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Bromine in PDB 1m3d: Structure of Type IV Collagen NC1 Domains

Protein crystallography data

The structure of Structure of Type IV Collagen NC1 Domains, PDB code: 1m3d was solved by M.Sundaramoorthy, M.Meiyappan, P.Todd, B.G.Hudson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.069, 137.963, 127.131, 90.00, 90.31, 90.00
R / Rfree (%) 16.9 / 19.7

Other elements in 1m3d:

The structure of Structure of Type IV Collagen NC1 Domains also contains other interesting chemical elements:

Lutetium (Lu) 4 atoms

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Bromine atom in the Structure of Type IV Collagen NC1 Domains (pdb code 1m3d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 36 binding sites of Bromine where determined in the Structure of Type IV Collagen NC1 Domains, PDB code: 1m3d:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 36 in 1m3d

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Bromine binding site 1 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3001

b:16.4
occ:1.00
 OH B:TYR189 3.3 13.6 1.0
N D:ALA186 3.3 8.9 1.0
O A:HOH4014 3.5 13.7 1.0
ND2 A:ASN66 3.5 13.5 1.0
O D:HOH4049 3.6 16.8 1.0
CE2 B:TYR189 3.8 14.7 1.0
CB D:ALA186 3.9 8.6 1.0
CA D:TYR185 4.0 8.5 1.0
CZ B:TYR189 4.0 13.7 1.0
CD2 D:TYR185 4.0 9.4 1.0
CE1 A:PHE64 4.0 12.2 1.0
C D:TYR185 4.2 7.9 1.0
CB D:TYR185 4.2 7.5 1.0
CA D:ALA186 4.2 9.3 1.0
ND2 A:ASN72 4.5 9.6 1.0
CG A:ASN66 4.5 12.5 1.0
CB A:ASN66 4.5 10.8 1.0
CG D:TYR185 4.5 9.5 1.0
CZ A:PHE64 4.6 11.3 1.0
O D:HOH4007 4.8 12.7 1.0
CE2 D:TYR185 4.9 8.4 1.0

Bromine binding site 2 out of 36 in 1m3d

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Bromine binding site 2 out of 36 in the Structure of Type IV Collagen NC1 Domains


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3002

b:15.6
occ:0.99
 OH E:TYR189 3.3 13.8 1.0
N A:ALA186 3.3 9.6 1.0
O A:HOH4075 3.4 26.6 1.0
ND2 D:ASN66 3.5 11.3 1.0
O D:HOH4077 3.5 17.1 1.0
CE2 E:TYR189 3.8 16.0 1.0
CE1 D:PHE64 3.9 13.2 1.0
CB A:ALA186 3.9 9.5 1.0
CA A:TYR185 4.0 9.9 1.0
CZ E:TYR189 4.0 13.5 1.0
CD2 A:TYR185 4.0 10.6 1.0
CB A:TYR185 4.1 9.7 1.0
C A:TYR185 4.1 9.4 1.0
CA A:ALA186 4.2 9.3 1.0
ND2 D:ASN72 4.4 14.3 1.0
CZ D:PHE64 4.5 14.2 1.0
CG D:ASN66 4.5 12.1 1.0
CG A:TYR185 4.5 9.8 1.0
CB D:ASN66 4.6 10.8 1.0
CD1 D:PHE64 5.0 14.7 1.0
CD2 E:TYR189 5.0 12.1 1.0
CE2 A:TYR185 5.0 11.2 1.0
O A:HOH4024 5.0 11.4 1.0

Bromine binding site 3 out of 36 in 1m3d

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Bromine binding site 3 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3004

