Iodine in PDB 3d11: Crystal Structures of the Nipah G Attachment Glycoprotein

All present enzymatic activity of Crystal Structures of the Nipah G Attachment Glycoprotein:
3.2.1.18;

The structure of Crystal Structures of the Nipah G Attachment Glycoprotein, PDB code: 3d11 was solved by K.Xu, K.R.Rajashankar, Y.P.Chan, P.Himanen, C.C.Broder, D.B.Nikolov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.25 / 2.31
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	130.161, 130.161, 130.161, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structures of the Nipah G Attachment Glycoprotein (pdb code 3d11). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structures of the Nipah G Attachment Glycoprotein, PDB code: 3d11:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1 b:44.4 occ:1.00 O A:HOH1464 3.7 37.8 1.0 CB A:SER204 4.0 33.6 1.0 CD2 A:LEU202 4.2 41.3 1.0 N A:TYR205 4.2 34.6 1.0 CD1 A:TYR205 4.3 38.5 1.0 CG A:LEU202 4.3 38.3 1.0 CB A:TYR205 4.4 35.3 1.0 OG A:SER204 4.6 33.1 1.0 N A:SER204 4.6 33.3 1.0 CG2 A:VAL210 4.7 39.0 1.0 CA A:SER204 4.7 33.6 1.0 CA A:TYR205 4.7 36.2 1.0 C A:SER204 4.8 36.0 1.0 CG A:TYR205 4.8 37.5 1.0

Iodine binding site 2 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I2 b:43.8 occ:1.00 O A:HOH1366 2.7 37.3 1.0 N A:TYR508 3.5 32.1 1.0 CG2 A:VAL507 3.9 34.5 1.0 CB A:LYS560 4.0 31.5 1.0 O A:HOH1519 4.1 39.4 1.0 CB A:TYR508 4.1 30.5 1.0 CA A:VAL507 4.1 35.1 1.0 C A:VAL507 4.3 33.0 1.0 CA A:TYR508 4.4 31.2 1.0 O A:HOH1550 4.4 46.5 1.0 CA A:LYS560 4.4 30.4 1.0 N A:LYS560 4.5 31.2 1.0 CZ A:PHE458 4.5 33.5 1.0 O A:HOH1524 4.5 45.8 1.0 CB A:VAL507 4.6 34.2 1.0 O A:HOH1536 4.7 45.1 1.0 CE A:LYS560 4.7 37.2 1.0 OE1 A:GLN559 4.7 42.6 1.0 CD A:LYS560 4.7 32.1 1.0 CG A:LYS560 4.9 30.7 1.0 O A:TYR508 5.0 29.9 1.0

Iodine binding site 3 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I3 b:47.2 occ:1.00 O A:HOH1381 3.4 36.5 1.0 N A:TYR407 3.8 43.5 1.0 N A:HIS406 3.8 45.1 1.0 OG A:SER307 3.9 38.3 1.0 CD1 A:TYR407 4.1 41.9 1.0 O A:HOH1415 4.1 40.1 1.0 CB A:SER405 4.2 45.5 1.0 CB A:TYR407 4.2 42.1 1.0 CB A:HIS406 4.4 43.6 1.0 O A:HOH1472 4.4 42.3 1.0 CB A:SER307 4.4 37.8 1.0 CA A:HIS406 4.5 43.8 1.0 O A:HOH1402 4.5 38.5 1.0 CA A:SER405 4.5 46.5 1.0 CA A:TYR407 4.5 42.7 1.0 C A:SER405 4.6 45.5 1.0 C A:HIS406 4.6 43.5 1.0 O A:TYR407 4.6 41.6 1.0 NH1 A:ARG402 4.6 49.0 1.0 CG A:TYR407 4.7 41.6 1.0 CG2 A:THR308 4.9 38.7 1.0

Iodine binding site 4 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I4 b:47.3 occ:0.50 CG A:LYS246 4.1 34.6 1.0 CD1 A:ILE237 4.3 38.8 1.0 O A:HOH1516 4.7 39.7 1.0 CA A:LYS246 4.7 32.0 1.0 CB A:LYS246 4.7 32.8 1.0 O A:LYS246 5.0 31.8 1.0

