Atomistry » Calcium » PDB 6x6m-6xqn » 6x7x
Atomistry »
  Calcium »
    PDB 6x6m-6xqn »
      6x7x »

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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Go back to Calcium Binding Sites List in 6x7x
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy