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Bromine in PDB 6tqd: D00-D0 Domain of Intimin

Protein crystallography data

The structure of D00-D0 Domain of Intimin, PDB code: 6tqd was solved by J.Weikum, J.C.Leo, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.83 / 1.48
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.039, 65.473, 79.378, 77.78, 76.55, 84.76
R / Rfree (%) 17.9 / 21.6

Other elements in 6tqd:

The structure of D00-D0 Domain of Intimin also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 6 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the D00-D0 Domain of Intimin (pdb code 6tqd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the D00-D0 Domain of Intimin, PDB code: 6tqd:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 6tqd

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Bromine binding site 1 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br701

b:19.1
occ:0.38
O A:HOH1010 2.9 20.9 1.0
O A:HOH1064 3.1 25.4 1.0
HG A:SER597 3.1 14.7 0.7
HA A:ALA639 3.2 10.5 1.0
HB2 A:SER597 3.2 13.4 0.7
HG2 A:LYS637 3.3 12.6 1.0
O F:HOH1050 3.3 30.8 1.0
HZ2 A:LYS637 3.3 18.6 1.0
HB3 A:SER597 3.3 13.1 0.3
HB2 A:SER597 3.5 13.1 0.3
C A:THR638 3.5 6.6 1.0
HB3 A:LYS637 3.5 10.7 1.0
OG A:SER597 3.5 12.2 0.7
HD3 A:LYS637 3.5 13.9 1.0
HZ1 A:LYS637 3.6 18.6 1.0
O A:LYS637 3.6 9.2 1.0
HA A:THR638 3.6 7.9 1.0
O A:THR638 3.6 8.3 1.0
N A:ALA639 3.7 9.5 1.0
NZ A:LYS637 3.8 15.5 1.0
C A:LYS637 3.8 8.6 1.0
CB A:SER597 3.9 11.1 0.7
CB A:SER597 3.9 10.9 0.3
CA A:THR638 3.9 6.7 1.0
CG A:LYS637 3.9 10.5 1.0
CA A:ALA639 3.9 8.7 1.0
N A:THR638 4.1 8.7 1.0
CB A:LYS637 4.1 9.1 1.0
CD A:LYS637 4.1 11.5 1.0
H A:ALA639 4.1 11.4 1.0
H A:SER597 4.2 9.9 0.3
H A:SER597 4.2 9.8 0.7
HB3 A:SER597 4.4 13.4 0.7
O A:HOH1135 4.4 32.7 1.0
O A:HOH1060 4.4 48.6 1.0
HZ3 A:LYS637 4.5 18.6 1.0
CE A:LYS637 4.6 14.3 1.0
HB2 A:ALA639 4.6 17.6 1.0
CA A:LYS637 4.6 8.7 1.0
H A:THR638 4.7 10.5 1.0
OG A:SER597 4.7 13.1 0.3
N A:SER597 4.8 8.2 0.3
HG3 A:LYS637 4.8 12.6 1.0
N A:SER597 4.8 8.1 0.7
CB A:ALA639 4.9 14.6 1.0
O A:HOH839 4.9 14.3 1.0
HB2 A:LYS637 4.9 10.7 1.0
HD2 A:LYS637 5.0 13.9 1.0
O A:HOH834 5.0 26.4 1.0
CA A:SER597 5.0 8.8 0.7
CA A:SER597 5.0 9.1 0.3

Bromine binding site 2 out of 9 in 6tqd

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Bromine binding site 2 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br702

b:19.1
occ:0.37
HD22 A:ASN457 2.5 16.0 1.0
HE22 B:GLN511 2.7 18.5 1.0
HB3 A:ASN457 2.8 9.0 1.0
HA A:PRO459 3.1 18.4 1.0
O B:HOH858 3.2 28.1 1.0
O A:HOH966 3.2 9.5 1.0
ND2 A:ASN457 3.3 13.3 1.0
NE2 B:GLN511 3.4 15.4 1.0
HE21 B:GLN511 3.6 18.5 1.0
CB A:ASN457 3.7 7.6 1.0
H A:ILE458 3.8 11.3 1.0
OE1 B:GLN500 3.9 18.7 1.0
HD21 A:ASN457 3.9 16.0 1.0
CA A:PRO459 4.0 15.3 1.0
O A:ILE458 4.0 14.4 1.0
CG A:ASN457 4.0 11.6 1.0
C A:ILE458 4.2 11.6 1.0
N A:ILE458 4.2 9.4 1.0
HB3 A:PRO459 4.3 20.0 1.0
N A:PRO459 4.3 13.0 1.0
HB2 A:ASN457 4.3 9.0 1.0
HA A:ASN457 4.3 9.8 1.0
CA A:ASN457 4.5 8.1 1.0
CD B:GLN511 4.6 15.3 1.0
O B:HOH862 4.6 27.6 1.0
HA B:SER502 4.6 19.6 1.0
C A:ASN457 4.7 9.9 1.0
NA A:NA703 4.7 23.0 1.0
CB A:PRO459 4.7 16.6 1.0
O B:SER502 4.8 17.0 1.0
HD3 A:PRO459 4.9 21.9 1.0
CD B:GLN500 4.9 14.9 1.0
OE1 B:GLN511 4.9 17.2 1.0
CA A:ILE458 4.9 11.3 1.0

Bromine binding site 3 out of 9 in 6tqd

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Bromine binding site 3 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br701

b:19.6
occ:0.26
OD1 B:ASN457 1.9 25.3 0.4
HD22 B:ASN457 2.5 15.6 0.6
CG B:ASN457 2.7 17.5 0.4
HE22 C:GLN511 2.8 23.9 1.0
HD21 B:ASN457 2.9 25.9 0.4
HB3 B:ASN457 2.9 13.8 0.6
O B:HOH905 3.1 10.8 1.0
ND2 B:ASN457 3.1 21.6 0.4
HA B:PRO459 3.1 16.4 1.0
O C:HOH808 3.3 34.4 1.0
ND2 B:ASN457 3.4 12.9 0.6
NE2 C:GLN511 3.5 19.9 1.0
HE21 C:GLN511 3.6 23.9 1.0
H B:ILE458 3.6 9.7 0.4
H B:ILE458 3.7 9.7 0.6
O B:ILE458 3.8 13.0 1.0
CB B:ASN457 3.8 11.5 0.6
OE1 C:GLN500 3.8 23.6 1.0
HD22 B:ASN457 3.9 25.9 0.4
HD21 B:ASN457 3.9 15.6 0.6
CB B:ASN457 3.9 11.7 0.4
O B:HOH1073 4.0 48.3 1.0
CA B:PRO459 4.0 13.7 1.0
HB2 B:ASN457 4.1 14.1 0.4
C B:ILE458 4.1 12.4 1.0
CG B:ASN457 4.1 10.7 0.6
N B:ILE458 4.2 8.1 1.0
HA B:ASN457 4.2 11.4 0.4
N B:PRO459 4.3 12.2 1.0
HA B:ASN457 4.3 11.5 0.6
HA C:SER502 4.4 26.7 1.0
HB3 B:PRO459 4.4 18.6 1.0
NA B:NA703 4.5 29.4 1.0
HB2 B:ASN457 4.5 13.8 0.6
CA B:ASN457 4.5 9.6 0.6
O C:SER502 4.5 25.6 1.0
CA B:ASN457 4.5 9.5 0.4
CD C:GLN511 4.6 16.4 1.0
C B:ASN457 4.6 8.1 0.6
HB3 B:ASN457 4.7 14.1 0.4
CD C:GLN500 4.7 21.0 1.0
C B:ASN457 4.8 8.0 0.4
CB B:PRO459 4.8 15.5 1.0
CA B:ILE458 4.8 9.1 1.0
O B:HOH997 4.9 20.2 1.0
HD3 B:PRO459 4.9 18.3 1.0
O C:HOH839 5.0 35.8 1.0
C B:PRO459 5.0 13.3 1.0

Bromine binding site 4 out of 9 in 6tqd

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Bromine binding site 4 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br702

b:17.0
occ:0.28
H B:ASP627 2.7 18.8 1.0
HA B:ALA605 2.9 12.9 1.0
HA B:SER626 2.9 15.3 1.0
HG23 B:VAL606 3.0 20.3 1.0
HG22 B:THR604 3.2 13.9 1.0
O B:HOH840 3.3 33.5 1.0
N B:ASP627 3.5 15.6 1.0
O B:HOH1004 3.6 17.0 1.0
OG B:SER626 3.7 14.7 1.0
CA B:ALA605 3.7 10.8 1.0
HB2 B:ASP627 3.7 32.5 1.0
HG2 B:LYS628 3.7 37.9 1.0
CA B:SER626 3.8 12.9 1.0
CG2 B:VAL606 3.9 16.9 1.0
C B:ALA605 4.0 10.1 1.0
N B:ALA605 4.0 11.1 1.0
HG21 B:VAL606 4.1 20.3 1.0
CG2 B:THR604 4.2 11.5 1.0
O B:THR604 4.2 14.7 1.0
CB B:SER626 4.2 14.5 1.0
C B:SER626 4.2 14.2 1.0
HG22 B:VAL606 4.2 20.3 1.0
C B:THR604 4.3 11.5 1.0
H B:LYS628 4.3 21.5 1.0
HB2 B:SER626 4.3 17.5 1.0
HG B:SER626 4.3 17.6 1.0
H B:ALA605 4.4 13.3 1.0
HG23 B:THR604 4.4 13.9 1.0
N B:VAL606 4.4 10.8 1.0
O B:LYS625 4.4 12.8 1.0
O B:ALA605 4.4 11.4 1.0
H B:VAL606 4.5 13.1 1.0
CB B:ASP627 4.5 27.0 1.0
OD2 B:ASP627 4.5 40.6 1.0
CA B:ASP627 4.5 20.7 1.0
HG21 B:THR604 4.5 13.9 1.0
CG B:LYS628 4.7 31.5 1.0
N B:LYS628 4.8 17.9 1.0
HG3 B:LYS628 4.8 37.9 1.0
N B:SER626 4.9 13.2 1.0
HB B:VAL606 4.9 19.3 1.0
CB B:VAL606 4.9 16.1 1.0
CB B:ALA605 4.9 11.3 1.0
CG B:ASP627 5.0 35.7 1.0

Bromine binding site 5 out of 9 in 6tqd

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Bromine binding site 5 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br701

b:24.3
occ:0.44
HA C:ALA639 3.1 24.6 1.0
O C:HOH1027 3.1 34.2 1.0
HZ1 C:LYS637 3.2 32.2 1.0
HG C:SER597 3.2 36.9 1.0
HG2 C:LYS637 3.4 23.9 1.0
HD3 C:LYS637 3.4 27.9 1.0
HB2 C:SER597 3.5 28.6 1.0
C C:THR638 3.5 16.6 1.0
HB3 C:LYS637 3.5 22.6 1.0
HZ2 C:LYS637 3.5 32.2 1.0
HA C:THR638 3.6 18.5 1.0
N C:ALA639 3.6 19.6 1.0
OG C:SER597 3.7 30.7 1.0
O C:THR638 3.7 17.9 1.0
O C:LYS637 3.8 15.4 1.0
NZ C:LYS637 3.8 26.9 1.0
CA C:ALA639 3.8 20.5 1.0
CA C:THR638 4.0 15.4 1.0
CG C:LYS637 4.0 19.9 1.0
C C:LYS637 4.0 14.1 1.0
H C:ALA639 4.0 23.6 1.0
CD C:LYS637 4.1 23.2 1.0
CB C:SER597 4.1 23.8 1.0
CB C:LYS637 4.2 18.9 1.0
N C:THR638 4.2 14.5 1.0
HB2 C:ALA639 4.3 29.9 1.0
H C:SER597 4.4 16.3 1.0
HZ3 C:LYS637 4.5 32.2 1.0
CE C:LYS637 4.5 26.0 1.0
HB3 C:SER597 4.6 28.6 1.0
CB C:ALA639 4.7 24.9 1.0
CA C:LYS637 4.8 14.2 1.0
H C:THR638 4.8 17.2 1.0
HG3 C:LYS637 4.9 23.9 1.0
HD2 C:LYS637 4.9 27.9 1.0
C C:ALA639 4.9 23.7 1.0
O C:HOH925 5.0 19.8 1.0
HB2 C:LYS637 5.0 22.6 1.0
HE3 C:LYS637 5.0 31.2 1.0

