Calcium in PDB 6mlt: Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1

Protein crystallography data

The structure of Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1, PDB code: 6mlt was solved by K.Kaus, A.Biester, E.Chupp, K.Lu, C.Vidsudharomn, R.Olson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.951, 70.951, 303.957, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 17.6

Other elements in 6mlt:

The structure of Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1 also contains other interesting chemical elements:

Sodium (Na) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1 (pdb code 6mlt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1, PDB code: 6mlt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6mlt

Go back to Calcium Binding Sites List in 6mlt
Calcium binding site 1 out of 2 in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:32.2
occ:1.00
OD1 A:ASP63 2.2 32.2 1.0
O A:HOH1116 2.2 35.7 1.0
O A:LYS69 2.3 27.8 1.0
OD1 A:ASP67 2.4 45.3 1.0
OD1 A:ASN65 2.4 36.9 1.0
OD1 A:ASP74 2.5 24.3 1.0
OD2 A:ASP74 2.6 24.6 1.0
CG A:ASP74 2.9 23.9 1.0
CG A:ASP67 3.2 43.2 1.0
CG A:ASP63 3.3 31.9 1.0
CG A:ASN65 3.3 40.3 1.0
HA A:ASP63 3.3 37.9 1.0
H A:ASP67 3.4 49.0 1.0
C A:LYS69 3.4 25.8 1.0
HD21 A:ASN65 3.4 53.2 1.0
H A:LYS69 3.5 42.3 1.0
H A:ASN65 3.5 50.1 1.0
OD2 A:ASP67 3.6 46.3 1.0
HA A:ILE70 3.6 30.5 1.0
ND2 A:ASN65 3.7 44.3 1.0
CA A:ASP63 4.0 31.6 1.0
H A:GLY66 4.1 76.9 1.0
H A:ASP64 4.1 37.0 1.0
OD2 A:ASP63 4.1 31.5 1.0
H A:ASP71 4.1 37.9 1.0
CB A:ASP63 4.1 32.8 1.0
N A:LYS69 4.1 35.2 1.0
N A:ASP67 4.2 40.9 1.0
N A:ASN65 4.2 41.8 1.0
CA A:LYS69 4.2 28.8 1.0
HB2 A:ASP63 4.2 39.4 1.0
N A:ILE70 4.3 25.7 1.0
CB A:ASP74 4.4 24.7 1.0
N A:ASP64 4.4 30.8 1.0
CA A:ILE70 4.4 25.4 1.0
C A:ASP63 4.4 34.0 1.0
N A:GLY66 4.5 64.0 1.0
CB A:ASP67 4.5 37.3 1.0
HD22 A:ASN65 4.5 53.2 1.0
CB A:ASN65 4.5 42.3 1.0
OD1 A:ASP71 4.5 43.4 1.0
CB A:LYS69 4.6 29.8 1.0
HB3 A:ASP67 4.7 44.7 1.0
CA A:ASN65 4.7 48.4 1.0
H A:GLY68 4.7 42.0 1.0
N A:ASP71 4.8 31.6 1.0
CA A:ASP67 4.8 35.4 1.0
HB3 A:ASP74 4.8 29.7 1.0
C A:ASN65 4.8 59.7 1.0
HB2 A:ASP74 4.8 29.7 1.0
HB3 A:ASN65 4.8 50.8 1.0
HA A:ASP74 4.9 31.5 1.0
N A:GLY68 4.9 35.0 1.0
HG12 A:ILE70 4.9 31.5 1.0
HB3 A:ASP63 5.0 39.4 1.0
C A:ASP67 5.0 34.0 1.0
H A:ASP74 5.0 35.9 1.0

Calcium binding site 2 out of 2 in 6mlt

Go back to Calcium Binding Sites List in 6mlt
Calcium binding site 2 out of 2 in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:22.0
occ:1.00
O A:VAL75 2.2 21.5 1.0
OD1 A:ASN62 2.3 23.3 1.0
O A:HOH1121 2.3 19.6 1.0
OD1 A:ASP77 2.4 18.6 1.0
OD2 A:ASP64 2.5 22.7 1.0
OD2 A:ASP77 2.5 19.6 1.0
O A:HOH1114 2.5 19.5 1.0
CG A:ASP77 2.8 19.2 1.0
CG A:ASP64 3.4 24.8 1.0
C A:VAL75 3.4 20.8 1.0
CG A:ASN62 3.4 22.1 1.0
HB A:VAL75 3.5 25.5 1.0
H A:ASN62 3.5 28.3 1.0
OD1 A:ASP64 3.6 25.2 1.0
H A:VAL75 3.6 25.1 1.0
H A:LEU61 3.8 26.0 1.0
H A:GLY99 3.9 25.1 1.0
HD21 A:ASN62 3.9 28.2 1.0
HD11 A:LEU105 4.1 26.8 1.0
N A:VAL75 4.1 20.9 1.0
CA A:VAL75 4.1 21.8 1.0
ND2 A:ASN62 4.1 23.5 1.0
O A:ASN62 4.1 21.4 1.0
HB3 A:ASP74 4.2 29.7 1.0
N A:ASN62 4.2 23.6 1.0
CB A:VAL75 4.2 21.2 1.0
CB A:ASP77 4.3 19.5 1.0
OE1 A:GLN60 4.4 19.9 1.0
HA A:SER98 4.4 29.6 1.0
HA A:ALA76 4.4 22.2 1.0
C A:ALA76 4.4 19.7 1.0
N A:ALA76 4.5 20.6 1.0
HG12 A:VAL75 4.5 26.5 1.0
HA A:GLN60 4.5 23.0 1.0
CB A:ASN62 4.6 21.1 1.0
N A:ASP77 4.6 18.2 1.0
N A:LEU61 4.6 21.7 1.0
O A:ALA76 4.7 18.2 1.0
C A:ASN62 4.7 23.8 1.0
N A:GLY99 4.7 20.9 1.0
HB2 A:ASP77 4.7 23.4 1.0
CA A:ALA76 4.7 18.4 1.0
HD13 A:LEU105 4.7 26.8 1.0
HD21 A:LEU105 4.7 28.9 1.0
CA A:ASN62 4.7 22.3 1.0
HG23 A:VAL100 4.7 36.7 1.0
HB3 A:ASP77 4.7 23.4 1.0
CB A:ASP64 4.8 26.6 1.0
HA A:ASP77 4.8 21.7 1.0
HB3 A:ASN62 4.8 25.4 1.0
OG A:SER98 4.8 26.4 1.0
CD1 A:LEU105 4.8 22.3 1.0
CA A:ASP77 4.8 18.1 1.0
HB2 A:ASP64 4.9 32.0 1.0
H A:ASP77 4.9 21.8 1.0
HB2 A:LEU61 4.9 24.5 1.0
CG1 A:VAL75 4.9 22.1 1.0
H A:ASP64 5.0 37.0 1.0
HD22 A:ASN62 5.0 28.2 1.0

Reference:

K.Kaus, A.Biester, E.Chupp, J.Lu, C.Visudharomn, R.Olson. The 1.9 Angstrom Crystal Structure of the Extracellular Matrix Protein BAP1 Fromvibrio Choleraeprovides Insights Into Bacterial Biofilm Adhesion. J.Biol.Chem. V. 294 14499 2019.
ISSN: ESSN 1083-351X
PubMed: 31439670
DOI: 10.1074/JBC.RA119.008335
Page generated: Sat Dec 12 07:03:31 2020

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