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Cadmium in PDB 4fdw: Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution, PDB code: 4fdw was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.80 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.140, 112.320, 55.990, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution (pdb code 4fdw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution, PDB code: 4fdw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15;

Cadmium binding site 1 out of 15 in 4fdw

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Cadmium binding site 1 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:29.8
occ:0.70
O A:HOH615 2.1 26.3 1.0
O A:HOH609 2.1 25.1 1.0
OD1 A:ASP82 2.4 49.5 1.0
OD2 A:ASP82 2.4 53.5 1.0
O A:HOH781 2.5 54.4 1.0
CG A:ASP82 2.7 48.0 1.0
O A:HOH801 4.0 57.9 1.0
CB A:ASP82 4.2 40.5 1.0
OE2 A:GLU51 4.6 65.9 1.0
O A:ASP82 4.8 44.5 1.0

Cadmium binding site 2 out of 15 in 4fdw

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Cadmium binding site 2 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:49.6
occ:0.50
OD2 A:ASP52 2.3 61.0 1.0
O A:HOH676 2.4 39.6 1.0
CG A:ASP52 3.2 53.1 1.0
OD1 A:ASP52 3.4 53.0 1.0
NZ A:LYS119 3.6 67.5 1.0
CE A:LYS119 4.3 57.7 1.0
O A:HOH693 4.3 41.9 1.0
O A:HOH851 4.5 69.3 1.0
O A:HOH797 4.5 57.3 1.0
CB A:ASP52 4.6 40.0 1.0
O A:HOH852 5.0 50.7 1.0

Cadmium binding site 3 out of 15 in 4fdw

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Cadmium binding site 3 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:44.1
occ:0.70
O A:HOH601 2.0 16.0 1.0
OE1 A:GLU56 2.5 59.8 1.0
OE2 A:GLU56 2.6 39.9 1.0
CD A:GLU56 2.9 56.6 1.0
OG A:SER54 3.8 52.0 1.0
O A:HOH721 4.0 49.8 1.0
CD A:CD511 4.1 67.2 0.7
CG A:GLU56 4.4 47.3 1.0
CB A:SER54 4.8 39.1 1.0
CA A:GLU56 5.0 38.7 1.0

Cadmium binding site 4 out of 15 in 4fdw

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Cadmium binding site 4 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:31.6
occ:0.80
OD1 A:ASN370 2.3 36.9 1.0
OG A:SER367 2.4 29.2 0.4
O A:HOH603 2.4 20.6 1.0
O A:SER367 2.4 31.7 1.0
CL A:CL518 2.5 33.7 1.0
O A:HOH605 2.6 24.3 1.0
CB A:SER367 3.0 32.2 0.6
CB A:SER367 3.1 28.7 0.4
C A:SER367 3.3 33.3 1.0
OG A:SER367 3.4 44.6 0.6
CG A:ASN370 3.4 42.1 1.0
CA A:SER367 3.6 29.4 0.4
CA A:SER367 3.6 30.4 0.6
CD A:CD514 3.9 54.6 0.4
ND2 A:ASN370 3.9 36.4 1.0
CA A:GLY344 4.1 25.4 1.0
N A:GLY344 4.3 26.4 1.0
N A:ASN371 4.3 31.6 1.0
O A:HOH735 4.4 49.4 1.0
N A:ALA368 4.5 29.2 1.0
O A:HOH706 4.5 43.0 1.0
N A:ASN370 4.5 28.3 1.0
CB A:ASN371 4.5 30.8 1.0
CB A:ASN370 4.7 30.3 1.0
C A:ALA368 4.8 29.9 1.0
CG A:GLN343 4.9 35.1 1.0
CA A:ASN370 5.0 30.0 1.0

