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Calcium in PDB 6x7x: Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain

Protein crystallography data

The structure of Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x7x 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) 39.56 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.299, 50.358, 79.13, 90, 90, 90
R / Rfree (%) 15.8 / 18.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain (pdb code 6x7x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x7x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6x7x

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Calcium binding site 1 out of 9 in the Mannose-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 Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:2.7
occ:1.00
 OD1 A:ASP155 2.3 2.7 1.0
OD1 A:ASP110 2.3 2.8 1.0
O A:GLY157 2.4 3.8 1.0
O A:ASP159 2.4 3.3 0.5
O A:ASP159 2.4 2.8 0.5
OD2 A:ASP111 2.4 3.2 1.0
O3 A:BMA211 2.5 0.3 0.2
O3 A:MAN210 2.5 8.4 0.6
O3 A:BMA211 2.5 5.5 0.2
O4 A:BMA211 2.5 5.8 0.2
O4 A:MAN210 2.5 9.1 0.6
O2 A:BMA211 2.5 0.4 0.2
C3 A:BMA211 3.3 6.7 0.2
C3 A:MAN210 3.3 11.4 0.6
CG A:ASP110 3.3 3.6 1.0
C2 A:BMA211 3.3 0.8 0.2
CG A:ASP111 3.3 2.6 1.0
C4 A:BMA211 3.3 6.7 0.2
C4 A:MAN210 3.4 11.0 0.6
C3 A:BMA211 3.4 1.0 0.2
C A:GLY157 3.4 3.3 1.0
CG A:ASP155 3.5 2.4 1.0
C A:ASP159 3.6 3.8 0.5
C A:ASP159 3.6 3.3 0.5
OD2 A:ASP110 3.6 5.1 1.0
OD1 A:ASP111 3.7 3.7 1.0
N A:ASP159 3.9 4.8 0.5
N A:ASP159 3.9 4.3 0.5
N A:GLY157 3.9 3.5 1.0
C4 A:BMA211 4.1 1.6 0.2
C A:GLY158 4.2 4.4 1.0
N A:GLN156 4.2 2.9 0.4
N A:GLN156 4.2 3.0 0.6
N A:GLY158 4.3 3.0 1.0
CG A:GLN156 4.3 4.6 0.4
CA A:GLY157 4.3 3.9 1.0
CA A:ASP159 4.3 5.5 0.5
CA A:ASP159 4.3 4.5 0.5
OD2 A:ASP155 4.3 3.2 1.0
CA A:GLY158 4.4 4.0 1.0
CG A:GLN156 4.4 4.2 0.6
CB A:ASP155 4.4 2.7 1.0
CA A:ASP155 4.5 1.7 1.0
NE2 A:GLN156 4.5 4.0 0.6
N A:ASP111 4.5 2.4 1.0
C A:ASP110 4.5 2.3 1.0
CB A:ASP111 4.6 3.4 1.0
N A:TYR160 4.6 3.7 1.0
CB A:ASP110 4.6 3.3 1.0
O A:ASP110 4.7 2.6 1.0
C5 A:BMA211 4.7 8.1 0.2
C5 A:MAN210 4.7 14.0 0.6
C2 A:BMA211 4.7 7.8 0.2
C2 A:MAN210 4.7 14.3 0.6
C1 A:BMA211 4.8 1.6 0.2
C A:ASP155 4.8 2.4 1.0
CA A:TYR160 4.8 3.5 1.0
O A:GLY158 4.8 5.0 1.0
C A:GLN156 4.8 3.4 0.6
O4 A:BMA211 4.9 1.4 0.2
C A:GLN156 4.9 3.5 0.4
O A:GLN129 4.9 6.0 1.0
CA A:ASP111 4.9 3.0 1.0

Calcium binding site 2 out of 9 in 6x7x

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Calcium binding site 2 out of 9 in the Mannose-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 Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:4.5
occ:1.00
 OE1 A:GLN27 2.3 5.9 1.0
O A:HOH457 2.3 11.0 1.0
O A:GLN156 2.3 4.0 0.4
O A:GLN156 2.3 4.2 0.6
O A:HOH312 2.4 10.0 1.0
O A:HOH500 2.4 6.7 1.0
OD1 A:ASP87 2.5 3.9 1.0
OD2 A:ASP87 2.5 3.4 1.0
CG A:ASP87 2.8 3.6 1.0
C A:GLN156 3.5 3.5 0.4
C A:GLN156 3.5 3.4 0.6
CD A:GLN27 3.5 5.2 1.0
OE1 A:GLN156 4.0 5.3 0.6
CA A:GLN156 4.0 3.6 0.4
CA A:GLN156 4.0 3.6 0.6
CB A:GLN156 4.2 3.7 0.4
CA A:GLN27 4.2 3.8 1.0
CB A:GLN156 4.2 3.6 0.6
O A:HOH525 4.2 9.3 1.0
NE2 A:GLN27 4.3 5.0 1.0
CB A:ASP87 4.3 3.7 1.0
O A:HOH359 4.4 9.4 1.0
O A:HOH371 4.5 7.3 1.0
OE1 A:GLN156 4.5 5.4 0.4
CD A:GLN156 4.5 4.4 0.6
CB A:GLN27 4.5 4.9 1.0
OG1 A:THR86 4.5 4.0 1.0
CG A:GLN27 4.6 5.3 1.0
N A:GLY157 4.6 3.5 1.0
O A:SER26 4.7 5.6 1.0
N A:LEU28 4.7 4.1 1.0
O A:THR86 4.8 4.3 1.0
CG A:GLN156 4.9 4.6 0.4
CG A:GLN156 5.0 4.2 0.6
CB A:THR86 5.0 4.0 1.0
CA A:GLY157 5.0 3.9 1.0

