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Calcium in PDB 6xac: Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

Protein crystallography data

The structure of Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6xac 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) 42.20 / 1.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.224, 50.012, 78.662, 90, 90, 90
R / Rfree (%) 13.4 / 16

Calcium Binding Sites:

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

Calcium binding site 1 out of 7 in 6xac

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Calcium binding site 1 out of 7 in the Galactose-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 Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:7.3
occ:1.00
 OD1 A:ASP155 2.3 7.0 1.0
OD1 A:ASP110 2.3 7.8 1.0
O A:ASP159 2.4 7.7 1.0
O A:GLY157 2.4 8.4 1.0
OD2 A:ASP111 2.4 7.2 1.0
O2 A:GAL201 2.5 8.3 1.0
O1 A:GAL201 2.5 8.7 1.0
CG A:ASP110 3.3 7.8 1.0
CG A:ASP111 3.3 7.2 1.0
C2 A:GAL201 3.3 9.3 1.0
C1 A:GAL201 3.4 9.1 1.0
C A:GLY157 3.4 7.8 1.0
CG A:ASP155 3.5 7.0 1.0
C A:ASP159 3.5 7.7 1.0
OD2 A:ASP110 3.6 8.4 1.0
OD1 A:ASP111 3.7 8.0 1.0
N A:ASP159 3.8 8.3 1.0
N A:GLY157 4.0 7.5 1.0
C A:GLY158 4.2 8.3 1.0
N A:GLN156 4.2 6.7 1.0
CA A:ASP159 4.3 8.7 1.0
N A:GLY158 4.3 8.8 1.0
CA A:GLY157 4.3 8.1 1.0
OD2 A:ASP155 4.3 6.9 1.0
CG A:GLN156 4.3 9.2 1.0
CA A:GLY158 4.4 9.3 1.0
CB A:ASP155 4.4 7.3 1.0
C A:ASP110 4.4 6.9 1.0
CA A:ASP155 4.4 6.5 1.0
N A:ASP111 4.4 7.0 1.0
CB A:ASP111 4.6 7.7 1.0
N A:TYR160 4.6 8.0 1.0
CB A:ASP110 4.6 8.0 1.0
O5 A:GAL201 4.6 12.5 1.0
O A:ASP110 4.6 7.2 1.0
C3 A:GAL201 4.7 12.9 1.0
C A:ASP155 4.7 6.5 1.0
CA A:TYR160 4.8 7.6 1.0
O A:GLY158 4.8 9.0 1.0
C A:GLN156 4.9 7.0 1.0
CA A:ASP111 4.9 7.3 1.0
O A:GLN129 4.9 9.6 1.0

Calcium binding site 2 out of 7 in 6xac

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Calcium binding site 2 out of 7 in the Galactose-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 Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:7.8
occ:1.00
 O A:GLN156 2.3 8.2 1.0
OE1 A:GLN27 2.3 9.2 1.0
O A:HOH485 2.4 9.5 1.0
O A:HOH441 2.4 14.1 1.0
OD1 A:ASP87 2.4 7.6 1.0
O A:HOH500 2.4 9.8 1.0
OD2 A:ASP87 2.5 7.4 1.0
CG A:ASP87 2.8 7.7 1.0
C A:GLN156 3.4 7.0 1.0
CD A:GLN27 3.5 9.0 1.0
CA A:GLN156 3.9 7.4 1.0
CB A:GLN156 4.1 8.4 1.0
CA A:GLN27 4.2 8.0 1.0
CB A:ASP87 4.3 7.4 1.0
O A:HOH515 4.3 13.3 1.0
NE2 A:GLN27 4.3 10.1 1.0
OE1 A:GLN156 4.4 14.9 1.0
O A:HOH362 4.4 9.4 1.0
O A:HOH358 4.5 11.5 1.0
O A:HOH512 4.5 30.6 1.0
CB A:GLN27 4.5 8.7 1.0
OG1 A:THR86 4.5 7.6 1.0
N A:GLY157 4.6 7.5 1.0
CG A:GLN27 4.6 9.2 1.0
N A:LEU28 4.7 8.0 1.0
O A:SER26 4.7 9.7 1.0
O A:THR86 4.8 8.0 1.0
CG A:GLN156 4.9 9.2 1.0
CB A:THR86 5.0 8.4 1.0

Calcium binding site 3 out of 7 in 6xac

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Calcium binding site 3 out of 7 in the Galactose-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 Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:13.8
occ:0.50
 O A:SER73 2.3 359.6 1.0
O A:HOH510 2.4 36.3 1.0
O A:HOH489 2.5 17.6 1.0
O A:HOH508 2.6 31.1 1.0
OG A:SER76 2.6 11.6 1.0
C A:SER73 3.2 442.9 1.0
CB A:SER76 3.6 10.3 1.0
CA A:SER73 3.7 112.4 1.0
CB A:SER73 4.1 99.6 1.0
N A:ASP74 4.3 18.7 1.0
O A:HOH375 4.4 16.6 1.0
N A:SER76 4.5 8.3 1.0
CA A:SER76 4.6 9.1 1.0
O A:HOH547 4.7 23.7 1.0
O A:HOH326 4.7 15.0 1.0
CA A:ASP74 4.8 8.5 1.0