Bromine binding site 6 out of 9 in 6tqd

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Bromine binding site 6 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br702

b:48.7
occ:0.44
HZ2 C:LYS625 2.9 37.9 1.0
HB2 C:ALA577 3.1 18.0 1.0
O C:HOH880 3.2 26.5 1.0
HE2 C:LYS625 3.3 34.0 1.0
NZ C:LYS625 3.6 31.6 1.0
HB3 C:ALA577 3.7 18.0 1.0
HE3 C:LYS625 3.7 34.0 1.0
CE C:LYS625 3.7 28.3 1.0
CB C:ALA577 3.8 15.0 1.0
HZ3 C:LYS625 3.9 37.9 1.0
HB1 C:ALA577 4.2 18.0 1.0
HZ1 C:LYS625 4.3 37.9 1.0
HG21 C:THR623 4.6 19.7 1.0
O C:THR575 4.7 17.6 1.0
H C:ALA577 4.9 16.1 1.0
O C:HOH1078 5.0 49.4 1.0

Bromine binding site 7 out of 9 in 6tqd

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Bromine binding site 7 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br702

b:17.9
occ:0.39
HG D:SER597 3.0 22.9 1.0
HA D:ALA639 3.1 10.1 1.0
HZ1 D:LYS637 3.1 18.5 1.0
O D:HOH1007 3.2 23.8 1.0
O D:HOH1119 3.2 20.1 1.0
O C:HOH1039 3.2 27.2 1.0
HB2 D:SER597 3.3 16.3 1.0
HG2 D:LYS637 3.3 14.2 1.0
OG D:SER597 3.4 19.1 1.0
HZ2 D:LYS637 3.4 18.5 1.0
C D:THR638 3.5 5.9 1.0
HD3 D:LYS637 3.5 14.7 1.0
HB3 D:LYS637 3.6 9.7 1.0
O D:THR638 3.6 7.1 1.0
N D:ALA639 3.6 6.7 1.0
O D:LYS637 3.6 8.9 1.0
HA D:THR638 3.7 10.1 1.0
NZ D:LYS637 3.7 15.4 1.0
O D:HOH902 3.7 28.7 1.0
CA D:ALA639 3.8 8.4 1.0
CB D:SER597 3.9 13.6 1.0
C D:LYS637 3.9 6.8 1.0
CA D:THR638 4.0 8.4 1.0
CG D:LYS637 4.0 11.8 1.0
H D:ALA639 4.0 8.1 1.0
CD D:LYS637 4.1 12.2 1.0
H D:SER597 4.1 7.8 1.0
N D:THR638 4.2 7.3 1.0
CB D:LYS637 4.2 8.0 1.0
HB2 D:ALA639 4.3 11.3 1.0
HZ3 D:LYS637 4.4 18.5 1.0
HB3 D:SER597 4.5 16.3 1.0
CE D:LYS637 4.5 14.6 1.0
CB D:ALA639 4.7 9.4 1.0
O D:HOH1128 4.7 39.1 1.0
CA D:LYS637 4.7 4.8 1.0
N D:SER597 4.8 6.5 1.0
H D:THR638 4.8 8.8 1.0
O D:HOH1165 4.8 34.8 1.0
O D:HOH892 4.8 14.0 1.0
HG3 D:LYS637 4.9 14.2 1.0
C D:ALA639 4.9 9.7 1.0
CA D:SER597 5.0 6.7 1.0
HD2 D:LYS637 5.0 14.7 1.0

Bromine binding site 8 out of 9 in 6tqd

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Bromine binding site 8 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br701

