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Calcium in PDB 6xaq: Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

Protein crystallography data

The structure of Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6xaq 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) 42.57 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.107, 50.477, 79.239, 90, 90, 90
R / Rfree (%) 16.3 / 16.7

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 6xaq

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Calcium binding site 1 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:5.8
occ:1.00
 HO4 A:GYP307 2.0 8.5 1.0
HO3 A:GYP307 2.0 8.6 1.0
OD1 A:ASP155 2.3 5.6 1.0
OD1 A:ASP110 2.3 6.2 1.0
O A:GLY157 2.3 6.5 1.0
O A:ASP159 2.4 6.1 1.0
OD2 A:ASP111 2.4 5.8 1.0
O3 A:GYP307 2.5 7.2 1.0
O4 A:GYP307 2.5 7.1 1.0
CG A:ASP110 3.3 6.8 1.0
H A:GLY157 3.3 8.4 1.0
C3 A:GYP307 3.3 8.0 1.0
CG A:ASP111 3.3 5.1 1.0
C4 A:GYP307 3.4 8.0 1.0
C A:GLY157 3.4 6.5 1.0
H3 A:GYP307 3.5 9.6 1.0
CG A:ASP155 3.5 5.4 1.0
HG3 A:GLN156 3.5 9.8 1.0
C A:ASP159 3.5 6.9 1.0
H4 A:GYP307 3.6 9.6 1.0
OD2 A:ASP110 3.7 7.6 1.0
OD1 A:ASP111 3.7 6.4 1.0
H A:GLN156 3.7 6.2 1.0
HE21 A:GLN156 3.7 12.2 1.0
H A:ASP159 3.7 9.4 0.4
HA A:ASP155 3.7 6.5 1.0
H A:ASP159 3.7 9.4 0.6
N A:ASP159 3.8 7.9 1.0
N A:GLY157 3.9 7.0 1.0
HA A:TYR160 4.2 7.9 1.0
C A:GLY158 4.2 7.2 1.0
N A:GLN156 4.2 5.2 1.0
HA3 A:GLY158 4.2 9.8 1.0
N A:GLY158 4.3 6.5 1.0
CA A:GLY157 4.3 7.6 1.0
CA A:ASP159 4.3 7.5 0.6
CA A:ASP159 4.3 7.6 0.4
OD2 A:ASP155 4.3 6.0 1.0
CA A:ASP155 4.4 5.4 1.0
CB A:ASP155 4.4 5.5 1.0
N A:ASP111 4.4 5.8 1.0
HB3 A:TYR160 4.4 8.7 1.0
C A:ASP110 4.5 5.2 1.0
CA A:GLY158 4.5 8.2 1.0
CG A:GLN156 4.5 8.1 1.0
H A:ASP111 4.5 7.0 1.0
HB2 A:ASP155 4.6 6.7 1.0
NE2 A:GLN156 4.6 10.2 1.0
CB A:ASP111 4.6 6.2 1.0
N A:TYR160 4.6 7.1 1.0
CB A:ASP110 4.6 6.5 1.0
O A:ASP110 4.6 5.4 1.0
HB2 A:ASP159 4.7 11.5 0.4
C A:ASP155 4.7 6.4 1.0
C2 A:GYP307 4.7 12.5 1.0
HB2 A:ASP111 4.7 7.4 1.0
HA A:ASP111 4.7 6.6 1.0
C5 A:GYP307 4.7 12.4 1.0
HB2 A:ASP159 4.8 11.4 0.6
CA A:TYR160 4.8 6.6 1.0
HB3 A:ASP110 4.8 7.9 1.0
O A:GLY158 4.8 7.9 1.0
HG2 A:GLN156 4.8 9.8 1.0
HA2 A:GLY157 4.8 9.1 1.0
H2 A:GYP307 4.9 15.1 1.0
C A:GLN156 4.9 6.9 1.0
H5 A:GYP307 4.9 14.8 1.0
CA A:ASP111 4.9 5.5 1.0
O A:GLN129 4.9 8.4 1.0
HD1 A:TYR160 4.9 7.5 1.0
HA3 A:GLY157 5.0 9.1 1.0

