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

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

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

Calcium

(Ca)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1, PDB code: 6mlt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1003 b:21.1 occ:1.00 O A:LEU131 2.3 24.8 1.0 OE2 A:GLU133 2.3 33.9 1.0 OD1 A:ASP127 2.3 29.8 1.0 OD1 A:ASP129 2.3 30.4 1.0 OD1 A:ASP125 2.4 28.1 1.0 OE1 A:GLU133 2.5 28.8 1.0 CD A:GLU133 2.7 30.8 1.0 H A:LEU131 3.1 36.1 1.0 H A:ASP129 3.2 39.8 1.0 HA A:ASP125 3.2 28.7 1.0 H A:ASP127 3.2 30.3 1.0 CG A:ASP129 3.2 31.0 1.0 CG A:ASP125 3.3 31.2 1.0 C A:LEU131 3.4 23.2 1.0 HZ3 A:LYS154 3.4 49.5 1.0 CG A:ASP127 3.4 29.9 1.0 H A:LEU126 3.5 30.0 1.0 HB2 A:LEU131 3.6 34.1 1.0 OD2 A:ASP129 3.7 32.3 1.0 H A:GLY128 3.8 32.9 1.0 N A:LEU131 3.8 30.0 1.0 CA A:ASP125 3.9 23.9 1.0 HZ1 A:LYS154 3.9 49.5 1.0 N A:LEU126 4.0 25.0 1.0 N A:ASP129 4.0 33.1 1.0 OD2 A:ASP127 4.0 29.9 1.0 CA A:LEU131 4.0 25.4 1.0 N A:ASP127 4.0 25.2 1.0 NZ A:LYS154 4.1 41.3 1.0 OD2 A:ASP125 4.1 31.6 1.0 CB A:ASP125 4.1 28.4 1.0 C A:ASP125 4.2 24.9 1.0 CG A:GLU133 4.2 26.4 1.0 CB A:LEU131 4.3 28.4 1.0 N A:GLY128 4.3 27.4 1.0 CB A:ASP129 4.3 28.6 1.0 H A:GLY130 4.3 34.4 1.0 HB2 A:ASP125 4.4 34.1 1.0 N A:ILE132 4.5 22.2 1.0 HZ2 A:LYS154 4.5 49.5 1.0 HB3 A:ASP129 4.5 34.4 1.0 H A:GLU133 4.5 24.4 1.0 HA A:ILE132 4.5 26.9 1.0 O A:HOH1416 4.5 41.8 1.0 CA A:ASP129 4.6 30.4 1.0 HG3 A:GLU133 4.6 31.8 1.0 N A:GLY130 4.6 28.6 1.0 CB A:ASP127 4.6 28.6 1.0 O A:HOH1312 4.6 30.6 1.0 CA A:ASP127 4.7 26.6 1.0 N A:GLU133 4.7 20.4 1.0 HG2 A:GLU133 4.7 31.8 1.0 C A:ILE132 4.7 21.8 1.0 C A:ASP127 4.7 27.4 1.0 C A:ASP129 4.8 30.1 1.0 HB3 A:LEU131 4.8 34.1 1.0 HB2 A:GLU133 4.8 27.5 1.0 CA A:ILE132 4.8 22.4 1.0 HA A:LEU131 5.0 30.5 1.0 HB3 A:ASP127 5.0 34.4 1.0 HB3 A:ASP125 5.0 34.1 1.0 C A:GLY130 5.0 37.4 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1004 b:27.1 occ:1.00 O A:ASN180 2.3 27.8 1.0 OD1 A:ASN176 2.3 31.4 1.0 OE1 A:GLU182 2.4 27.6 1.0 OD1 A:ASP174 2.4 28.4 1.0 OE2 A:GLU182 2.4 30.5 1.0 OD1 A:ASP178 2.5 32.8 1.0 CD A:GLU182 2.7 29.5 1.0 H A:ASP178 3.2 36.0 1.0 CG A:ASP174 3.2 31.2 1.0 H A:ASN176 3.3 25.0 1.0 HA A:ASP174 3.3 26.6 1.0 C A:ASN180 3.3 30.5 1.0 CG A:ASP178 3.3 34.4 1.0 CG A:ASN176 3.4 36.1 1.0 H A:ASN180 3.4 40.6 1.0 HB2 A:ASN180 3.5 56.9 1.0 H A:ILE175 