Calcium binding site 4 out of 7 in 6xac

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Calcium binding site 4 out of 7 in the Galactose-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 Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:7.8
occ:1.00
 O A:PRO82 2.3 8.4 1.0
O A:HOH329 2.4 11.3 1.0
O A:HOH400 2.4 9.4 1.0
O A:GLY64 2.4 8.7 1.0
O A:HOH410 2.4 9.2 1.0
O A:HOH391 2.4 7.8 1.0
OD1 A:ASP81 2.5 7.8 1.0
CG A:ASP81 3.5 8.0 1.0
C A:GLY64 3.5 8.1 1.0
C A:PRO82 3.5 8.6 1.0
OD2 A:ASP81 3.9 8.6 1.0
O A:HOH330 4.1 7.8 1.0
N A:PRO82 4.2 8.2 1.0
CA A:GLY64 4.2 9.0 1.0
OE1 A:GLN68 4.4 8.1 1.0
C A:ASP81 4.4 8.2 1.0
CA A:PRO82 4.4 9.8 1.0
N A:GLY64 4.4 8.2 1.0
O A:GLY83 4.4 8.2 1.0
CD A:PRO82 4.5 8.8 1.0
N A:THR65 4.5 7.8 1.0
N A:GLY83 4.5 9.0 1.0
C A:GLY83 4.5 8.0 1.0
CA A:GLY83 4.6 9.5 1.0
NE2 A:GLN68 4.6 8.0 1.0
O A:ASP81 4.7 9.6 1.0
O A:HOH536 4.7 18.7 1.0
O A:HOH416 4.7 36.6 1.0
CA A:THR65 4.7 8.6 1.0
CB A:ASP81 4.8 8.8 1.0
CB A:PRO82 4.8 13.3 1.0
OD1 A:ASP84 4.8 9.9 1.0
CA A:ASP81 4.9 7.9 1.0
CD A:GLN68 4.9 7.7 1.0
C A:LYS63 5.0 7.8 1.0

Calcium binding site 5 out of 7 in 6xac

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Calcium binding site 5 out of 7 in the Galactose-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 Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:39.7
occ:0.78
 OD1 A:ASP7 2.3 60.5 1.0
O A:THR9 2.4 38.1 1.0
OD1 A:ASP11 2.6 283.2 1.0
CG A:ASP11 3.2 175.2 1.0
OD2 A:ASP11 3.2 171.9 1.0
CG A:ASP7 3.2 69.2 1.0
OD2 A:ASP7 3.5 73.8 1.0
C A:THR9 3.5 34.1 1.0
CB A:THR9 4.2 43.0 1.0
N A:ASP7 4.2 71.5 1.0
CA A:THR9 4.2 39.8 1.0
N A:THR9 4.2 34.8 1.0
N A:ASP11 4.4 73.1 1.0
C A:PRO10 4.5 28.3 1.0
CB A:ASP11 4.5 217.0 1.0
N A:PRO10 4.5 23.1 1.0
CB A:ASP7 4.6 45.8 1.0
CA A:PRO10 4.7 23.0 1.0
O A:PRO10 4.8 33.9 1.0
CA A:ASP11 4.8 380.8 1.0
CA A:ASP7 5.0 50.4 1.0

Calcium binding site 6 out of 7 in 6xac

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Calcium binding site 6 out of 7 in the Galactose-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 Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:22.6
occ:1.00
 O A:VAL38 2.3 12.8 1.0
O A:HOH479 2.3 27.0 1.0
O A:HOH502 2.3 31.7 1.0
O A:LYS41 2.4 12.3 1.0
O A:HOH498 2.5 25.1 1.0
OH A:TYR22 2.6 12.6 1.0
CZ A:TYR22 3.5 9.7 1.0
C A:VAL38 3.5 10.9 1.0
C A:LYS41 3.6 11.6 1.0
CE2 A:TYR22 3.7 11.0 1.0
O A:HOH407 3.8 32.0 1.0
CG1 A:VAL38 4.2 12.1 1.0
CA A:GLU42 4.2 13.6 1.0
N A:GLU42 4.3 12.8 1.0
O A:HOH455 4.3 21.3 1.0
CA A:VAL38 4.4 9.4 1.0
N A:LYS41 4.4 11.3 1.0
N A:ASP39 4.4 11.1 1.0
CA A:ASP39 4.5 13.4 1.0
N A:ALA43 4.6 10.5 1.0
C A:GLU42 4.6 11.4 1.0
OE2 A:GLU42 4.6 38.2 1.0
CA A:LYS41 4.6 12.2 1.0
OE1 A:GLU20 4.7 14.8 1.0
C A:ASP39 4.7 11.8 1.0
CE1 A:TYR22 4.7 9.8 1.0
CD2 A:TYR22 4.9 9.3 1.0
CB A:VAL38 5.0 10.6 1.0
O A:ASP39 5.0 17.0 1.0

Calcium binding site 7 out of 7 in 6xac

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Calcium binding site 7 out of 7 in the Galactose-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 Galactose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:11.3
occ:0.50
 O A:HOH521 2.4 25.6 1.0
O A:HOH371 2.4 18.5 1.0
O A:HOH537 2.4 23.3 1.0
O A:HOH471 2.4 17.2 1.0
O A:HOH403 2.4 16.8 1.0
O A:HOH495 2.8 26.7 1.0
O A:SER53 4.1 8.5 1.0
CA A:GLY72 4.3 10.6 1.0
O A:HOH328 4.4 15.3 1.0
O A:HOH360 4.5 24.5 1.0
O A:GLY55 4.5 13.6 1.0
O A:PHE70 4.7 7.9 1.0
O A:HOH511 4.7 27.3 1.0
O A:GLU69 4.7 9.0 1.0
N A:GLY72 4.8 9.9 1.0
O A:HOH426 4.9 20.6 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 17:57:45 2024

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