Calcium binding site 3 out of 9 in 6x7x

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Calcium binding site 3 out of 9 in the Mannose-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 Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:13.4
occ:0.71
 O A:HOH508 2.2 24.1 1.0
O A:HOH507 2.3 32.4 1.0
O A:HOH450 2.5 14.8 1.0
O A:SER73 2.6 11.3 1.0
OG A:SER76 2.6 7.9 1.0
O A:HOH479 2.6 16.0 1.0
O A:HOH388 2.8 32.0 1.0
C A:SER73 3.5 8.8 1.0
CB A:SER76 3.6 5.8 1.0
CA A:SER73 4.0 9.9 1.0
O A:HOH381 4.4 11.7 1.0
CB A:SER73 4.5 11.0 1.0
N A:SER76 4.5 3.8 1.0
N A:ASP74 4.5 6.1 1.0
CA A:SER76 4.6 4.2 1.0
CA A:ASP74 4.8 5.7 1.0
O A:HOH545 4.9 22.6 1.0
O A:HOH321 5.0 14.5 1.0

Calcium binding site 4 out of 9 in 6x7x

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Calcium binding site 4 out of 9 in the Mannose-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 Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:3.3
occ:1.00
 O A:PRO82 2.3 5.1 1.0
O A:HOH345 2.4 7.5 1.0
O A:GLY64 2.4 5.1 1.0
O A:HOH398 2.4 6.1 1.0
O A:HOH390 2.4 3.6 1.0
O A:HOH404 2.4 4.8 1.0
OD1 A:ASP81 2.5 4.3 1.0
CG A:ASP81 3.5 4.3 1.0
C A:GLY64 3.5 4.9 1.0
C A:PRO82 3.5 5.1 1.0
OD2 A:ASP81 3.9 4.2 1.0
O A:HOH353 4.1 3.2 1.0
N A:PRO82 4.2 4.2 1.0
CA A:GLY64 4.3 4.9 1.0
O A:HOH543 4.4 36.0 1.0
OE1 A:GLN68 4.4 3.2 1.0
N A:GLY64 4.4 4.2 1.0
CA A:PRO82 4.4 5.1 1.0
C A:ASP81 4.4 4.1 1.0
O A:GLY83 4.5 4.6 1.0
C A:GLY83 4.5 3.6 1.0
N A:GLY83 4.5 5.1 1.0
N A:THR65 4.5 3.8 1.0
CD A:PRO82 4.5 5.2 1.0
CA A:GLY83 4.6 4.5 1.0
NE2 A:GLN68 4.6 3.7 1.0
O A:HOH541 4.7 37.5 1.0
O A:ASP81 4.7 4.5 1.0
O A:HOH540 4.7 17.0 1.0
CA A:THR65 4.7 4.4 1.0
CB A:ASP81 4.8 4.3 1.0
OD1 A:ASP84 4.8 7.5 1.0
CB A:PRO82 4.8 6.5 1.0
C A:LYS63 4.9 3.6 1.0
CA A:ASP81 5.0 3.7 1.0
CD A:GLN68 5.0 3.2 1.0
CG A:PRO82 5.0 7.0 1.0

Calcium binding site 5 out of 9 in 6x7x

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Calcium binding site 5 out of 9 in the Mannose-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 Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:23.1
occ:0.74
 O A:HOH309 2.2 39.2 1.0
OD1 A:ASP11 2.4 19.0 1.0
OE1 A:GLN5 2.5 34.4 1.0
O A:THR9 2.6 24.2 1.0
OD2 A:ASP11 2.7 20.8 1.0
O A:HOH302 2.8 37.9 1.0
OD1 A:ASP7 2.9 39.9 1.0
CG A:ASP11 2.9 19.0 1.0
OG1 A:THR9 3.1 31.6 1.0
CD A:GLN5 3.4 35.2 1.0
NE2 A:GLN5 3.6 34.3 1.0
C A:THR9 3.7 24.3 1.0
OD1 A:ASP6 3.9 58.7 1.0
CG A:ASP7 4.0 39.6 1.0
N A:THR9 4.3 30.0 1.0
N A:ASP7 4.3 41.4 1.0
CB A:THR9 4.3 30.4 1.0
CA A:THR9 4.3 28.3 1.0
CB A:ASP11 4.3 16.4 1.0
N A:ASP11 4.6 15.1 1.0
N A:ASP6 4.6 47.0 1.0
OD2 A:ASP7 4.6 40.2 1.0
C A:PRO10 4.7 16.9 1.0
O A:ASP7 4.7 35.9 1.0
C A:ASP7 4.7 36.2 1.0
CA A:ASP7 4.8 38.6 1.0
N A:PRO10 4.8 20.4 1.0
CG A:GLN5 4.8 37.5 1.0
CA A:ASP11 4.9 13.9 1.0
O A:PRO10 4.9 17.4 1.0
CB A:ASP7 4.9 38.9 1.0
CA A:PRO10 5.0 17.8 1.0

