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Calcium in PDB 6x8a: Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain

Protein crystallography data

The structure of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x8a was solved by S.Guo, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.71 / 1.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.23, 50.61, 79.6, 90, 90, 90
R / Rfree (%) 14.2 / 16.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain (pdb code 6x8a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x8a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6x8a

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Calcium binding site 1 out of 7 in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:4.4
occ:1.00
 OD1 A:ASP110 2.3 5.0 1.0
OD1 A:ASP155 2.3 4.6 1.0
O A:ASP159 2.4 5.0 1.0
O A:GLY157 2.4 5.7 1.0
OD2 A:ASP111 2.4 4.5 1.0
O3 B:GLC1 2.5 6.3 1.0
O4 B:GLC1 2.5 6.1 1.0
CG A:ASP110 3.3 5.1 1.0
CG A:ASP111 3.3 4.6 1.0
C3 B:GLC1 3.3 8.0 1.0
C4 B:GLC1 3.4 7.6 1.0
C A:GLY157 3.5 5.7 1.0
CG A:ASP155 3.5 4.1 1.0
C A:ASP159 3.5 5.3 1.0
OD2 A:ASP110 3.6 6.2 1.0
OD1 A:ASP111 3.7 5.1 1.0
N A:ASP159 3.9 5.8 1.0
N A:GLY157 4.0 5.2 1.0
C A:GLY158 4.2 5.9 1.0
N A:GLN156 4.3 4.2 1.0
CA A:ASP159 4.3 5.9 1.0
N A:GLY158 4.3 5.9 1.0
CA A:GLY157 4.3 5.8 1.0
OD2 A:ASP155 4.3 5.2 1.0
CA A:GLY158 4.4 6.0 1.0
CB A:ASP155 4.4 4.3 1.0
CA A:ASP155 4.4 3.9 1.0
CG A:GLN156 4.5 6.9 1.0
N A:ASP111 4.5 4.2 1.0
C A:ASP110 4.5 3.9 1.0
NE2 A:GLN156 4.5 9.4 1.0
CB A:ASP111 4.5 4.8 1.0
N A:TYR160 4.6 5.2 1.0
CB A:ASP110 4.6 5.0 1.0
O A:ASP110 4.7 4.1 1.0
C2 B:GLC1 4.7 11.1 1.0
C5 B:GLC1 4.7 10.9 1.0
CA A:TYR160 4.7 5.5 1.0
C A:ASP155 4.8 4.1 1.0
O A:GLY158 4.8 6.6 1.0
C A:GLN156 4.9 5.0 1.0
CA A:ASP111 4.9 4.4 1.0
O A:GLN129 5.0 6.8 1.0

Calcium binding site 2 out of 7 in 6x8a

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Calcium binding site 2 out of 7 in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:6.5
occ:1.00
 O A:GLN156 2.3 6.3 1.0
OE1 A:GLN27 2.3 7.8 1.0
O A:HOH479 2.4 8.6 1.0
O A:HOH360 2.4 11.8 1.0
O A:HOH497 2.4 9.4 1.0
OD1 A:ASP87 2.4 6.6 1.0
OD2 A:ASP87 2.5 5.8 1.0
CG A:ASP87 2.8 5.6 1.0
C A:GLN156 3.4 5.0 1.0
CD A:GLN27 3.5 7.2 1.0
CA A:GLN156 4.0 4.8 1.0
OE1 A:GLN156 4.0 10.2 1.0
CB A:GLN156 4.2 5.7 1.0
CA A:GLN27 4.2 6.2 1.0
NE2 A:GLN27 4.3 8.5 1.0
CB A:ASP87 4.3 5.1 1.0
O A:HOH516 4.4 11.9 1.0
O A:HOH524 4.4 37.1 1.0
O A:HOH380 4.4 9.0 1.0
CD A:GLN156 4.5 8.6 1.0
CB A:GLN27 4.5 7.0 1.0
O A:HOH338 4.5 10.3 1.0
OG1 A:THR86 4.5 6.3 1.0
N A:GLY157 4.6 5.2 1.0
CG A:GLN27 4.6 7.5 1.0
O A:SER26 4.7 8.2 1.0
O A:THR86 4.8 6.0 1.0
N A:LEU28 4.8 6.0 1.0
CA A:GLY157 4.9 5.8 1.0
CG A:GLN156 4.9 6.9 1.0
CB A:THR86 5.0 6.4 1.0

