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Zinc in PDB 5g2t: BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate

Enzymatic activity of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate

All present enzymatic activity of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate:
3.1.6.18;

Protein crystallography data

The structure of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate, PDB code: 5g2t was solved by A.Cartmell, E.C.Lowe, A.Basle, L.I.Crouch, M.Czjzek, J.Turnbull, B.Henrissat, N.Terrapon, S.Thomas, H.Murray, S.J.Firbank, D.N.Bolam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 125.34 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.207, 114.526, 127.293, 90.00, 100.04, 90.00
R / Rfree (%) 16 / 19.8

Other elements in 5g2t:

The structure of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate (pdb code 5g2t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate, PDB code: 5g2t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5g2t

Go back to Zinc Binding Sites List in 5g2t
Zinc binding site 1 out of 4 in the BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.6
occ:1.00
 ND1 A:HIS477 2.2 21.2 1.0
NE2 A:HIS470 2.2 24.5 1.0
SG A:CYS233 2.3 18.5 1.0
SG A:CYS234 2.4 21.8 1.0
CE1 A:HIS477 3.1 20.6 1.0
N A:CYS234 3.1 18.1 1.0
CG A:HIS477 3.2 20.4 1.0
CD2 A:HIS470 3.2 22.8 1.0
CB A:CYS233 3.2 19.4 1.0
CE1 A:HIS470 3.2 25.1 1.0
C A:CYS233 3.4 17.7 1.0
CB A:HIS477 3.5 23.0 1.0
CB A:CYS234 3.6 20.9 1.0
CA A:CYS234 3.7 20.5 1.0
CA A:CYS233 3.9 18.0 1.0
O A:CYS233 3.9 18.1 1.0
CA A:HIS477 4.0 24.3 1.0
NE2 A:HIS477 4.2 21.4 1.0
CD2 A:HIS477 4.3 21.6 1.0
ND1 A:HIS470 4.3 24.4 1.0
CD1 A:TYR231 4.3 20.5 1.0
CG A:HIS470 4.4 24.4 1.0
N A:CYS233 4.6 16.4 1.0
O A:HOH2184 4.7 29.9 1.0
O A:TYR231 4.8 15.9 1.0
CA A:TYR231 4.8 16.9 1.0
N A:HIS477 5.0 24.9 1.0
N A:GLU478 5.0 28.3 1.0

Zinc binding site 2 out of 4 in 5g2t

Go back to Zinc Binding Sites List in 5g2t
Zinc binding site 2 out of 4 in the BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:20.0
occ:1.00
 ND1 B:HIS477 2.1 20.9 1.0
NE2 B:HIS470 2.2 25.4 1.0
SG B:CYS233 2.3 21.6 1.0
SG B:CYS234 2.4 23.0 1.0
CD2 B:HIS470 3.0 26.1 1.0
CE1 B:HIS477 3.0 22.1 1.0
CG B:HIS477 3.1 22.1 1.0
N B:CYS234 3.2 20.9 1.0
CB B:CYS233 3.2 20.9 1.0
CE1 B:HIS470 3.2 25.6 1.0
CB B:HIS477 3.4 24.7 1.0
C B:CYS233 3.5 20.8 1.0
CB B:CYS234 3.6 21.8 1.0
CA B:CYS234 3.7 21.1 1.0
CA B:CYS233 3.9 19.8 1.0
O B:CYS233 4.0 20.7 1.0
CA B:HIS477 4.0 25.9 1.0
NE2 B:HIS477 4.2 21.3 1.0
CG B:HIS470 4.2 26.2 1.0
CD2 B:HIS477 4.2 21.8 1.0
ND1 B:HIS470 4.3 25.6 1.0
CD1 B:TYR231 4.4 24.5 1.0
N B:CYS233 4.6 19.2 1.0
O B:HOH2176 4.7 31.1 1.0
O B:TYR231 4.8 15.8 1.0
N B:GLU478 4.8 33.4 1.0
CA B:TYR231 4.9 18.3 1.0
C B:HIS477 5.0 29.8 1.0