Calcium binding site 2 out of 8 in 6xaq

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Calcium binding site 2 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:6.8
occ:1.00
 OE1 A:GLN27 2.3 7.8 1.0
O A:GLN156 2.3 7.1 1.0
O A:HOH565 2.3 8.9 1.0
OD1 A:ASP87 2.4 6.2 1.0
O A:HOH594 2.4 8.2 1.0
O A:HOH483 2.4 11.3 1.0
OD2 A:ASP87 2.5 6.8 1.0
CG A:ASP87 2.8 6.1 1.0
HA A:GLN27 3.2 9.5 1.0
C A:GLN156 3.4 6.9 1.0
HB2 A:GLN156 3.5 7.8 1.0
CD A:GLN27 3.5 7.7 1.0
HA A:GLN156 3.7 7.0 1.0
HG1 A:THR86 3.9 7.9 1.0
CA A:GLN156 4.0 5.8 1.0
HB2 A:GLN27 4.0 9.7 1.0
H A:LEU28 4.0 8.9 1.0
OE1 A:GLN156 4.1 9.7 1.0
HE22 A:GLN27 4.1 10.1 1.0
CA A:GLN27 4.2 7.9 1.0
CB A:GLN156 4.2 6.5 1.0
CB A:ASP87 4.3 6.5 1.0
NE2 A:GLN27 4.3 8.4 1.0
HB A:THR86 4.4 8.3 1.0
HA3 A:GLY157 4.4 9.1 1.0
CB A:GLN27 4.4 8.0 1.0
O A:HOH470 4.4 8.3 1.0
CD A:GLN156 4.5 9.3 1.0
OG1 A:THR86 4.5 6.6 1.0
N A:GLY157 4.5 7.0 1.0
CG A:GLN27 4.6 8.5 1.0
O A:HOH466 4.6 9.5 1.0
HB3 A:ASP87 4.7 7.8 1.0
O A:SER26 4.7 9.3 1.0
N A:LEU28 4.7 7.4 1.0
O A:THR86 4.8 6.6 1.0
HB2 A:ASP87 4.8 7.8 1.0
HA A:ASP87 4.9 7.3 1.0
CG A:GLN156 4.9 8.1 1.0
CB A:THR86 4.9 6.9 1.0
HB3 A:GLN156 4.9 7.8 1.0
CA A:GLY157 4.9 7.6 1.0
N A:GLN27 5.0 7.2 1.0

Calcium binding site 3 out of 8 in 6xaq

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Calcium binding site 3 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:9.7
occ:0.61
 O A:SER73 2.2 12.3 1.0
O A:HOH603 2.3 19.0 1.0
O A:HOH591 2.3 20.9 1.0
O A:HOH549 2.6 14.2 1.0
O A:HOH496 2.6 18.7 1.0
OG A:SER76 2.6 9.3 1.0
O A:HOH532 2.6 13.5 1.0
C A:SER73 3.3 11.8 1.0
HA A:SER73 3.5 14.6 1.0
HB3 A:SER76 3.5 9.7 1.0
CB A:SER76 3.6 8.1 1.0
H A:SER76 3.7 7.7 1.0
CA A:SER73 3.9 12.2 1.0
HB2 A:SER73 4.0 14.5 1.0
HB2 A:SER76 4.3 9.7 1.0
HA A:ASP74 4.3 8.6 1.0
N A:ASP74 4.4 8.2 1.0
N A:SER76 4.4 6.4 1.0
O A:HOH647 4.5 23.2 0.5
CB A:SER73 4.5 12.1 1.0
CA A:SER76 4.6 7.0 1.0
HG23 A:THR77 4.7 10.9 1.0
CA A:ASP74 4.8 7.2 1.0
O A:HOH440 4.9 13.2 1.0
C A:ASP74 5.0 7.4 1.0

