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Calcium in PDB 5fq6: Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron

Protein crystallography data

The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq6 was solved by A.J.Glenwright, K.R.Pothula, D.S.Chorev, A.Basle, C.V.Robinson, U.Kleinekathoefer, D.N.Bolam, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 222.027, 91.941, 261.219, 90.00, 98.23, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 5fq6:

The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron (pdb code 5fq6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5fq6

Go back to Calcium Binding Sites List in 5fq6
Calcium binding site 1 out of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1987

b:51.4
occ:1.00
 OD1 B:ASP280 2.2 62.8 1.0
O B:GLY281 2.3 54.3 1.0
O B:THR285 2.4 48.5 1.0
O B:ILE283 2.4 45.8 1.0
OD1 B:ASP288 2.5 40.5 1.0
C B:GLY281 3.4 51.8 1.0
CG B:ASP288 3.4 56.8 1.0
CG B:ASP280 3.4 56.1 1.0
OD2 B:ASP288 3.5 54.6 1.0
C B:THR285 3.6 49.6 1.0
C B:ILE283 3.6 44.7 1.0
N B:GLY281 3.8 48.1 1.0
C B:ASP280 4.0 45.5 1.0
OD2 B:ASP280 4.0 55.5 1.0
O B:ASP280 4.1 44.9 1.0
CA B:GLY281 4.2 56.4 1.0
C B:PRO284 4.2 50.5 1.0
N B:ILE283 4.2 53.0 1.0
N B:THR285 4.2 40.3 1.0
N B:MET282 4.4 58.0 1.0
CA B:PRO284 4.5 50.6 1.0
CA B:ILE283 4.5 42.8 1.0
N B:ASP286 4.5 61.1 1.0
C B:MET282 4.5 57.0 1.0
N B:PRO284 4.5 47.1 1.0
O B:PRO284 4.5 47.3 1.0
CB B:ASP280 4.5 40.8 1.0
CA B:THR285 4.5 46.9 1.0
O B:ASP288 4.6 67.3 1.0
CA B:ASP286 4.6 55.1 1.0
CA B:ASP280 4.6 42.0 1.0
CA B:MET282 4.8 61.3 1.0
CB B:ASP288 4.9 53.5 1.0
N B:ASP288 5.0 39.9 1.0

Calcium binding site 2 out of 4 in 5fq6

Go back to Calcium Binding Sites List in 5fq6
Calcium binding site 2 out of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1987

b:47.4
occ:1.00
 O D:ILE283 2.3 58.0 1.0
O D:GLY281 2.3 46.4 1.0
O D:THR285 2.4 44.1 1.0
OD1 D:ASP280 2.4 59.3 1.0
OD1 D:ASP288 2.9 61.7 1.0
C D:GLY281 3.4 49.7 1.0
C D:ILE283 3.5 44.4 1.0
C D:THR285 3.6 41.2 1.0
CG D:ASP280 3.6 54.2 1.0
CG D:ASP288 3.7 66.8 1.0
N D:GLY281 3.9 42.8 1.0
N D:ILE283 4.0 52.2 1.0
C D:PRO284 4.1 38.9 1.0
N D:THR285 4.1 39.9 1.0
C D:ASP280 4.1 45.2 1.0
CA D:GLY281 4.2 49.2 1.0
OD2 D:ASP280 4.2 65.6 1.0
C D:MET282 4.2 57.7 1.0
CA D:ILE283 4.3 30.9 1.0
O D:ASP280 4.3 40.4 1.0
N D:MET282 4.3 64.5 1.0
CA D:PRO284 4.3 44.2 1.0
N D:PRO284 4.4 43.2 1.0
O D:ASP288 4.4 83.2 1.0
CA D:THR285 4.4 38.9 1.0
OD2 D:ASP288 4.4 66.5 1.0
O D:PRO284 4.4 34.6 1.0
CB D:ASP288 4.4 70.7 1.0
N D:ASP286 4.5 51.8 1.0
N D:ASP288 4.5 44.6 1.0
CA D:MET282 4.6 62.6 1.0
CA D:ASP286 4.7 41.2 1.0
O D:MET282 4.7 52.7 1.0
CB D:ASP280 4.7 31.7 1.0
N D:ALA287 4.8 35.8 1.0
CA D:ASP280 4.8 44.1 1.0
CB D:ILE283 4.8 30.2 1.0
CA D:ASP288 5.0 56.2 1.0

