Chlorine in PDB 6u7n: Crystal Structure of Neurotrimin (Ntm)

The structure of Crystal Structure of Neurotrimin (Ntm), PDB code: 6u7n was solved by M.Machius, H.Venkannagari, A.Misra, G.Rudenko, S.Rush, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 3.32
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	106.049, 106.049, 227.819, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 25

The binding sites of Chlorine atom in the Crystal Structure of Neurotrimin (Ntm) (pdb code 6u7n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Neurotrimin (Ntm), PDB code: 6u7n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl409 b:75.1 occ:1.00 H A:ILE138 2.7 51.5 1.0 HG3 A:LYS137 2.9 0.2 1.0 HB A:ILE138 3.3 71.2 1.0 HB A:VAL211 3.5 70.2 1.0 N A:ILE138 3.5 42.9 1.0 HA A:LYS137 3.6 63.1 1.0 O A:ILE138 3.7 44.0 1.0 HE3 A:LYS137 3.8 0.3 1.0 CG A:LYS137 3.8 94.3 1.0 HG21 A:VAL211 4.0 63.1 1.0 HG2 A:LYS137 4.0 0.2 1.0 HG23 A:VAL211 4.0 63.1 1.0 CB A:ILE138 4.1 59.3 1.0 HH11 A:ARG213 4.1 0.5 1.0 CA A:ILE138 4.2 49.7 1.0 HD12 A:ILE138 4.2 0.1 1.0 HG13 A:ILE138 4.2 87.6 1.0 CB A:VAL211 4.3 58.5 1.0 HD2 A:ARG213 4.3 96.5 1.0 CG2 A:VAL211 4.3 52.6 1.0 HG11 A:VAL211 4.3 67.2 1.0 CA A:LYS137 4.3 52.5 1.0 C A:ILE138 4.4 49.9 1.0 C A:LYS137 4.4 47.2 1.0 HB2 A:ARG213 4.4 68.2 1.0 HD3 A:ARG213 4.4 96.5 1.0 CE A:LYS137 4.6 0.2 1.0 O A:VAL212 4.6 34.2 1.0 CG1 A:ILE138 4.6 73.0 1.0 CB A:LYS137 4.6 69.1 1.0 CD A:LYS137 4.7 1.0 1.0 HE2 A:LYS137 4.8 0.3 1.0 HD2 A:LYS137 4.8 0.8 1.0 CG1 A:VAL211 4.8 56.0 1.0 CD A:ARG213 4.8 80.4 1.0 HB2 A:LYS137 4.9 82.9 1.0 CD1 A:ILE138 4.9 85.9 1.0 NH1 A:ARG213 4.9 0.0 1.0

Chlorine binding site 2 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl410 b:53.1 occ:1.00 H A:ARG214 2.4 55.3 1.0 HG3 A:ARG213 3.1 69.1 1.0 HB2 A:ARG214 3.2 55.5 1.0 N A:ARG214 3.2 46.1 1.0 HA A:ARG213 3.2 68.1 1.0 CG A:ARG213 4.0 57.6 1.0 HG3 A:ARG214 4.0 55.3 1.0 CB A:ARG214 4.0 46.3 1.0 CA A:ARG213 4.0 56.8 1.0 HG2 A:ARG213 4.0 69.1 1.0 CA A:ARG214 4.1 45.9 1.0 C A:ARG213 4.1 56.6 1.0 O A:ARG214 4.2 46.9 1.0 CG A:ARG214 4.5 46.0 1.0 HD2 A:ARG214 4.5 55.8 1.0 C A:ARG214 4.6 46.3 1.0 CB A:ARG213 4.6 56.9 1.0 HB3 A:ARG214 4.8 55.5 1.0 HA A:ARG214 4.9 55.1 1.0

Chlorine binding site 3 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl411 b:65.9 occ:1.00 HH A:TYR224 2.1 37.1 1.0 HE1 A:TYR224 2.9 37.5 1.0 OH A:TYR224 2.9 30.9 1.0 HG A:SER226 3.3 61.2 1.0 CE1 A:TYR224 3.6 31.3 1.0 CZ A:TYR224 3.7 31.1 1.0 OG A:SER226 4.1 51.0 1.0 HB3 A:SER226 4.1 63.9 1.0 HA A:SER226 4.3 54.9 1.0 CB A:SER226 4.6 53.2 1.0 HH22 A:ARG193 4.7 37.0 1.0 CD1 A:TYR224 4.9 31.6 1.0 HH12 A:ARG193 4.9 36.2 1.0 HG A:SER246 4.9 41.0 1.0 CA A:SER226 4.9 45.7 1.0