Calcium binding site 4 out of 8 in 6xaq

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Calcium binding site 4 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:6.1
occ:1.00
 O A:HOH425 2.3 10.0 1.0
O A:PRO82 2.4 6.7 1.0
O A:HOH514 2.4 7.5 1.0
O A:GLY64 2.4 6.7 1.0
OD1 A:ASP81 2.4 7.3 1.0
O A:HOH523 2.5 7.7 1.0
O A:HOH501 2.5 6.3 1.0
CG A:ASP81 3.5 6.8 1.0
C A:GLY64 3.5 6.6 1.0
C A:PRO82 3.5 7.3 1.0
HD2 A:PRO82 3.8 8.4 1.0
HE22 A:GLN68 3.8 8.2 1.0
OD2 A:ASP81 3.9 7.5 1.0
HA A:THR65 4.0 8.0 1.0
HA2 A:GLY64 4.1 9.0 1.0
O A:HOH441 4.1 6.1 1.0
HA2 A:GLY83 4.2 9.3 1.0
N A:PRO82 4.2 7.3 1.0
CA A:GLY64 4.2 7.5 1.0
HB2 A:PRO82 4.3 12.4 1.0
O A:HOH642 4.4 31.7 1.0
C A:ASP81 4.4 7.7 1.0
OE1 A:GLN68 4.4 6.2 1.0
CA A:PRO82 4.4 7.0 1.0
O A:GLY83 4.4 7.0 1.0
N A:GLY64 4.4 6.7 1.0
CD A:PRO82 4.5 7.0 1.0
H A:GLY64 4.5 8.1 0.4
N A:GLY83 4.5 7.4 1.0
N A:THR65 4.5 6.7 1.0
C A:GLY83 4.5 6.8 1.0
H A:GLY64 4.5 8.1 0.6
CA A:GLY83 4.6 7.7 1.0
NE2 A:GLN68 4.6 6.8 1.0
O A:HOH590 4.6 32.3 1.0
O A:ASP81 4.7 8.5 1.0
HG22 A:THR65 4.7 11.9 1.0
CA A:THR65 4.7 6.6 1.0
CB A:ASP81 4.8 7.1 1.0
O A:HOH435 4.8 30.3 1.0
O A:HOH639 4.8 14.7 1.0
CB A:PRO82 4.8 10.3 1.0
OD1 A:ASP84 4.8 8.5 1.0
HA A:ASP81 4.8 8.6 1.0
CA A:ASP81 4.9 7.1 1.0
CD A:GLN68 4.9 6.3 1.0
C A:LYS63 5.0 6.8 0.6

Calcium binding site 5 out of 8 in 6xaq

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Calcium binding site 5 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:18.3
occ:0.51
 O A:HOH578 2.4 28.1 1.0
O A:VAL38 2.5 11.7 1.0
O A:HOH602 2.6 32.0 1.0
O A:LYS41 2.6 10.9 1.0
OH A:TYR22 2.7 12.0 1.0
HH A:TYR22 3.1 14.4 1.0
HE2 A:TYR22 3.3 10.9 1.0
HG13 A:VAL38 3.5 12.1 1.0
O A:HOH527 3.6 23.2 1.0
CZ A:TYR22 3.7 9.2 1.0
C A:VAL38 3.7 10.9 1.0
C A:LYS41 3.7 10.6 1.0
HA A:GLU42 3.8 16.3 1.0
CE2 A:TYR22 3.8 9.1 1.0
HA A:ASP39 3.9 14.2 0.6
HG12 A:VAL38 3.9 12.1 1.0
H A:LYS41 3.9 13.6 1.0
CG1 A:VAL38 4.1 10.1 1.0
HA A:VAL38 4.2 11.1 1.0
O A:HOH529 4.3 24.3 1.0
HA A:ASP39 4.3 15.5 0.5
H A:ALA43 4.4 12.4 1.0
CA A:GLU42 4.4 13.6 1.0
N A:GLU42 4.5 11.7 1.0
CA A:VAL38 4.5 9.2 1.0
CA A:ASP39 4.6 11.9 0.6
N A:LYS41 4.6 11.3 1.0
N A:ASP39 4.6 9.6 1.0
N A:ALA43 4.7 10.3 1.0
OE1 A:GLU20 4.7 13.4 1.0
CA A:ASP39 4.8 12.9 0.5
C A:GLU42 4.8 10.3 1.0
C A:ASP39 4.8 12.2 1.0
CA A:LYS41 4.8 11.3 1.0
HG11 A:VAL38 4.8 12.1 1.0
CE1 A:TYR22 4.9 8.5 1.0
OE2 A:GLU42 4.9 42.9 1.0
O A:ASP39 5.0 14.5 1.0
CB A:VAL38 5.0 9.5 1.0

