG2 A:ARG366 3.7 74.3 1.0
HD2 A:ARG366 3.8 89.9 1.0
CD1 A:LEU426 3.9 35.6 1.0
HB3 A:LEU426 3.9 37.2 1.0
CG1 A:VAL354 4.0 26.5 1.0
HG12 A:VAL354 4.0 31.8 1.0
CB A:VAL354 4.0 31.1 1.0
HD12 A:LEU426 4.1 42.7 1.0
CG2 A:VAL354 4.1 30.2 1.0
CZ A:ARG351 4.2 28.6 1.0
HG3 A:ARG366 4.2 74.3 1.0
CG A:ARG366 4.3 61.9 1.0
NE A:ARG351 4.4 25.0 1.0
CD A:ARG366 4.4 74.9 1.0
HD11 A:LEU426 4.4 42.7 1.0
CA A:ARG351 4.5 23.7 1.0
HG23 A:VAL354 4.6 36.3 1.0
CB A:LEU426 4.6 31.0 1.0
HD11 A:ILE369 4.6 39.7 1.0
HB3 A:ARG351 4.7 32.5 1.0
HB2 A:LEU426 4.7 37.2 1.0
HD22 A:LEU426 4.7 42.2 1.0
HB3 A:PRO362 4.7 46.9 1.0
CG A:LEU426 4.8 35.5 1.0
HE A:ARG366 4.8 0.7 1.0
HD12 A:ILE369 4.8 39.7 1.0
NE A:ARG366 4.8 85.6 1.0
CG A:ARG351 4.8 25.1 1.0
HB2 A:PRO362 4.9 46.9 1.0
HG13 A:VAL354 4.9 31.8 1.0
HG22 A:VAL354 4.9 36.3 1.0
CB A:ARG351 4.9 27.1 1.0

Chlorine binding site 3 out of 4 in 6hwj

Go back to Chlorine Binding Sites List in 6hwj
Chlorine binding site 3 out of 4 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Glucosamine Kinase (Crystal Form A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:33.0
occ:1.00
HE2 B:HIS419 2.3 35.9 1.0
HE B:ARG356 2.4 48.7 1.0
HH B:TYR422 2.4 34.4 1.0
HH21 B:ARG356 2.5 49.6 1.0
HE2 B:TYR422 3.0 34.0 1.0
NE2 B:HIS419 3.1 29.9 1.0
NE B:ARG356 3.2 40.6 1.0
HZ3 B:TRP420 3.2 31.6 1.0
OH B:TYR422 3.2 28.6 1.0
NH2 B:ARG356 3.2 41.4 1.0
HE3 B:TRP420 3.3 34.3 1.0
HD2 B:PHE355 3.5 37.3 1.0
CZ B:ARG356 3.7 44.2 1.0
CE2 B:TYR422 3.8 28.4 1.0
HG22 B:VAL352 3.8 31.9 1.0
CZ3 B:TRP420 3.9 26.3 1.0
HE2 B:PHE355 3.9 34.1 1.0
CE3 B:TRP420 3.9 28.6 1.0
CZ B:TYR422 3.9 28.4 1.0
CD2 B:PHE355 4.0 31.1 1.0
HH22 B:ARG356 4.0 49.6 1.0
HG3 B:ARG356 4.0 40.2 1.0
CD2 B:HIS419 4.0 26.7 1.0
HD2 B:HIS419 4.1 32.0 1.0
CE1 B:HIS419 4.1 29.1 1.0
HG2 B:ARG356 4.1 40.2 1.0
HE1 B:HIS419 4.2 34.9 1.0
CE2 B:PHE355 4.2 28.4 1.0
CD B:ARG356 4.3 37.5 1.0
CG B:ARG356 4.4 33.5 1.0
HG13 B:VAL352 4.4 36.1 1.0
HD21 B:LEU417 4.7 39.6 1.0
HB3 B:PHE355 4.7 37.1 1.0
CG2 B:VAL352 4.7 26.6 1.0
HA B:VAL352 4.7 32.6 1.0
HD3 B:ARG356 4.9 45.0 1.0
HD2 B:ARG356 4.9 45.0 1.0
CG B:PHE355 4.9 29.6 1.0
HG11 B:VAL352 5.0 36.1 1.0
HG21 B:VAL352 5.0 31.9 1.0
NH1 B:ARG356 5.0 42.7 1.0

Chlorine binding site 4 out of 4 in 6hwj

Go back to Chlorine Binding Sites List in 6hwj
Chlorine binding site 4 out of 4 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Glucosamine Kinase (Crystal Form A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:34.8
occ:1.00
HE B:ARG366 2.4 55.9 1.0
HH11 B:ARG351 2.4 37.3 1.0
HH21 B:ARG366 2.6 60.0 1.0
HD13 B:LEU426 2.9 37.3 1.0
HD3 B:ARG351 3.1 35.5 1.0
O B:HOH739 3.1 41.4 1.0
NE B:ARG366 3.2 46.6 1.0
HG21 B:VAL354 3.2 40.1 1.0
NH1 B:ARG351 3.2 31.1 1.0
NH2 B:ARG366 3.3 50.0 1.0
HD2 B:ARG351 3.3 35.5 1.0
O B:HOH668 3.4 29.0 1.0
HA B:ARG351 3.5 32.8 1.0
HG11 B:VAL354 3.5 41.4 1.0
HB B:VAL354 3.5 38.6 1.0
HH12 B:ARG351 3.5 37.3 1.0
CD B:ARG351 3.7 29.6 1.0
CZ B:ARG366 3.7 50.1 1.0
CD1 B:LEU426 3.9 31.1 1.0
HG2 B:ARG366 4.0 48.6 1.0
CG2 B:VAL354 4.0 33.4 1.0
HG3 B:ARG366 4.0 48.6 1.0
HH22 B:ARG366 4.0 60.0 1.0
CB B:VAL354 4.0 32.2 1.0
HB3 B:LEU426 4.1 32.0 1.0
CG1 B:VAL354 4.1 34.5 1.0
HD12 B:LEU426 4.2 37.3 1.0
CZ B:ARG351 4.3 29.8 1.0
CG B:ARG366 4.3 40.5 1.0
HD11 B:LEU426 4.3 37.3 1.0
CD B:ARG366 4.3 45.0 1.0
HG23 B:VAL354 4.3 40.1 1.0
HG12 B:VAL354 4.4 41.4 1.0
CA B:ARG351 4.4 27.4 1.0
NE B:ARG351 4.4 29.0 1.0
HD22 B:LEU426 4.4 39.5 1.0
HB3 B:ARG351 4.7 31.7 1.0
HD11 B:ILE369 4.7 39.6 1.0
HG22 B:VAL354 4.7 40.1 1.0
HD3 B:ARG366 4.7 54.0 1.0
CG B:LEU426 4.8 30.0 1.0
CB B:LEU426 4.8 26.7 1.0
O B:HOH748 4.8 46.4 1.0
HD12 B:ILE369 4.9 39.6 1.0
CG B:ARG351 4.9 27.4 1.0
CB B:ARG351 4.9 26.4 1.0
HB2 B:LEU426 4.9 32.0 1.0
O B:GLY350 5.0 26.9 1.0
HG13 B:VAL354 5.0 41.4 1.0

Reference:

J.A.Manso, D.Nunes-Costa, S.Macedo-Ribeiro, N.Empadinhas, P.J.B.Pereira. Molecular Fingerprints For A Novel Enzyme Family Inactinobacteriawith Glucosamine Kinase Activity. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 31088917
DOI: 10.1128/MBIO.00239-19
Page generated: Sat Dec 12 13:08:49 2020

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