Gadolinium in PDB 7o9p: Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster

The structure of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster, PDB code: 7o9p was solved by V.Reithofer, P.De Groot, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.42 / 1.99
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	144.397, 144.397, 113.95, 90, 90, 120
R / Rfree (%)	16.9 / 21

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Gadolinium atom in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster (pdb code 7o9p). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 42 binding sites of Gadolinium where determined in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster, PDB code: 7o9p:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gadolinium binding site 1 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd401 b:28.6 occ:0.44 O A:HOH552 2.1 47.9 1.0 CD A:GLU141 2.3 62.8 1.0 OE2 A:GLU141 2.3 69.2 1.0 OE1 A:GLU141 2.3 64.7 1.0 O A:LYS109 2.4 37.2 1.0 O A:GLY139 2.4 36.4 1.0 O A:ARG110 2.4 64.8 1.0 OD2 A:ASP169 2.4 50.6 1.0 OD1 A:ASP169 2.4 45.5 1.0 CG A:ASP169 2.7 52.8 1.0 C A:ARG110 3.3 64.7 1.0 GD A:GD441 3.3 95.2 0.6 C A:LYS109 3.4 45.5 1.0 CG A:GLU141 3.4 54.0 1.0 C A:GLY139 3.5 38.3 1.0 CA A:ARG110 3.5 60.2 1.0 N A:ARG110 3.8 57.5 1.0 CA A:GLY139 3.9 37.8 1.0 CB A:ASP169 4.3 44.1 1.0 O A:HOH592 4.4 37.2 1.0 N A:HIS111 4.5 74.5 1.0 O A:ALA112 4.5 75.1 1.0 CA A:LYS109 4.6 45.6 1.0 CB A:GLU141 4.6 56.7 1.0 N A:VAL140 4.6 40.0 1.0 O A:HOH695 4.6 36.4 1.0 CB A:LYS109 4.7 50.3 1.0 N A:GLU141 4.8 49.4 1.0 O A:HOH570 4.8 47.9 1.0 CA A:VAL140 4.9 49.5 1.0

Gadolinium binding site 2 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd402 b:56.9 occ:0.60 O A:HOH767 2.6 65.4 1.0 O A:HOH550 2.7 51.0 1.0 O A:HOH676 2.8 42.7 1.0 O A:HOH512 2.9 41.8 1.0 O A:HOH674 3.1 50.3 1.0 O A:HOH522 3.2 57.5 1.0 OD1 A:ASN223 4.3 29.9 1.0 O A:GLY241 4.5 28.9 1.0 OG A:SER243 4.5 33.4 1.0 ND2 A:ASN223 4.7 33.8 1.0 CG A:ASN223 4.9 29.0 1.0

Gadolinium binding site 3 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd403 b:51.5 occ:0.46 O A:HOH647 2.0 71.3 1.0 OE1 A:GLN102 2.4 54.4 1.0 OE2 A:GLU132 2.4 56.8 1.0 OE1 A:GLU132 2.4 62.9 1.0 CD A:GLU132 2.7 49.3 1.0 GD A:GD405 3.0 52.9 0.5 O A:HOH603 3.2 60.5 1.0 CD A:GLN102 3.3 47.3 1.0 GD A:GD417 3.5 115.3 0.8 GD A:GD416 3.5 75.4 0.4 CG A:GLN102 3.8 41.7 1.0 CG A:GLU132 4.1 46.4 1.0 OE1 A:GLU134 4.2 43.8 1.0 O A:HOH644 4.3 74.1 1.0 NE2 A:GLN102 4.4 51.0 1.0 O A:HOH654 4.5 53.2 1.0 CB A:GLU132 4.8 34.6 1.0 O A:HOH591 4.9 53.9 1.0

Gadolinium binding site 4 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd404 b:36.0 occ:0.45 O A:HOH594 2.2 43.1 1.0 O A:HOH661 2.3 42.3 1.0 OE2 A:GLU70 2.3 56.1 1.0 OE2 A:GLU106 2.4 41.2 1.0 O A:HOH501 2.4 44.1 1.0 O A:HOH630 2.5 53.2 1.0 OE1 A:GLU106 2.5 36.9 1.0 CD A:GLU106 2.8 34.7 1.0 CD A:GLU70 3.6 66.7 1.0 CG A:GLU70 4.3 59.0 1.0 CG A:GLU106 4.3 32.9 1.0 O A:HOH623 4.3 54.1 1.0 OH A:TYR66 4.3 27.5 1.0 OE1 A:GLU70 4.6 72.0 1.0 O A:SER71 4.9 37.6 1.0