b:14.5
occ:0.93
 O D:HOH4039 3.3 14.6 1.0
N D:ASP78 3.4 9.3 1.0
NH2 A:ARG179 3.5 7.6 0.5
N D:ARG76 3.5 11.4 1.0
CA D:ALA74 3.6 9.3 1.0
C D:ARG76 3.7 11.7 1.0
CA D:GLY178 3.7 9.4 1.0
C D:ALA74 3.7 10.9 1.0
N D:ASN77 3.8 12.2 1.0
O D:ARG76 3.8 12.8 1.0
N D:SER75 3.9 9.6 1.0
CB D:ASP78 4.1 9.0 1.0
O A:HOH4045 4.1 14.6 1.0
CA D:ARG76 4.1 12.2 1.0
CE D:MET60 4.2 7.1 1.0
CA D:ASP78 4.2 9.3 1.0
CA D:ASN77 4.2 11.6 1.0
O D:ALA74 4.2 9.5 1.0
C D:ASN77 4.3 11.9 1.0
N D:GLY178 4.3 8.4 1.0
O D:ASP78 4.4 7.9 1.0
C D:GLY178 4.4 10.2 1.0
N D:ALA74 4.5 9.2 1.0
O D:HOH4024 4.5 11.0 1.0
C D:SER75 4.6 11.8 1.0
CB D:ALA74 4.6 10.4 1.0
O D:HOH4004 4.6 9.1 1.0
CB D:ARG76 4.6 10.1 1.0
NH2 A:ARG179 4.6 12.1 0.5
CZ A:ARG179 4.7 8.9 0.5
CA D:SER75 4.7 10.9 1.0
C D:ASP78 4.7 9.1 1.0
CG D:ASP78 4.7 10.8 1.0
CG D:MET60 4.7 8.1 1.0
SD D:MET60 4.8 9.8 1.0
OD1 D:ASP78 4.9 13.6 1.0
O D:GLY178 4.9 9.2 1.0
N D:ARG179 5.0 9.2 1.0

Bromine binding site 4 out of 36 in 1m3d

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Bromine binding site 4 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3005

b:14.6
occ:0.94
 O A:HOH4027 3.2 10.0 1.0
N A:ASP78 3.3 10.1 1.0
NH2 D:ARG179 3.4 19.2 1.0
N A:ARG76 3.5 12.2 1.0
CA A:ALA74 3.6 8.9 1.0
C A:ARG76 3.7 11.8 1.0
CA A:GLY178 3.7 9.9 1.0
C A:ALA74 3.7 9.1 1.0
N A:ASN77 3.7 11.1 1.0
O A:ARG76 3.9 12.9 1.0
N A:SER75 3.9 9.3 1.0
CB A:ASP78 4.1 7.8 1.0
CE A:MET60 4.1 9.1 1.0
CA A:ARG76 4.1 11.4 1.0
CA A:ASN77 4.2 9.9 1.0
CA A:ASP78 4.2 8.7 1.0
O A:ALA74 4.2 7.9 1.0
C A:ASN77 4.2 11.2 1.0
N A:GLY178 4.3 7.9 1.0
O D:HOH4065 4.4 16.6 1.0
O A:ASP78 4.4 5.8 1.0
C A:GLY178 4.4 10.1 1.0
N A:ALA74 4.4 7.8 1.0
O A:HOH4005 4.5 6.7 1.0
C A:SER75 4.6 13.1 1.0
CB A:ALA74 4.6 8.2 1.0
CB A:ARG76 4.6 11.5 1.0
O A:HOH4002 4.6 8.2 1.0
CG A:ASP78 4.6 11.3 1.0
C A:ASP78 4.7 7.2 1.0
CZ D:ARG179 4.7 18.6 1.0
CA A:SER75 4.7 10.8 1.0
OD1 A:ASP78 4.8 11.3 1.0
CG A:MET60 4.8 8.6 1.0
SD A:MET60 4.9 8.4 1.0
O A:GLY178 4.9 10.5 1.0
N A:ARG179 5.0 8.9 1.0

Bromine binding site 5 out of 36 in 1m3d

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Bromine binding site 5 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3012