Calcium binding site 3 out of 7 in 6x8a

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Calcium binding site 3 out of 7 in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:10.4
occ:0.76
 O A:HOH496 2.3 20.2 1.0
O A:SER73 2.4 11.0 1.0
O A:HOH457 2.5 13.8 1.0
OG A:SER76 2.6 8.6 1.0
O A:HOH442 2.6 11.0 1.0
O A:HOH418 2.6 21.1 1.0
C A:SER73 3.4 9.6 1.0
CB A:SER76 3.6 7.4 1.0
CA A:SER73 4.0 10.3 1.0
O A:HOH351 4.4 12.4 1.0
N A:SER76 4.4 5.7 1.0
N A:ASP74 4.5 7.3 1.0
CB A:SER73 4.6 11.0 1.0
CA A:SER76 4.6 6.2 1.0
O A:HOH551 4.8 19.2 1.0
CA A:ASP74 4.8 6.5 1.0
O A:HOH341 4.9 14.9 1.0
C A:ASP74 5.0 6.7 1.0

Calcium binding site 4 out of 7 in 6x8a

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Calcium binding site 4 out of 7 in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:5.6
occ:1.00
 O A:PRO82 2.3 6.2 1.0
O A:HOH396 2.4 5.6 1.0
O A:HOH336 2.4 11.9 1.0
O A:GLY64 2.4 6.8 1.0
O A:HOH408 2.4 8.2 1.0
OD1 A:ASP81 2.4 6.4 1.0
O A:HOH414 2.4 7.5 1.0
CG A:ASP81 3.5 6.1 1.0
C A:GLY64 3.5 6.0 1.0
C A:PRO82 3.5 6.4 1.0
OD2 A:ASP81 3.9 7.0 1.0
O A:HOH327 4.1 5.4 1.0
N A:PRO82 4.2 6.4 1.0
CA A:GLY64 4.3 6.7 1.0
O A:HOH539 4.3 37.3 1.0
CA A:PRO82 4.4 6.9 1.0
C A:ASP81 4.4 6.7 1.0
OE1 A:GLN68 4.4 6.0 1.0
N A:GLY64 4.4 6.4 1.0
CD A:PRO82 4.5 7.1 1.0
O A:GLY83 4.5 6.4 1.0
N A:GLY83 4.5 6.8 1.0
N A:THR65 4.5 6.1 1.0
C A:GLY83 4.5 5.9 1.0
CA A:GLY83 4.6 7.0 1.0
NE2 A:GLN68 4.6 6.8 1.0
CA A:THR65 4.7 6.2 1.0
O A:ASP81 4.7 7.5 1.0
O A:HOH535 4.7 16.6 1.0
CB A:ASP81 4.8 6.4 1.0
CB A:PRO82 4.8 9.7 1.0
OD1 A:ASP84 4.8 9.1 1.0
O A:HOH420 4.9 31.9 1.0
CA A:ASP81 4.9 6.6 1.0
C A:LYS63 5.0 6.2 1.0
CD A:GLN68 5.0 5.6 1.0

