Chlorine in PDB 7jhi: Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative

Enzymatic activity of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative

All present enzymatic activity of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative:
2.4.1.149;

Protein crystallography data

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative, PDB code: 7jhi was solved by Y.Hao, X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.33 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.431, 81.385, 157.138, 90.00, 98.63, 90.00
R / Rfree (%) 20.2 / 24.8

Other elements in 7jhi:

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Iodine (I) 41 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative (pdb code 7jhi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative, PDB code: 7jhi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 7jhi

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Chlorine binding site 1 out of 5 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:31.8
occ:1.00
 CD A:LYS266 3.4 28.7 1.0
CB B:SER263 3.5 20.2 1.0
N A:SER263 3.7 20.7 1.0
OG A:SER263 3.7 24.8 1.0
CA B:SER263 4.1 23.2 1.0
CB A:SER263 4.1 22.2 1.0
CB A:LYS266 4.2 20.1 1.0
O A:HOH502 4.2 25.1 1.0
CD2 A:LEU262 4.3 21.0 1.0
CA A:LEU262 4.3 21.8 1.0
CG A:LYS266 4.4 17.8 1.0
CE A:LYS266 4.4 23.4 1.0
N B:SER263 4.5 25.2 1.0
C A:LEU262 4.5 28.3 1.0
CA A:SER263 4.5 22.4 1.0
OG B:SER263 4.6 26.7 1.0
O A:SER261 4.7 22.9 1.0
CB A:LEU262 5.0 18.6 1.0

Chlorine binding site 2 out of 5 in 7jhi

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Chlorine binding site 2 out of 5 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl416

b:56.0
occ:1.00
 OE2 A:GLU359 3.6 60.1 1.0
CD A:GLU359 3.9 61.9 1.0
OD1 A:ASN362 3.9 48.4 1.0
CB A:ASN362 4.0 46.8 1.0
CG A:ASN362 4.0 46.3 1.0
OE1 A:GLU359 4.0 60.1 1.0
NH1 A:ARG354 4.0 23.0 1.0
OG A:SER368 4.2 43.4 1.0
N A:GLU359 4.4 45.3 1.0
CB A:ILE358 4.4 40.6 1.0
NH2 A:ARG354 4.5 32.8 1.0
CB A:GLU359 4.5 47.2 1.0
CB A:SER368 4.5 31.1 1.0
CG A:GLU359 4.6 44.1 1.0
CZ A:ARG354 4.7 41.1 1.0
ND2 A:ASN362 4.8 48.9 1.0
CG1 A:ILE358 4.9 35.4 1.0

Chlorine binding site 3 out of 5 in 7jhi

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Chlorine binding site 3 out of 5 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl414

b:11.2
occ:1.00
 CB C:PRO380 3.8 12.9 1.0
CG C:PRO380 4.0 13.1 1.0
CB C:ALA156 4.1 11.8 1.0
CG C:GLN381 4.3 31.2 1.0
CD C:PRO380 4.5 10.5 1.0
N C:GLN381 4.8 18.0 1.0
CD C:GLN381 4.8 25.6 1.0
NE2 C:GLN381 4.8 34.9 1.0
CA C:PRO380 5.0 14.2 1.0

Chlorine binding site 4 out of 5 in 7jhi

Go back to Chlorine Binding Sites List in 7jhi
Chlorine binding site 4 out of 5 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl409

b:45.0
occ:1.00
 N D:ASP237 3.3 39.5 1.0
CD D:PRO236 3.5 31.5 1.0
CB D:ASP237 3.5 43.5 1.0
O D:CYS138 3.7 49.5 1.0
N D:PRO236 3.7 38.0 1.0
CA D:CYS235 3.8 28.1 1.0
C D:CYS235 3.8 36.5 1.0
CA D:ASP237 3.9 39.6 1.0
CB D:CYS138 3.9 43.7 1.0
CG D:ASP237 4.2 61.2 1.0
OD2 D:ASP237 4.2 67.6 1.0
C D:ASP237 4.2 38.5 1.0
N D:THR238 4.3 34.1 1.0
O D:SER234 4.4 32.8 1.0
C D:PRO236 4.4 31.8 1.0
CD D:PRO142 4.4 39.2 1.0
SG D:CYS235 4.4 35.5 1.0
O D:CYS235 4.6 33.9 1.0
CA D:PRO236 4.6 34.9 1.0
C D:CYS138 4.7 52.4 1.0
CB D:CYS235 4.7 18.8 1.0
N D:CYS235 4.7 30.7 1.0
CG D:PRO236 4.8 32.8 1.0
C D:SER234 4.9 27.8 1.0
CA D:CYS138 4.9 42.6 1.0
O D:ASP237 4.9 38.6 1.0

Chlorine binding site 5 out of 5 in 7jhi

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Chlorine binding site 5 out of 5 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl410

b:48.0
occ:1.00
 CD D:ARG214 3.3 39.9 1.0
O D:HOH503 3.8 22.7 1.0
CG D:ARG214 4.0 32.3 1.0
CG D:PRO186 4.2 19.5 1.0
C5 H:NAG2 4.3 44.9 1.0
OE1 D:GLU188 4.4 37.7 1.0
NE D:ARG214 4.5 25.2 1.0
CB D:GLU188 4.5 33.8 1.0
O6 H:NAG1 4.5 42.9 1.0
O6 H:NAG2 4.6 48.0 1.0
CB D:PRO186 4.6 23.2 1.0
C1 H:NAG2 4.8 33.9 1.0
O4 H:NAG2 4.8 66.6 1.0
C3 H:NAG2 4.8 45.3 1.0
CG D:GLU188 4.8 39.5 1.0
OD1 D:ASP189 4.9 43.2 1.0
C4 H:NAG2 4.9 47.2 1.0
CD D:GLU188 4.9 51.0 1.0
CB D:ARG214 4.9 29.8 1.0
O5 H:NAG2 4.9 44.3 1.0
NH1 D:ARG214 5.0 34.1 1.0

Reference:

Y.Hao, A.Crequer-Grandhomme, N.Javier, A.Singh, H.Chen, P.Manzanillo, M.C.Lo, X.Huang. Structures and Mechanism of Human Glycosyltransferase Beta 1,3-N-Acetylglucosaminyltransferase 2 (B3GNT2), An Important Player in Immune Homeostasis. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33158990
DOI: 10.1074/JBC.RA120.015306
Page generated: Mon Jul 29 23:04:33 2024

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