b:18.3
occ:0.98
 O B:HOH4012 3.3 14.0 1.0
N B:ASP78 3.4 7.5 1.0
O B:HOH4041 3.5 16.5 1.0
CA B:GLY178 3.6 14.7 1.0
C B:ARG76 3.6 10.4 1.0
O B:ARG76 3.6 10.2 1.0
CA B:ALA74 3.6 11.3 1.0
N B:ARG76 3.6 11.2 1.0
C B:ALA74 3.7 12.1 1.0
N B:ASN77 3.9 8.3 1.0
N B:SER75 3.9 12.1 1.0
CB B:ASP78 4.0 6.5 1.0
N B:GLY178 4.1 11.5 1.0
CA B:ARG76 4.1 10.1 1.0
CA B:ASP78 4.2 8.4 1.0
CE B:MET60 4.2 6.3 1.0
CA B:ASN77 4.2 8.5 1.0
O B:ASP78 4.2 8.8 1.0
O B:ALA74 4.3 12.6 1.0
C B:ASN77 4.3 8.6 1.0
C B:GLY178 4.4 16.5 1.0
NH2 F:ARG177 4.4 39.9 1.0
N B:ALA74 4.5 9.9 1.0
O B:HOH4029 4.5 10.8 1.0
C B:SER75 4.5 12.6 1.0
CB B:ALA74 4.6 10.4 1.0
C B:ASP78 4.6 7.9 1.0
O B:HOH4014 4.7 5.5 1.0
CB B:ARG76 4.7 10.7 1.0
CG B:MET60 4.7 7.1 1.0
CG B:ASP78 4.7 10.3 1.0
CA B:SER75 4.8 13.1 1.0
SD B:MET60 4.8 10.0 1.0
OD1 B:ASP78 4.8 10.1 1.0
O B:GLY178 5.0 18.7 1.0
N B:ARG179 5.0 17.9 1.0

Bromine binding site 6 out of 36 in 1m3d

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Bromine binding site 6 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3021

b:23.1
occ:0.87
 ND2 B:ASN66 3.2 11.4 1.0
OH C:TYR187 3.2 12.1 1.0
N F:ALA184 3.3 9.1 1.0
O B:HOH4027 3.3 14.5 1.0
CE2 C:TYR187 3.7 12.4 1.0
CD2 F:TYR183 3.7 10.2 1.0
CB F:ALA184 3.8 8.4 1.0
CB B:ASN66 3.8 10.5 1.0
CA F:TYR183 3.8 9.7 1.0
CZ C:TYR187 3.9 12.1 1.0
CE1 B:PHE64 3.9 12.6 1.0
CB F:TYR183 3.9 9.5 1.0
CG B:ASN66 4.0 11.6 1.0
C F:TYR183 4.1 9.9 1.0
CA F:ALA184 4.2 8.6 1.0
ND2 B:ASN72 4.2 12.7 1.0
CG F:TYR183 4.3 10.6 1.0
CE2 F:TYR183 4.8 12.1 1.0
CD1 B:PHE64 4.8 11.7 1.0
CZ B:PHE64 4.8 11.5 1.0
CD2 C:TYR187 4.9 11.7 1.0

Bromine binding site 7 out of 36 in 1m3d

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Bromine binding site 7 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3026

b:32.6
occ:0.73
 NH2 B:ARG55 3.4 16.3 1.0
NH1 B:ARG55 3.8 17.5 1.0
CD2 B:TYR28 3.8 13.3 1.0
O B:LEU27 4.0 15.8 1.0
CG C:PRO128 4.0 18.1 1.0
CZ B:ARG55 4.0 18.3 1.0
CB B:LEU27 4.3 18.9 1.0
C B:LEU27 4.3 16.2 1.0
CB B:TYR28 4.3 12.9 1.0
O C:HIS126 4.4 17.8 1.0
CG B:TYR28 4.5 12.2 1.0
CG1 C:VAL117 4.6 9.5 1.0
CE2 B:TYR28 4.6 13.7 1.0
CB C:PRO128 4.6 18.3 1.0
CA C:PRO128 4.7 18.6 1.0
CD C:PRO128 4.7 18.7 1.0
CA B:LEU27 4.7 16.2 1.0
N C:PRO128 4.8 17.9 1.0
CG B:LEU27 4.9 20.4 1.0
CD2 B:LEU27 4.9 21.2 1.0
N B:TYR28 4.9 14.2 1.0