Gadolinium binding site 5 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd405 b:52.9 occ:0.51 O A:HOH654 2.3 53.2 1.0 OE2 A:GLU132 2.4 56.8 1.0 OE2 A:GLU134 2.4 47.6 1.0 OE1 A:GLU134 2.4 43.8 1.0 O A:HOH660 2.7 48.9 1.0 CD A:GLU134 2.8 39.3 1.0 GD A:GD403 3.0 51.5 0.5 GD A:GD416 3.2 75.4 0.4 CD A:GLU132 3.4 49.3 1.0 O A:HOH644 3.5 74.1 1.0 GD A:GD417 3.6 115.3 0.8 OE1 A:GLU132 3.7 62.9 1.0 NZ A:LYS165 4.0 63.9 1.0 CG A:GLU134 4.2 31.0 1.0 OE1 A:GLN102 4.4 54.4 1.0 CD2 A:TYR163 4.5 37.8 1.0 O A:HOH697 4.5 62.7 1.0 CE2 A:TYR163 4.6 36.4 1.0 CG A:GLU132 4.6 46.4 1.0 CB A:GLU134 4.7 25.6 1.0 CE A:LYS165 4.8 54.5 1.0 O A:HOH603 4.9 60.5 1.0 O A:HOH647 5.0 71.3 1.0

Gadolinium binding site 6 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd406 b:60.9 occ:0.58 O A:HOH511 2.3 57.0 1.0 O A:HOH589 2.8 37.8 1.0 GD A:GD407 3.4 32.4 0.3 GD A:GD408 4.1 100.4 0.8 OD2 A:ASP183 4.7 37.4 1.0

Gadolinium binding site 7 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 7 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd407 b:32.4 occ:0.28 O A:HOH511 2.0 57.0 1.0 O A:HOH589 2.2 37.8 1.0 OD1 A:ASN181 2.4 52.1 1.0 OD1 A:ASP183 2.5 33.5 1.0 CG A:ASP183 3.2 32.5 1.0 OD2 A:ASP183 3.3 37.4 1.0 GD A:GD406 3.4 60.9 0.6 CG A:ASN181 3.4 48.3 1.0 CG A:GLN206 3.9 31.9 1.0 ND2 A:ASN181 4.0 51.3 1.0 O A:HOH557 4.0 52.3 1.0 CB A:GLN206 4.5 24.6 1.0 CB A:ASN181 4.6 35.4 1.0 CB A:ASP183 4.7 28.4 1.0 CD A:GLN206 4.8 35.2 1.0 O A:HOH645 4.9 31.4 1.0 GD A:GD408 4.9 100.4 0.8

Gadolinium binding site 8 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 8 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd408 b:100.4 occ:0.82 OG A:SER323 2.5 68.5 1.0 O A:HOH610 3.1 77.2 1.0 CB A:SER323 3.9 64.8 1.0 GD A:GD406 4.1 60.9 0.6 O A:HOH589 4.3 37.8 1.0 NE2 A:GLN206 4.7 39.7 1.0 CD A:GLN206 4.8 35.2 1.0 CA A:SER323 4.9 63.4 1.0 GD A:GD407 4.9 32.4 0.3 OE1 A:GLN206 4.9 36.5 1.0 O A:HOH519 5.0 36.6 1.0 O A:HOH701 5.0 53.0 1.0

Gadolinium binding site 9 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 9 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd409 b:76.7 occ:0.60 O A:HOH769 2.7 62.4 1.0 GD A:GD429 3.6 112.0 0.8 GD A:GD415 3.8 106.6 0.8 GD A:GD410 3.8 108.5 1.0 GD A:GD412 3.8 133.4 1.0 OE1 A:GLU59 4.0 96.5 1.0 GD A:GD422 4.2 72.1 0.4 O A:HOH771 4.5 53.5 1.0 O A:HOH753 4.7 50.2 1.0 O A:HOH663 4.9 55.3 1.0

Gadolinium binding site 10 out of 42 in the Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 10 of Crystal Structure of the AWP3B (Adhesin-Like Wall Protein 3B) A-Domain From Candida Glabrata Showing A Gadolinium Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd410 b:108.5 occ:1.00 OE2 A:GLU59 2.4 99.1 1.0 OE1 A:GLU59 2.4 96.5 1.0 O A:HOH578 2.6 49.0 1.0 CD A:GLU59 2.7 79.2 1.0 O A:HOH657 3.4 66.9 1.0 O A:HOH555 3.8 69.2 1.0 GD A:GD415 3.8 106.6 0.8 GD A:GD409 3.8 76.7 0.6 GD A:GD412 3.9 133.4 1.0 CG A:GLU59 4.1 62.5 1.0

V.Reithofer, J.Fernandez-Pereira, M.Alvarado, P.De Groot, L.-O.Essen. A Novel Class of Candida Glabrata Cell Wall Proteins with Beta-Helix Fold Mediates Adhesion in Clinical Isolates Plos Pathog. 2021.
ISSN: ESSN 1553-7374