Calcium binding site 6 out of 8 in 6xaq

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Calcium binding site 6 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:9.6
occ:0.66
 O A:HOH637 2.4 18.1 1.0
O A:HOH484 2.4 13.3 1.0
O A:HOH550 2.4 12.9 1.0
O A:HOH608 2.4 20.4 1.0
O A:HOH511 2.5 11.9 1.0
O A:HOH582 2.6 18.1 1.0
HA3 A:GLY72 3.5 11.2 1.0
O A:SER53 4.0 7.3 1.0
O A:HOH659 4.4 31.0 1.0
CA A:GLY72 4.4 9.3 1.0
H A:SER73 4.4 10.8 1.0
O A:GLY55 4.4 10.0 1.0
HA A:TYR54 4.5 7.4 1.0
H A:GLY55 4.5 9.3 1.0
O A:HOH477 4.5 19.3 1.0
O A:HOH531 4.6 12.8 1.0
HA2 A:GLY72 4.7 11.2 1.0
O A:PHE70 4.7 5.8 1.0
O A:GLU69 4.8 7.1 1.0
N A:GLY72 4.9 7.9 1.0
N A:GLY55 5.0 7.8 1.0

Calcium binding site 7 out of 8 in 6xaq

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Calcium binding site 7 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca308

b:14.9
occ:0.47
 O A:HOH542 2.4 33.5 1.0
O A:HOH588 2.5 18.2 1.0
OG A:SER130 2.7 13.9 1.0
HG A:SER130 3.2 16.7 1.0
H A:SER130 3.4 10.8 1.0
HB3 A:SER130 3.5 13.2 1.0
CB A:SER130 3.7 10.9 1.0
N A:SER130 4.2 9.0 1.0
HB2 A:SER130 4.4 13.2 1.0
O A:HOH538 4.4 19.1 1.0
CA A:SER130 4.6 9.1 1.0
O A:HOH631 4.6 31.0 1.0
O5 A:GYP307 4.8 14.6 1.0
HA A:GLN129 4.8 10.1 1.0
H1 A:GYP307 4.9 17.9 1.0
H62 A:GYP307 4.9 17.3 1.0
O A:HOH467 5.0 16.6 1.0

Calcium binding site 8 out of 8 in 6xaq

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Calcium binding site 8 out of 8 in the Alpha-Methyl-Glucose-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 Alpha-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca309

b:30.5
occ:0.43
 O A:SER172 2.2 12.2 0.6
O A:HOH459 2.3 26.9 0.5
O A:HOH502 2.4 27.2 1.0
O A:HOH459 2.4 22.2 0.5
O A:HOH620 2.6 23.7 1.0
O A:SER172 2.6 12.6 0.4
C A:SER172 3.5 12.7 0.6
C A:SER172 3.6 14.9 0.4
HA A:THR173 3.7 14.5 1.0
O A:HOH555 3.7 34.5 1.0
HA A:SER172 3.9 15.4 0.6
HA A:SER172 4.1 17.1 0.4
CA A:SER172 4.3 12.8 0.6
N A:THR173 4.4 12.3 1.0
CA A:SER172 4.4 14.2 0.4
HG22 A:THR173 4.4 18.9 1.0
CA A:THR173 4.5 12.0 1.0
O A:GLY171 4.5 14.5 1.0
HD1 A:TYR174 4.6 11.2 1.0
HG A:SER172 4.9 23.6 0.4
HB3 A:SER172 5.0 17.6 0.6

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: Wed Jul 9 19:57:47 2025

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