Calcium binding site 3 out of 4 in 5fq6

Go back to Calcium Binding Sites List in 5fq6
Calcium binding site 3 out of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca1987

b:58.7
occ:1.00
 OD1 I:ASP280 2.1 49.3 1.0
O I:ILE283 2.2 63.4 1.0
O I:GLY281 2.4 66.6 1.0
O I:THR285 2.4 42.2 1.0
OD1 I:ASP288 2.7 45.7 1.0
CG I:ASP280 3.3 55.2 1.0
C I:ILE283 3.4 47.5 1.0
C I:GLY281 3.4 57.2 1.0
CG I:ASP288 3.5 51.4 1.0
OD2 I:ASP288 3.5 56.7 1.0
C I:THR285 3.6 44.7 1.0
OD2 I:ASP280 3.8 60.7 1.0
C I:PRO284 3.9 50.5 1.0
N I:GLY281 3.9 48.1 1.0
N I:THR285 4.0 53.9 1.0
N I:ILE283 4.1 47.4 1.0
C I:ASP280 4.1 49.6 1.0
O I:PRO284 4.2 51.0 1.0
CA I:PRO284 4.2 41.5 1.0
CA I:GLY281 4.2 52.2 1.0
N I:PRO284 4.2 41.5 1.0
C I:MET282 4.3 62.9 1.0
CA I:ILE283 4.3 44.1 1.0
O I:ASP280 4.3 46.1 1.0
CA I:THR285 4.4 51.6 1.0
N I:MET282 4.4 56.7 1.0
CB I:ASP280 4.5 41.4 1.0
N I:ASP286 4.6 50.6 1.0
O I:MET282 4.7 68.6 1.0
CA I:MET282 4.7 62.2 1.0
CA I:ASP280 4.7 41.5 1.0
OD2 I:ASP250 4.7 82.1 1.0
CA I:ASP286 4.8 50.0 1.0
O I:ASP288 4.8 59.5 1.0
CB I:ILE283 4.9 46.5 1.0

Calcium binding site 4 out of 4 in 5fq6

Go back to Calcium Binding Sites List in 5fq6
Calcium binding site 4 out of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca1987

b:0.0
occ:1.00
 O M:ILE283 2.2 53.9 1.0
OD1 M:ASP280 2.3 70.2 1.0
O M:THR285 2.5 74.6 1.0
OD2 M:ASP288 2.6 46.4 1.0
O M:GLY281 2.7 52.0 1.0
OD1 M:ASP288 3.0 60.1 1.0
CG M:ASP288 3.2 52.1 1.0
CG M:ASP280 3.3 58.0 1.0
C M:ILE283 3.4 43.5 1.0
C M:GLY281 3.6 44.8 1.0
C M:THR285 3.6 54.2 1.0
OD2 M:ASP280 3.7 55.9 1.0
C M:PRO284 3.9 41.5 1.0
N M:THR285 3.9 42.4 1.0
N M:GLY281 4.0 33.5 1.0
N M:ILE283 4.1 49.8 1.0
C M:ASP280 4.2 50.0 1.0
O M:PRO284 4.2 42.1 1.0
CA M:PRO284 4.2 37.6 1.0
N M:PRO284 4.3 46.5 1.0
CA M:GLY281 4.3 43.2 1.0
CA M:ILE283 4.3 41.5 1.0
CA M:THR285 4.4 52.1 1.0
O M:ASP280 4.4 41.8 1.0
C M:MET282 4.4 54.8 1.0
N M:MET282 4.5 48.5 1.0
CB M:ASP280 4.6 34.2 1.0
N M:ASP286 4.7 45.9 1.0
CB M:ASP288 4.7 47.1 1.0
O M:MET282 4.8 57.1 1.0
OD2 M:ASP250 4.8 76.6 1.0
CA M:ASP280 4.8 41.0 1.0
CA M:MET282 4.9 48.0 1.0

Reference:

A.J.Glenwright, K.R.Pothula, S.P.Bhamidimarri, D.S.Chorev, A.Basle, S.J.Firbank, H.Zheng, C.V.Robinson, M.Winterhalter, U.Kleinekathofer, D.N.Bolam, B.Van Den Berg. Structural Basis For Nutrient Acquisition By Dominant Members of the Human Gut Microbiota. Nature V. 541 407 2017.
ISSN: ESSN 1476-4687
PubMed: 28077872
DOI: 10.1038/NATURE20828
Page generated: Sun Jul 14 19:18:12 2024

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