Bromine binding site 8 out of 36 in 1m3d

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Bromine binding site 8 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3028

b:29.7
occ:0.62
 O B:HOH4074 2.9 23.3 1.0
NH1 B:ARG216 3.0 46.7 1.0
CZ B:ARG216 3.2 45.2 1.0
N B:PHE168 3.4 12.0 1.0
NE B:ARG216 3.7 43.6 1.0
CA B:GLU167 3.8 13.6 1.0
NH2 B:ARG216 3.8 47.1 1.0
CE1 B:TYR141 3.9 15.4 1.0
CD B:ARG216 4.0 39.6 1.0
C B:GLU167 4.1 12.9 1.0
OH B:TYR141 4.1 15.9 1.0
CB B:GLU167 4.2 15.3 1.0
O B:PHE168 4.3 10.3 1.0
CG B:GLU167 4.3 22.1 1.0
O B:GLU166 4.3 10.6 1.0
CZ B:TYR141 4.4 16.2 1.0
CB B:PHE168 4.4 11.0 1.0
CA B:PHE168 4.4 12.1 1.0
CD1 B:TYR141 4.8 14.4 1.0
C B:PHE168 4.8 11.1 1.0
N B:GLU167 4.9 11.9 1.0
CG B:ARG216 5.0 37.1 1.0

Bromine binding site 9 out of 36 in 1m3d

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Bromine binding site 9 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3034

b:43.8
occ:0.70
 N B:ARG216 3.2 31.5 1.0
N B:LEU215 3.3 31.4 1.0
CA B:GLY213 3.4 31.7 1.0
C B:GLY213 3.4 33.5 1.0
N B:GLY213 3.5 29.8 1.0
CG B:ARG216 3.6 37.1 1.0
N B:GLU214 3.7 33.7 1.0
CB B:LEU215 3.7 30.1 1.0
CA B:LEU215 3.8 31.0 1.0
O B:GLY213 3.9 34.0 1.0
CB B:ARG216 3.9 34.5 1.0
C B:LEU215 4.0 30.5 1.0
CA B:ARG216 4.2 32.9 1.0
C B:GLU214 4.2 32.9 1.0
CD B:ARG216 4.3 39.6 1.0
NE B:ARG216 4.4 43.6 1.0
CA B:GLU214 4.5 33.7 1.0
C B:ALA212 4.7 28.2 1.0
CG B:LEU215 4.8 30.0 1.0

Bromine binding site 10 out of 36 in 1m3d

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Bromine binding site 10 out of 36 in the Structure of Type IV Collagen NC1 Domains


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Structure of Type IV Collagen NC1 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br3007

b:15.8
occ:0.92
 O C:HOH3064 3.1 9.8 1.0
O C:HOH3067 3.1 17.0 1.0
N C:ARG75 3.4 10.5 1.0
N C:ASP77 3.4 8.6 1.0
CA C:ALA73 3.5 9.4 1.0
C C:ARG75 3.6 9.3 1.0
N C:ASN76 3.8 9.2 1.0
C C:ALA73 3.8 10.0 1.0
N C:SER74 3.8 9.3 1.0
O C:ARG75 3.9 10.0 1.0
O C:HOH3050 3.9 6.5 1.0
CA C:ARG75 4.0 10.5 1.0
CB C:ASP77 4.0 8.7 1.0
CA C:ASP77 4.2 8.4 1.0
N C:ALA73 4.2 8.1 1.0
CE C:MET59 4.2 9.8 1.0
O C:HOH3031 4.2 7.6 1.0
O C:ASP77 4.3 9.2 1.0
CA C:ASN76 4.3 9.6 1.0
C C:ASN76 4.3 9.3 1.0
CB C:ARG75 4.4 10.4 1.0
CB C:ALA176 4.4 11.0 1.0
N C:ALA176 4.4 10.4 1.0
O C:ALA73 4.5 9.1 1.0
C C:SER74 4.5 11.4 1.0
CG C:MET59 4.6 8.4 1.0
C C:ASP77 4.6 9.0 1.0
CG C:ASP77 4.7 11.2 1.0
CB C:ALA73 4.7 9.7 1.0
CA C:SER74 4.7 11.2 1.0
OD1 C:ASP77 4.7 9.9 1.0
SD C:MET59 4.8 9.7 1.0
CA C:ALA176 5.0 10.8 1.0

Reference:

M.Sundaramoorthy, M.Meiyappan, P.Todd, B.G.Hudson. Crystal Structure of NC1 Domains. Structural Basis For Type IV Collagen Assembly in Basement Membranes J.Biol.Chem. V. 277 31142 2002.
ISSN: ISSN 0021-9258
PubMed: 11970952
DOI: 10.1074/JBC.M201740200
Page generated: Wed Jul 10 16:52:11 2024

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