b:16.1
occ:0.44
O E:HOH994 3.0 20.2 1.0
O E:HOH1043 3.1 22.6 1.0
HZ1 E:LYS637 3.1 19.3 1.0
HA E:ALA639 3.2 12.2 1.0
HG2 E:LYS637 3.2 13.5 1.0
HZ3 E:LYS637 3.2 19.3 1.0
HD3 E:LYS637 3.4 13.0 1.0
HB2 E:SER597 3.4 15.6 0.5
HB3 E:SER597 3.5 15.6 0.5
C E:THR638 3.5 9.6 1.0
HB3 E:LYS637 3.5 12.5 1.0
O E:THR638 3.6 10.1 1.0
NZ E:LYS637 3.6 16.1 1.0
HA E:THR638 3.6 13.7 1.0
HB2 E:SER597 3.6 15.6 0.5
OG E:SER597 3.7 15.1 0.5
N E:ALA639 3.7 9.3 1.0
O E:LYS637 3.7 11.4 1.0
O B:HOH1054 3.8 37.1 1.0
CG E:LYS637 3.9 11.2 1.0
CA E:ALA639 3.9 10.2 1.0
C E:LYS637 3.9 10.7 1.0
CA E:THR638 3.9 11.4 1.0
CB E:SER597 4.0 12.9 0.5
CD E:LYS637 4.0 10.8 1.0
CB E:SER597 4.0 13.0 0.5
N E:THR638 4.1 10.5 1.0
CB E:LYS637 4.1 10.6 1.0
H E:ALA639 4.1 11.2 1.0
HZ2 E:LYS637 4.3 19.3 1.0
H E:SER597 4.4 13.5 0.5
H E:SER597 4.4 13.5 0.5
HG E:SER597 4.4 18.1 0.5
CE E:LYS637 4.4 15.0 1.0
HB2 E:ALA639 4.5 14.3 1.0
HB3 E:SER597 4.6 15.6 0.5
O B:HOH1019 4.6 35.3 1.0
H E:THR638 4.7 12.4 1.0
CA E:LYS637 4.7 11.0 1.0
HG3 E:LYS637 4.7 13.5 1.0
CB E:ALA639 4.8 11.9 1.0
OG E:SER597 4.8 14.6 0.5
HD2 E:LYS637 4.9 13.0 1.0
O E:HOH845 4.9 14.8 1.0
N E:SER597 5.0 11.4 0.5
HB2 E:LYS637 5.0 12.5 1.0
N E:SER597 5.0 11.4 0.5
HE3 E:LYS637 5.0 18.1 1.0
C E:ALA639 5.0 11.9 1.0

Bromine binding site 9 out of 9 in 6tqd

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Bromine binding site 9 out of 9 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of D00-D0 Domain of Intimin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br701

b:57.9
occ:1.00
H F:ASP627 2.5 30.7 1.0
HA F:SER626 2.9 26.0 1.0
HG22 F:THR604 3.1 32.3 1.0
HG23 F:VAL606 3.1 28.1 1.0
HA F:ALA605 3.2 26.4 1.0
N F:ASP627 3.3 25.6 1.0
HB2 F:ASP627 3.4 42.8 1.0
O F:HOH1024 3.5 38.4 1.0
O F:HOH1026 3.7 35.9 1.0
CA F:SER626 3.8 21.7 1.0
OG F:SER626 3.8 23.5 1.0
CG2 F:THR604 3.9 26.9 1.0
CA F:ALA605 4.0 22.0 1.0
CG2 F:VAL606 4.0 23.4 1.0
C F:SER626 4.1 22.1 1.0
HG23 F:THR604 4.1 32.3 1.0
OD1 F:ASP627 4.1 37.7 1.0
H F:LYS628 4.1 41.2 1.0
CB F:ASP627 4.1 35.6 1.0
HG21 F:VAL606 4.2 28.1 1.0
N F:ALA605 4.2 22.2 1.0
C F:ALA605 4.2 21.1 1.0
CA F:ASP627 4.3 32.2 1.0
HG21 F:THR604 4.3 32.3 1.0
CB F:SER626 4.3 22.6 1.0
HG22 F:VAL606 4.4 28.1 1.0
C F:THR604 4.4 23.9 1.0
HG F:SER626 4.5 28.2 1.0
O F:THR604 4.5 24.9 1.0
HB2 F:SER626 4.5 27.1 1.0
H F:ALA605 4.6 26.7 1.0
O F:LYS625 4.6 21.4 1.0
CG F:ASP627 4.6 36.9 1.0
N F:VAL606 4.6 20.1 1.0
N F:LYS628 4.6 34.3 1.0
O F:ALA605 4.6 23.0 1.0
H F:VAL606 4.7 24.1 1.0
HB3 F:LYS628 4.8 45.6 1.0
C F:ASP627 4.9 34.7 1.0
N F:SER626 4.9 19.2 1.0
HB3 F:ASP627 4.9 42.8 1.0
HB2 F:LYS628 5.0 45.6 1.0

Reference:

J.Weikum, A.Kulakova, G.Tesei, S.Yoshimoto, L.V.Jaegerum, M.Schutz, K.Hori, M.Skepo, P.Harris, J.C.Leo, J.P.Morth. The Extracellular Juncture Domains in the Intimin Passenger Adopt A Constitutively Extended Conformation Inducing Restraints to Its Sphere of Action. Sci Rep V. 10 21249 2020.
ISSN: ESSN 2045-2322
PubMed: 33277518
DOI: 10.1038/S41598-020-77706-7
Page generated: Thu Jul 11 02:46:32 2024

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Cl in 4NM0
Cl in 4NHQ
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