Calcium binding site 6 out of 9 in 6x7x

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Calcium binding site 6 out of 9 in the Mannose-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 Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:14.3
occ:0.72
 O A:HOH502 2.3 25.7 1.0
O A:HOH504 2.3 20.8 1.0
O A:VAL38 2.4 7.3 1.0
O A:LYS41 2.4 8.0 1.0
O A:HOH494 2.4 20.6 1.0
OH A:TYR22 2.6 8.0 1.0
CZ A:TYR22 3.5 5.8 1.0
C A:LYS41 3.6 7.9 1.0
C A:VAL38 3.6 6.7 1.0
CE2 A:TYR22 3.7 5.8 1.0
O A:HOH487 3.7 25.0 1.0
CG1 A:VAL38 4.2 6.9 1.0
CA A:GLU42 4.2 9.4 1.0
N A:GLU42 4.3 8.4 1.0
O A:HOH425 4.3 18.2 1.0
N A:LYS41 4.4 7.7 1.0
CA A:VAL38 4.5 5.6 1.0
N A:ASP39 4.5 7.4 1.0
CA A:ASP39 4.6 9.5 1.0
OE2 A:GLU42 4.6 24.7 1.0
O A:HOH491 4.6 28.9 1.0
N A:ALA43 4.6 7.1 1.0
C A:ASP39 4.6 8.6 1.0
C A:GLU42 4.6 7.8 1.0
CA A:LYS41 4.6 8.1 1.0
OE1 A:GLU20 4.7 11.8 1.0
CE1 A:TYR22 4.7 4.5 1.0
O A:ASP39 4.9 10.5 1.0
CD2 A:TYR22 5.0 4.2 1.0

Calcium binding site 7 out of 9 in 6x7x

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Calcium binding site 7 out of 9 in the Mannose-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 Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:12.3
occ:0.70
 O A:HOH470 2.3 17.8 1.0
O A:HOH548 2.3 23.2 1.0
O A:HOH528 2.4 22.8 1.0
O A:HOH366 2.4 17.0 1.0
O A:HOH407 2.5 13.9 1.0
O A:HOH467 2.7 30.8 1.0
O A:SER53 4.1 3.5 1.0
CA A:GLY72 4.2 6.7 1.0
O A:HOH564 4.4 34.5 1.0
O A:HOH387 4.4 12.7 1.0
O A:GLY55 4.5 8.2 1.0
O A:HOH389 4.6 18.9 1.0
O A:PHE70 4.7 3.2 1.0
O A:HOH431 4.7 14.1 1.0
O A:GLU69 4.7 5.1 1.0
N A:GLY72 4.8 5.1 1.0

Calcium binding site 8 out of 9 in 6x7x

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Calcium binding site 8 out of 9 in the Mannose-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 8 of Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:24.0
occ:0.60
 O A:HOH442 2.3 33.1 1.0
O A:SER172 2.4 13.8 1.0
O A:HOH496 2.4 14.0 1.0
O A:HOH539 2.7 27.5 1.0
C A:SER172 3.5 12.2 1.0
CA A:SER172 4.3 13.7 1.0
N A:THR173 4.4 10.1 1.0
CA A:THR173 4.5 8.4 1.0
O A:HOH497 4.5 39.1 1.0
O A:GLY171 4.5 12.2 1.0
OG A:SER172 4.8 19.3 1.0

Calcium binding site 9 out of 9 in 6x7x

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Calcium binding site 9 out of 9 in the Mannose-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 9 of Mannose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca213

b:22.9
occ:0.50
 O A:ALA168 2.2 9.4 1.0
O A:HOH429 2.4 15.8 1.0
O A:HOH511 2.4 33.7 1.0
C A:ALA168 3.4 8.4 1.0
CA A:ASP169 4.3 9.0 1.0
N A:ASP169 4.3 7.5 1.0
CA A:ALA168 4.4 7.5 1.0
CB A:ALA168 4.4 8.2 1.0
O A:HOH451 4.4 53.4 1.0
O A:THR102 4.6 7.6 1.0
O A:HOH519 4.9 24.8 1.0
CB A:ASP169 4.9 9.8 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 17:50:57 2024

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