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Terbium in PDB 1m9s: Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.

Protein crystallography data

The structure of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains., PDB code: 1m9s was solved by M.Marino, M.Banerjee, R.Jonquieres, P.Cossart, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.500, 330.900, 182.400, 90.00, 90.00, 90.00
R / Rfree (%) 27.3 / 30.2

Terbium Binding Sites:

The binding sites of Terbium atom in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. (pdb code 1m9s). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 7 binding sites of Terbium where determined in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains., PDB code: 1m9s:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7;

Terbium binding site 1 out of 7 in 1m9s

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Terbium binding site 1 out of 7 in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb639

b:0.1
occ:1.00
O A:HOH688 2.8 70.9 1.0
OD1 A:ASN173 2.9 66.7 1.0
OE1 A:GLU194 3.3 91.0 1.0
O A:HOH661 3.5 59.5 1.0
OE2 A:GLU194 3.6 91.5 1.0
OE2 A:GLU150 3.6 65.7 1.0
O A:HOH660 3.7 56.6 1.0
TB A:TB640 3.7 0.2 1.0
CD A:GLU194 3.8 81.3 1.0
TB A:TB641 3.9 0.9 1.0
CG A:ASN173 4.0 61.8 1.0
CD A:GLU150 4.1 79.5 1.0
O A:HOH657 4.1 62.8 1.0
OE1 A:GLU150 4.2 87.3 1.0
ND2 A:ASN173 4.6 69.3 1.0

Terbium binding site 2 out of 7 in 1m9s

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Terbium binding site 2 out of 7 in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb640

b:0.2
occ:1.00
TB A:TB639 3.7 0.1 1.0
OE1 A:GLU194 3.7 91.0 1.0
O A:HOH658 3.9 75.3 1.0
O A:HOH661 3.9 59.5 1.0
CD A:GLU194 3.9 81.3 1.0
O A:HOH660 4.2 56.6 1.0
O A:HOH659 4.2 71.0 1.0
OE2 A:GLU194 4.4 91.5 1.0
CG A:GLU194 4.4 79.1 1.0
OE1 A:GLU236 4.8 76.0 1.0

Terbium binding site 3 out of 7 in 1m9s

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Terbium binding site 3 out of 7 in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb641

b:0.9
occ:1.00
O A:HOH688 3.5 70.9 1.0
OE1 A:GLU150 3.5 87.3 1.0
TB A:TB639 3.9 0.1 1.0
CD A:GLU150 4.5 79.5 1.0
OE2 A:GLU150 5.0 65.7 1.0

Terbium binding site 4 out of 7 in 1m9s

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Terbium binding site 4 out of 7 in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb642

b:0.2
occ:1.00
OD1 A:ASP275 2.9 84.4 1.0
CG A:ASP275 3.6 86.8 1.0
OD2 A:ASP275 3.7 88.2 1.0
OD2 A:ASP277 3.9 96.5 1.0
O A:ASP275 4.3 72.8 1.0
OD1 A:ASP277 4.4 0.0 1.0
CG A:ASP277 4.6 98.3 1.0
CB A:ASP275 4.8 75.2 1.0
C A:ASP275 4.9 72.1 1.0
CA A:ASP275 4.9 72.6 1.0

Terbium binding site 5 out of 7 in 1m9s

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Terbium binding site 5 out of 7 in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb643

b:0.2
occ:0.50
O A:GLU293 3.7 70.5 1.0
CG A:GLU293 4.2 84.5 1.0
C A:GLU293 4.5 69.8 1.0
N A:GLU293 4.7 81.9 1.0
OD2 A:ASP274 4.9 72.5 1.0

Terbium binding site 6 out of 7 in 1m9s

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Terbium binding site 6 out of 7 in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb644

b:0.6
occ:1.00
O A:PRO49 2.8 0.3 1.0
OD1 A:ASP51 2.9 0.8 1.0
C A:PRO49 3.8 0.5 1.0
CG A:ASP51 4.0 0.2 1.0
CA A:PRO49 4.2 0.4 1.0
CE A:LYS45 4.6 0.3 1.0
OD2 A:ASP51 4.6 0.0 1.0
N A:ASP51 4.7 0.2 1.0
O A:PHE48 4.7 0.7 1.0
O A:LYS45 4.7 0.6 1.0
NZ A:LYS45 4.8 0.7 1.0
CA A:ASP51 5.0 0.6 1.0

Terbium binding site 7 out of 7 in 1m9s

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Terbium binding site 7 out of 7 in the Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains.


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 of Crystal Structure of Internalin B (Inlb), A Listeria Monocytogenes Virulence Protein Containing SH3-Like Domains. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb645

b:0.2
occ:1.00
O A:ASN231 3.3 62.6 1.0
OD1 A:ASP233 3.3 64.4 1.0
OD2 A:ASP233 3.6 79.6 1.0
CG A:ASP233 3.7 71.1 1.0
C A:ASN231 4.0 56.2 1.0
CA A:ASN231 4.2 53.3 1.0
CD A:LYS306 4.2 94.2 1.0
CE A:LYS306 4.4 97.2 1.0
NZ A:LYS306 4.4 0.6 1.0
ND2 A:ASN231 4.5 44.2 1.0
CB A:ASN231 4.6 51.4 1.0
O A:LEU232 4.7 55.4 1.0
OE1 A:GLN211 4.8 74.1 1.0
CG A:LYS306 4.9 86.5 1.0
C A:LEU232 4.9 57.4 1.0
N A:LEU232 5.0 54.1 1.0

Reference:

M.Marino, M.Banerjee, R.Jonquieres, P.Cossart, P.Ghosh. Gw Domains of the Listeria Monocytogenes Invasion Protein Inlb Are SH3-Like and Mediate Binding to Host Ligands Embo J. V. 21 5623 2002.
ISSN: ISSN 0261-4189
PubMed: 12411480
DOI: 10.1093/EMBOJ/CDF558
Page generated: Wed Dec 16 02:26:37 2020

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