Chlorine binding site 4 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl412 b:69.5 occ:1.00 HG A:SER250 2.0 62.4 1.0 OG A:SER250 2.9 52.0 1.0 HA A:SER250 3.2 62.2 1.0 HB3 A:PHE276 3.2 73.3 1.0 HB3 A:SER250 3.5 63.7 1.0 O A:PRO275 3.5 75.0 1.0 CB A:SER250 3.6 53.1 1.0 HB2 A:PRO275 3.7 75.5 1.0 O A:ALA247 3.8 35.8 1.0 H A:ALA247 3.8 42.3 1.0 CA A:SER250 3.9 51.8 1.0 H A:ALA251 4.0 75.2 1.0 C A:PRO275 4.0 76.4 1.0 CB A:PHE276 4.1 61.1 1.0 HA A:PHE276 4.1 74.8 1.0 HB3 A:PRO275 4.2 75.5 1.0 HB2 A:PHE276 4.3 73.3 1.0 CB A:PRO275 4.3 63.0 1.0 HA A:SER246 4.4 42.0 1.0 CA A:PHE276 4.4 62.3 1.0 N A:PHE276 4.5 63.7 1.0 HB2 A:SER250 4.5 63.7 1.0 N A:ALA247 4.7 35.2 1.0 N A:ALA251 4.7 62.7 1.0 CA A:PRO275 4.8 63.6 1.0 N A:SER250 4.8 51.5 1.0 C A:SER250 4.9 52.8 1.0 C A:ALA247 4.9 35.4 1.0 HD2 A:PHE276 4.9 75.6 1.0 HO2 A:EDO408 5.0 90.3 1.0

Chlorine binding site 5 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl413 b:84.0 occ:1.00 HZ3 A:LYS300 2.5 0.0 1.0 HZ2 A:LYS300 2.7 0.0 1.0 NZ A:LYS300 3.0 85.8 1.0 O A:SER146 3.5 41.2 1.0 HZ1 A:LYS300 3.5 0.0 1.0 HA A:ILE147 3.6 69.0 1.0 HD22 A:ASN220 3.6 48.8 1.0 HD21 A:ASN220 3.7 48.8 1.0 ND2 A:ASN220 3.9 40.7 1.0 HE2 A:LYS300 4.0 0.9 1.0 OD1 A:ASN148 4.1 82.5 1.0 CE A:LYS300 4.1 87.4 1.0 C A:SER146 4.3 40.2 1.0 CA A:ILE147 4.4 57.5 1.0 HD21 A:ASN148 4.5 97.1 1.0 C A:ILE147 4.6 49.5 1.0 HB3 A:SER146 4.6 49.1 1.0 OG A:SER146 4.6 41.0 1.0 N A:ILE147 4.7 54.9 1.0 HE3 A:LYS300 4.7 0.9 1.0 CG A:ASN148 4.7 71.8 1.0 HG A:SER146 4.8 49.2 1.0 ND2 A:ASN148 4.9 80.9 1.0 CG A:ASN220 4.9 40.6 1.0 N A:ASN148 4.9 38.5 1.0 H A:ASN148 4.9 46.2 1.0 O A:ILE147 4.9 49.2 1.0

Chlorine binding site 6 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl414 b:73.8 occ:1.00 HH22 A:ARG170 2.7 37.9 1.0 HH12 A:ARG170 2.9 47.1 1.0 HD12 A:ILE172 3.2 41.2 1.0 HG23 A:ILE172 3.4 42.3 1.0 NH2 A:ARG170 3.5 31.6 1.0 HH22 A:ARG214 3.6 56.3 1.0 NH1 A:ARG170 3.7 39.2 1.0 HH21 A:ARG214 4.1 56.3 1.0 NH2 A:ARG214 4.1 46.9 1.0 CD1 A:ILE172 4.1 34.4 1.0 CZ A:ARG170 4.1 40.6 1.0 HH21 A:ARG170 4.2 37.9 1.0 HG21 A:ILE172 4.2 42.3 1.0 CG2 A:ILE172 4.2 35.2 1.0 HD13 A:ILE172 4.2 41.2 1.0 HH11 A:ARG170 4.4 47.1 1.0 HD11 A:ILE172 4.6 41.2 1.0 HA A:ILE172 4.8 41.0 1.0 HG22 A:ILE172 4.8 42.3 1.0