Cadmium binding site 5 out of 15 in 4fdw

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Cadmium binding site 5 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd505

b:28.2
occ:0.70
OE2 A:GLU315 2.3 39.8 1.0
OE1 A:GLU315 2.4 38.2 1.0
O A:HOH700 2.6 42.8 1.0
CD A:GLU315 2.7 45.5 1.0
CG A:GLU315 4.2 38.3 1.0
CD A:CD506 4.5 35.1 0.7
O A:HOH772 4.6 52.3 1.0
O A:HOH677 4.8 39.1 1.0
CB A:GLU315 4.8 32.4 1.0

Cadmium binding site 6 out of 15 in 4fdw

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Cadmium binding site 6 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd506

b:35.1
occ:0.70
OE1 A:GLU315 2.4 38.2 1.0
OD1 A:ASP313 2.4 41.2 1.0
O A:HOH604 2.5 20.6 1.0
OD2 A:ASP313 2.7 53.0 1.0
CG A:ASP313 2.9 41.8 1.0
O A:HOH772 3.1 52.3 1.0
CD A:GLU315 3.4 45.5 1.0
CG A:GLU315 3.7 38.3 1.0
CB A:GLU315 4.0 32.4 1.0
O A:HOH785 4.4 54.7 1.0
CB A:ASP313 4.4 33.6 1.0
CD A:CD505 4.5 28.2 0.7
OE2 A:GLU315 4.6 39.8 1.0
N A:GLU315 4.8 30.3 1.0
O A:HOH700 4.9 42.8 1.0

Cadmium binding site 7 out of 15 in 4fdw

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Cadmium binding site 7 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd507

b:41.8
occ:0.40
O A:HOH686 2.1 42.1 1.0
O A:HOH668 2.2 36.3 1.0
OE2 A:GLU336 2.3 55.7 1.0
OE1 A:GLU336 2.6 47.6 1.0
OE1 A:GLU380 2.6 44.7 1.0
CD A:GLU336 2.8 59.6 1.0
CD A:CD508 3.7 48.5 0.5
CD A:GLU380 3.8 70.2 1.0
CB A:PRO358 4.2 29.4 1.0
CG A:GLU336 4.3 37.6 1.0
CA A:PRO358 4.3 28.4 1.0
OE2 A:GLU380 4.4 74.5 1.0
O A:HOH660 4.6 35.6 1.0
N A:ALA359 4.6 31.3 1.0
O A:HOH795 4.8 54.6 1.0
CG A:GLU380 4.9 45.2 1.0
CG A:PRO358 4.9 31.5 1.0

Cadmium binding site 8 out of 15 in 4fdw

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Cadmium binding site 8 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd508

b:48.5
occ:0.50
OE2 A:GLU380 2.4 74.5 1.0
OE1 A:GLU380 2.9 44.7 1.0
CD A:GLU380 3.0 70.2 1.0
O A:HOH800 3.5 54.4 1.0
CD A:CD507 3.7 41.8 0.4
O A:HOH668 4.0 36.3 1.0
NZ A:LYS378 4.0 71.6 1.0
CG A:GLU380 4.4 45.2 1.0
O A:HOH686 4.7 42.1 1.0

Cadmium binding site 9 out of 15 in 4fdw

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Cadmium binding site 9 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd509

b:48.7
occ:0.60
OD2 A:ASP178 2.2 64.2 1.0
O A:HOH650 2.2 34.0 1.0
O A:HOH719 2.2 49.4 1.0
O A:HOH687 2.5 42.1 1.0
O A:HOH779 2.7 62.5 1.0
OD1 A:ASP178 2.7 55.1 1.0
CG A:ASP178 2.8 54.0 1.0
CB A:ASP178 4.2 36.1 1.0
CG A:GLU200 4.5 45.8 0.5
CB A:LYS199 4.5 31.1 1.0
OE1 A:GLU200 4.6 61.4 0.5
OE1 A:GLU200 4.7 52.6 0.5
CD A:LYS199 4.8 45.6 1.0
N A:GLU200 4.8 33.8 1.0
CD A:GLU200 4.8 64.5 0.5
CG A:LYS199 4.9 34.7 1.0
CD A:GLU200 5.0 56.9 0.5