Zinc binding site 3 out of 4 in 5g2t

Go back to Zinc Binding Sites List in 5g2t
Zinc binding site 3 out of 4 in the BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:16.5
occ:1.00
 ND1 C:HIS477 2.1 17.1 1.0
NE2 C:HIS470 2.2 17.7 1.0
SG C:CYS233 2.3 15.9 1.0
SG C:CYS234 2.3 18.7 1.0
CE1 C:HIS477 3.0 17.3 1.0
CE1 C:HIS470 3.1 18.4 1.0
N C:CYS234 3.1 16.7 1.0
CG C:HIS477 3.2 17.8 1.0
CD2 C:HIS470 3.2 18.0 1.0
CB C:CYS233 3.2 16.1 1.0
C C:CYS233 3.4 16.5 1.0
CB C:CYS234 3.5 18.1 1.0
CB C:HIS477 3.6 18.2 1.0
CA C:CYS234 3.6 17.7 1.0
CA C:CYS233 3.9 15.7 1.0
O C:CYS233 4.0 18.5 1.0
CA C:HIS477 4.0 18.9 1.0
NE2 C:HIS477 4.2 17.6 1.0
ND1 C:HIS470 4.2 17.9 1.0
CD2 C:HIS477 4.3 17.9 1.0
CG C:HIS470 4.3 18.8 1.0
CD1 C:TYR231 4.4 14.6 1.0
N C:CYS233 4.5 14.3 1.0
O C:TYR231 4.7 12.8 1.0
O C:HOH2165 4.7 26.1 1.0
CA C:TYR231 4.9 13.7 1.0
N C:HIS477 5.0 18.8 1.0
C C:TYR231 5.0 13.2 1.0
N C:GLU478 5.0 25.1 1.0

Zinc binding site 4 out of 4 in 5g2t

Go back to Zinc Binding Sites List in 5g2t
Zinc binding site 4 out of 4 in the BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BT1596 in Complex with Its Substrate 4,5 Unsaturated Uronic Acid Alpha 1,4 D-Glucosamine-2-N, 6-O-Disulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:18.8
occ:1.00
 ND1 D:HIS477 1.9 19.0 1.0
NE2 D:HIS470 2.2 25.9 1.0
SG D:CYS233 2.3 16.9 1.0
SG D:CYS234 2.4 23.6 1.0
CE1 D:HIS477 2.7 20.6 1.0
N D:CYS234 3.1 18.5 1.0
CG D:HIS477 3.1 19.2 1.0
CD2 D:HIS470 3.2 25.2 1.0
CE1 D:HIS470 3.2 27.0 1.0
CB D:CYS233 3.3 17.0 1.0
C D:CYS233 3.4 17.3 1.0
CB D:CYS234 3.5 20.4 1.0
CA D:CYS234 3.6 19.9 1.0
CB D:HIS477 3.6 19.1 1.0
CA D:CYS233 3.9 17.1 1.0
NE2 D:HIS477 3.9 19.2 1.0
O D:CYS233 4.0 17.3 1.0
CA D:HIS477 4.1 20.6 1.0
CD2 D:HIS477 4.1 19.0 1.0
ND1 D:HIS470 4.3 26.9 1.0
CG D:HIS470 4.3 25.6 1.0
CD1 D:TYR231 4.4 18.7 1.0
N D:CYS233 4.5 16.2 1.0
O D:TYR231 4.6 15.9 1.0
O D:HOH2159 4.6 34.0 1.0
CA D:TYR231 4.9 17.2 1.0
N D:HIS477 4.9 20.8 1.0
C D:TYR231 5.0 16.7 1.0

Reference:

A.Cartmell, E.C.Lowe, A.Basle, S.J.Firbank, D.A.Ndeh, H.Murray, N.Terrapon, V.Lombard, B.Henrissat, J.E.Turnbull, M.Czjzek, H.J.Gilbert, D.N.Bolam. How Members of the Human Gut Microbiota Overcome the Sulfation Problem Posed By Glycosaminoglycans. Proc. Natl. Acad. Sci. V. 114 7037 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28630303
DOI: 10.1073/PNAS.1704367114
Page generated: Sun Oct 27 16:53:55 2024

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