Iodine binding site 5 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I5 b:57.1 occ:1.00 N A:ASN543 3.6 40.6 1.0 CB A:ASN543 3.8 42.0 1.0 CE A:LYS541 3.8 44.8 1.0 ND2 A:ASN543 4.0 43.8 1.0 CB A:LYS541 4.1 39.8 1.0 CA A:ASN543 4.1 41.0 1.0 N A:GLU544 4.3 42.8 1.0 C A:ASN543 4.4 42.3 1.0 CG A:ASN543 4.4 42.9 1.0 OE1 A:GLU544 4.5 46.3 1.0 N A:ASP542 4.5 40.1 1.0 CB A:GLU544 4.5 43.0 1.0 C A:ASP542 4.7 40.1 1.0 CB A:ASP542 4.7 41.8 1.0 NZ A:LYS541 4.8 46.6 1.0 O A:HOH1454 4.8 42.1 1.0 O A:HOH1426 4.8 43.7 1.0 CG A:LYS541 4.8 41.5 1.0 CA A:ASP542 4.8 39.5 1.0 C A:LYS541 4.9 39.8 1.0 CD A:LYS541 4.9 42.9 1.0 CG A:GLU544 5.0 46.9 1.0

Iodine binding site 6 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I6 b:61.4 occ:1.00 CG A:PRO208 3.7 37.5 1.0 CG A:MET267 4.0 37.7 1.0 CB A:MET267 4.0 36.5 1.0 O A:HOH1530 4.1 38.8 1.0 O A:HOH1388 4.3 42.0 1.0 CD A:PRO208 4.5 36.9 1.0 CB A:PRO208 4.5 38.2 1.0 CG1 A:VAL270 4.8 36.2 1.0

Iodine binding site 7 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I7 b:78.3 occ:1.00 I A:IOD16 2.6 0.3 1.0 N A:LYS376 3.2 57.2 1.0 CD1 A:PHE375 3.2 51.0 1.0 O A:HOH1397 3.6 57.5 1.0 CE1 A:PHE375 3.7 50.6 1.0 CA A:PHE375 3.8 54.2 1.0 O A:HOH1409 3.9 54.3 1.0 CD2 A:LEU370 3.9 50.1 1.0 O A:LYS376 4.0 59.5 1.0 C A:PHE375 4.0 55.2 1.0 CA A:LYS376 4.1 57.8 1.0 O A:GLU374 4.1 53.8 1.0 CB A:LYS376 4.2 58.0 1.0 CG A:PHE375 4.3 51.2 1.0 C A:LYS376 4.4 59.0 1.0 NH1 A:ARG410 4.5 47.3 1.0 CB A:PHE375 4.6 52.2 1.0 N A:PHE375 4.8 52.8 1.0 C A:GLU374 4.9 53.2 1.0 CZ A:PHE375 5.0 50.0 1.0

Iodine binding site 8 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I8 b:74.5 occ:1.00 O A:HOH1461 3.8 36.4 1.0 CA A:PRO208 3.9 37.5 1.0 C A:PRO208 3.9 38.0 1.0 O A:PRO208 4.0 39.3 1.0 CB A:PRO208 4.0 38.2 1.0 N A:VAL209 4.5 37.0 1.0 N A:GLY211 4.6 45.4 1.0 N A:VAL210 4.9 40.0 1.0

Iodine binding site 9 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I9 b:79.9 occ:1.00 I A:IOD14 3.2 95.1 1.0 O A:HOH1412 3.6 46.9 1.0 N A:CYS601 3.7 49.7 1.0 CA A:GLN600 3.9 49.9 1.0 C A:GLN600 4.3 49.5 1.0 CB A:GLN600 4.3 50.0 1.0 CB A:CYS601 4.7 51.3 1.0 CA A:CYS601 4.8 50.5 1.0

Iodine binding site 10 out of 19 in the Crystal Structures of the Nipah G Attachment Glycoprotein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structures of the Nipah G Attachment Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:I10 b:81.2 occ:1.00 O A:HOH1501 3.4 36.8 1.0 O A:HOH1481 3.4 45.2 1.0 SD A:MET315 3.6 54.7 1.0 CG A:MET315 4.0 44.1 1.0 NE2 A:GLN334 4.1 50.6 1.0 OE1 A:GLN334 4.2 52.3 1.0 CB A:PRO273 4.3 37.4 1.0 CG2 A:VAL279 4.4 31.3 1.0 CD A:PRO274 4.5 38.2 1.0 CD A:GLN334 4.6 50.5 1.0 CB A:MET315 4.7 39.6 1.0 CG A:PRO274 4.7 37.0 1.0 CH2 A:TRP271 4.8 41.4 1.0 CG2 A:VAL297 4.8 34.9 1.0

K.Xu, K.R.Rajashankar, Y.P.Chan, J.P.Himanen, C.C.Broder, D.B.Nikolov. Host Cell Recognition By the Henipaviruses: Crystal Structures of the Nipah G Attachment Glycoprotein and Its Complex with Ephrin-B3. Proc.Natl.Acad.Sci.Usa V. 105 9953 2008.
ISSN: ISSN 0027-8424
PubMed: 18632560
DOI: 10.1073/PNAS.0804797105