Cadmium binding site 10 out of 15 in 4fdw

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Cadmium binding site 10 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd510

b:96.4
occ:0.50
OE1 A:GLU233 2.6 64.2 1.0
OE2 A:GLU233 2.9 53.5 1.0
CD A:GLU233 3.0 59.4 1.0
O A:HOH812 3.3 61.6 1.0
NZ A:LYS256 4.3 47.5 1.0
CG A:GLU233 4.5 40.4 1.0
CE A:LYS256 4.6 44.6 1.0

Cadmium binding site 11 out of 15 in 4fdw

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Cadmium binding site 11 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd511

b:67.2
occ:0.70
OG A:SER54 2.2 52.0 1.0
O A:HOH721 2.6 49.8 1.0
O A:HOH601 2.6 16.0 1.0
O A:HOH693 2.7 41.9 1.0
O A:HOH634 3.0 31.5 1.0
O A:HOH816 3.0 63.0 1.0
CB A:SER54 3.4 39.1 1.0
CD A:CD503 4.1 44.1 0.7
CA A:SER54 4.1 33.6 1.0
OE2 A:GLU56 4.1 39.9 1.0
N A:ILE55 4.3 36.6 1.0
O A:ILE55 4.3 43.5 1.0
C A:SER54 4.6 36.9 1.0
C A:ILE55 4.8 42.1 1.0

Cadmium binding site 12 out of 15 in 4fdw

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Cadmium binding site 12 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd512

b:71.2
occ:0.50
OE1 A:GLU188 2.5 53.6 1.0
CD A:GLU188 3.3 67.1 1.0
OE2 A:GLU188 3.4 66.5 1.0
CG A:GLU188 4.7 47.0 1.0
NZ A:LYS166 4.8 62.5 1.0

Cadmium binding site 13 out of 15 in 4fdw

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Cadmium binding site 13 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd513

b:91.7
occ:0.50
OD1 A:ASP106 2.4 71.8 1.0
O A:HOH683 2.6 40.7 1.0
O A:HOH853 2.9 75.7 1.0
CG A:ASP106 3.3 71.6 1.0
OD2 A:ASP106 3.5 84.3 1.0
O A:HOH827 3.6 65.3 1.0
CL A:CL517 3.7 68.3 0.7
O A:GLU144 4.2 40.8 1.0
CL A:CL516 4.4 48.0 1.0
CE1 A:HIS124 4.6 41.7 1.0
CB A:ASP106 4.6 47.0 1.0

Cadmium binding site 14 out of 15 in 4fdw

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Cadmium binding site 14 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd514

b:54.6
occ:0.40
O A:HOH735 2.4 49.4 1.0
O A:HOH603 2.9 20.6 1.0
O A:HOH605 3.1 24.3 1.0
CD A:CD504 3.9 31.6 0.8
OG A:SER367 4.1 29.2 0.4
O A:HOH706 4.2 43.0 1.0
NE2 A:GLN343 4.3 25.9 1.0
OG A:SER367 4.4 44.6 0.6
OH A:TYR321 4.8 44.9 1.0
O A:HOH755 4.8 49.6 1.0
CB A:SER367 4.9 28.7 0.4
CB A:SER367 5.0 32.2 0.6

Cadmium binding site 15 out of 15 in 4fdw

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Cadmium binding site 15 out of 15 in the Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of Crystal Structure of A Putative Cell Surface Protein (BACOVA_01565) From Bacteroides Ovatus Atcc 8483 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd515

b:83.2
occ:0.30
OE2 A:GLU410 2.4 79.7 1.0
O A:HOH838 2.7 49.9 1.0
CD A:GLU410 3.0 87.2 1.0
OE1 A:GLU410 3.0 84.7 1.0
O A:HOH805 3.0 58.4 1.0
CG A:GLU410 4.4 57.1 1.0
CD A:LYS413 4.5 64.9 1.0
OD1 A:ASN414 4.7 68.2 1.0
CB A:LYS413 4.9 43.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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