Chlorine binding site 7 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl415 b:40.1 occ:1.00 HG21 A:VAL248 2.9 40.5 1.0 H A:VAL219 3.1 38.0 1.0 O A:VAL219 3.1 32.0 1.0 OG A:SER196 3.2 29.7 1.0 HE2 A:TYR221 3.4 41.6 1.0 HB A:VAL219 3.5 36.7 1.0 HB3 A:SER196 3.5 35.6 1.0 HG3 A:ARG193 3.5 35.3 1.0 HB2 A:SER196 3.5 35.6 1.0 CB A:SER196 3.7 29.7 1.0 HG11 A:VAL248 3.7 41.4 1.0 HG A:SER196 3.7 35.6 1.0 N A:VAL219 3.9 31.6 1.0 CG2 A:VAL248 3.9 33.7 1.0 HG23 A:THR218 4.0 44.3 1.0 C A:VAL219 4.1 32.1 1.0 CE2 A:TYR221 4.3 34.6 1.0 CB A:VAL219 4.3 30.6 1.0 CA A:VAL219 4.3 31.5 1.0 HG23 A:VAL248 4.3 40.5 1.0 HA A:ARG193 4.3 34.7 1.0 HD2 A:TYR221 4.3 41.5 1.0 HA A:THR218 4.4 42.4 1.0 HB A:VAL248 4.4 41.1 1.0 HG22 A:VAL248 4.4 40.5 1.0 CG1 A:VAL248 4.5 34.5 1.0 CG A:ARG193 4.5 29.4 1.0 CB A:VAL248 4.5 34.2 1.0 O A:ARG193 4.6 28.8 1.0 CD2 A:TYR221 4.7 34.6 1.0 HG2 A:ARG193 4.8 35.3 1.0 HH A:TYR221 4.8 42.2 1.0 HG12 A:VAL219 4.9 36.7 1.0 HG12 A:VAL248 4.9 41.4 1.0 C A:THR218 5.0 43.4 1.0 CG2 A:THR218 5.0 37.0 1.0 HG23 A:VAL219 5.0 36.2 1.0

Chlorine binding site 8 out of 8 in the Crystal Structure of Neurotrimin (Ntm)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Neurotrimin (Ntm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl416 b:96.8 occ:1.00 HB2 A:PRO249 2.8 52.8 1.0 H A:LYS300 3.0 75.3 1.0 OD1 A:ASN299 3.1 99.2 1.0 HA A:ASN299 3.5 73.0 1.0 HB2 A:LYS300 3.5 75.2 1.0 HG2 A:PRO249 3.5 52.3 1.0 N A:LYS300 3.6 62.8 1.0 CB A:PRO249 3.7 44.0 1.0 HB3 A:PRO249 3.9 52.8 1.0 OE2 A:GLU252 4.0 0.3 1.0 CG A:PRO249 4.1 43.6 1.0 HG3 A:GLU252 4.2 0.7 1.0 CB A:LYS300 4.2 62.6 1.0 O A:SER250 4.2 53.8 1.0 HB3 A:LYS300 4.3 75.2 1.0 CA A:ASN299 4.3 60.8 1.0 CG A:ASN299 4.3 82.7 1.0 C A:ASN299 4.3 61.3 1.0 CA A:LYS300 4.4 63.1 1.0 HD2 A:PRO249 4.5 50.6 1.0 HA A:LYS300 4.5 75.8 1.0 CD A:GLU252 4.6 0.2 1.0 CD A:PRO249 4.8 42.2 1.0 HG3 A:PRO249 4.9 52.3 1.0 CA A:PRO249 4.9 42.4 1.0 CG A:GLU252 4.9 92.3 1.0 CB A:ASN299 4.9 62.2 1.0 C A:PRO249 4.9 42.7 1.0

H.Venkannagari, J.M.Kasper, A.Misra, S.A.Rush, S.Fan, H.Lee, H.Sun, S.Seshadrinathan, M.Machius, J.D.Hommel, G.Rudenko. Highly Conserved Molecular Features in Iglons Contrast Their Distinct Structural and Biological Outcomes. J.Mol.Biol. V. 432 5287 2020.
ISSN: ESSN 1089-8638
PubMed: 32710982
DOI: 10.1016/J.JMB.2020.07.014