Calcium binding site 5 out of 7 in 6x8a

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Calcium binding site 5 out of 7 in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:21.9
occ:0.66
 OD1 A:ASP7 2.3 38.8 1.0
O A:HOH306 2.3 35.6 1.0
OE1 A:GLN5 2.4 24.5 1.0
O A:THR9 2.4 20.8 1.0
OD2 A:ASP11 2.5 29.0 1.0
OD1 A:ASP11 2.5 28.2 1.0
CG A:ASP11 2.8 22.8 1.0
CG A:ASP7 3.3 37.0 1.0
CD A:GLN5 3.3 23.6 1.0
C A:THR9 3.6 21.1 1.0
NE2 A:GLN5 3.6 23.6 1.0
OD2 A:ASP7 3.7 44.2 1.0
CB A:THR9 4.1 31.4 1.0
CA A:THR9 4.2 26.0 1.0
N A:THR9 4.2 26.7 1.0
CB A:ASP11 4.3 18.8 1.0
N A:ASP7 4.4 32.4 1.0
OD1 A:ASP6 4.5 56.2 1.0
N A:ASP11 4.6 17.3 1.0
C A:PRO10 4.6 18.0 1.0
CB A:ASP7 4.6 30.9 1.0
N A:PRO10 4.7 17.9 1.0
CG2 A:THR9 4.7 34.0 1.0
N A:ASP6 4.7 33.2 1.0
CG A:GLN5 4.7 26.8 1.0
CA A:ASP7 4.8 30.5 1.0
C A:ASP7 4.8 29.4 1.0
CA A:ASP11 4.9 15.1 1.0
CA A:PRO10 4.9 17.6 1.0
O A:ASP7 4.9 30.6 1.0
O A:PRO10 5.0 22.7 1.0
O A:HOH490 5.0 31.4 1.0

Calcium binding site 6 out of 7 in 6x8a

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Calcium binding site 6 out of 7 in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:22.1
occ:1.00
 O A:VAL38 2.4 10.3 1.0
O A:HOH494 2.4 33.2 1.0
O A:LYS41 2.4 9.8 1.0
O A:HOH487 2.5 26.7 1.0
OH A:TYR22 2.7 12.7 1.0
CZ A:TYR22 3.5 9.4 1.0
C A:VAL38 3.6 9.0 1.0
C A:LYS41 3.6 9.9 1.0
CE2 A:TYR22 3.6 8.9 1.0
O A:HOH448 3.9 26.4 1.0
CG1 A:VAL38 4.1 9.0 1.0
CA A:GLU42 4.3 11.8 1.0
O A:HOH429 4.4 21.1 1.0
N A:GLU42 4.4 11.1 1.0
CA A:VAL38 4.4 7.5 1.0
N A:LYS41 4.4 10.4 1.0
N A:ASP39 4.5 9.0 1.0
CA A:ASP39 4.6 11.5 1.0
C A:ASP39 4.6 10.9 1.0
N A:ALA43 4.7 9.4 1.0
C A:GLU42 4.7 10.7 1.0
CA A:LYS41 4.7 10.8 1.0
OE2 A:GLU42 4.7 35.4 1.0
OE1 A:GLU20 4.7 13.2 1.0
CE1 A:TYR22 4.8 7.3 1.0
O A:ASP39 4.9 14.3 1.0
CD2 A:TYR22 4.9 7.7 1.0
CB A:VAL38 5.0 8.4 1.0

Calcium binding site 7 out of 7 in 6x8a

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Calcium binding site 7 out of 7 in the Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Sucrose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:13.2
occ:1.00
 O A:HOH464 2.4 11.6 1.0
O A:HOH350 2.4 12.8 1.0
O A:HOH542 2.4 18.9 1.0
O A:HOH509 2.5 18.6 1.0
O A:HOH436 2.5 13.1 1.0
O A:HOH465 2.7 19.0 1.0
O A:SER53 4.1 6.4 1.0
CA A:GLY72 4.3 8.2 1.0
O A:GLY55 4.5 8.9 1.0
O A:HOH347 4.5 20.3 1.0
O A:HOH444 4.6 13.3 1.0
O A:HOH344 4.6 15.0 1.0
O A:PHE70 4.7 5.0 1.0
O A:GLU69 4.8 6.6 1.0
N A:GLY72 4.9 7.4 1.0
O A:HOH506 4.9 35.8 1.0

Reference:

S.Guo, T.D.R.Vance, H.Zahiri, R.Eves, C.Stevens, J.H.Hehemann, S.Vidal-Melgosa, P.L.Davies. Structural Basis of Ligand Selectivity By A Bacterial Adhesin Lectin Involved in Multispecies Biofilm Formation. Mbio V. 12 2021.
ISSN: ESSN 2150-7511
PubMed: 33824212
DOI: 10.1128/MBIO.00130-21
Page generated: Tue Jul 16 17:53:38 2024

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