3.6 24.0 1.0 HD21 A:ASN176 3.7 53.2 1.0 OD2 A:ASP178 3.7 35.6 1.0 O A:HOH1252 3.8 39.4 1.0 H A:GLY177 3.8 31.2 1.0 N A:ASN180 3.9 33.8 1.0 OD2 A:ASP174 3.9 33.6 1.0 ND2 A:ASN176 3.9 44.3 1.0 CA A:ASP174 4.0 22.1 1.0 CA A:ASN180 4.0 36.2 1.0 N A:ASP178 4.0 30.0 1.0 N A:ILE175 4.1 19.9 1.0 CB A:ASP174 4.1 27.2 1.0 N A:ASN176 4.1 20.8 1.0 CB A:ASN180 4.2 47.4 1.0 HA A:ILE181 4.2 28.3 1.0 H A:GLY179 4.2 42.1 1.0 CG A:GLU182 4.2 23.3 1.0 C A:ASP174 4.3 22.3 1.0 N A:GLY177 4.3 25.9 1.0 HB2 A:ASP174 4.3 32.6 1.0 N A:ILE181 4.3 25.1 1.0 CB A:ASP178 4.5 33.8 1.0 HG12 A:ILE175 4.5 30.6 1.0 H A:GLU182 4.5 24.4 1.0 O A:HOH1302 4.5 49.2 1.0 N A:GLY179 4.5 35.1 1.0 HG2 A:GLU182 4.6 28.0 1.0 CB A:ASN176 4.6 26.9 1.0 CA A:ASP178 4.6 33.0 1.0 HG3 A:GLU182 4.7 28.0 1.0 CA A:ILE181 4.7 23.6 1.0 CA A:ASN176 4.7 22.7 1.0 HB3 A:ASP178 4.7 40.6 1.0 HB3 A:ASN180 4.7 56.9 1.0 N A:GLU182 4.7 20.3 1.0 C A:ASN176 4.8 23.4 1.0 C A:ASP178 4.8 36.6 1.0 HD22 A:ASN176 4.8 53.2 1.0 C A:ILE181 4.8 23.0 1.0 C A:GLY179 4.9 35.7 1.0 HD22 A:ASN180 4.9 89.5 1.0 HA A:ASN180 4.9 43.4 1.0 HB2 A:GLU182 4.9 23.7 1.0 HB3 A:ASP174 4.9 32.6 1.0 C A:GLY177 5.0 30.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1005 b:23.9 occ:1.00 O A:GLN216 2.2 23.6 1.0 OD1 A:ASP210 2.3 27.9 1.0 OD1 A:ASP214 2.3 30.5 1.0 OD1 A:ASN212 2.4 31.9 1.0 OE2 A:GLU218 2.5 31.7 1.0 OE1 A:GLU218 2.6 30.7 1.0 CD A:GLU218 2.9 31.7 1.0 HA A:ASP210 3.2 29.8 1.0 H A:ASN212 3.2 30.6 1.0 H A:ASP214 3.2 36.0 1.0 CG A:ASP214 3.2 33.1 1.0 CG A:ASP210 3.3 28.0 1.0 C A:GLN216 3.3 23.9 1.0 CG A:ASN212 3.4 32.2 1.0 HB2 A:GLN216 3.4 27.8 1.0 H A:GLN216 3.4 32.1 1.0 H A:SER211 3.5 27.2 1.0 HD21 A:ASN212 3.6 42.4 1.0 OD2 A:ASP214 3.6 34.1 1.0 O A:HOH1177 3.7 32.2 1.0 N A:GLN216 3.8 26.8 1.0 ND2 A:ASN212 3.9 35.3 1.0 CA A:ASP210 3.9 24.8 1.0 CA A:GLN216 3.9 22.7 1.0 HG A:SER211 4.0 32.2 1.0 N A:SER211 4.0 22.6 1.0 OD2 A:ASP210 4.0 30.6 1.0 N A:ASP214 4.0 30.0 1.0 N A:ASN212 4.0 25.5 1.0 HA A:ARG217 4.0 26.5 1.0 H A:GLY213 4.1 37.3 1.0 CB A:GLN216 4.1 23.1 1.0 CB A:ASP210 4.1 25.8 1.0 H A:GLU218 4.2 25.1 1.0 H A:GLY215 4.2 34.2 1.0 C A:ASP210 4.2 24.0 1.0 N A:ARG217 4.3 24.4 1.0 CB A:ASP214 4.3 32.6 1.0 N A:GLY213 4.4 31.0 1.0 HB2 A:ASP210 4.4 31.0 1.0 CG A:GLU218 4.4 25.9 1.0 N A:GLY215 4.5 28.5 1.0 HB3 A:GLN216 4.5 27.8 1.0 CA A:ASP214 4.5 30.9 1.0 HB3 A:ASP214 4.6 39.1 1.0 CB A:ASN212 4.6 27.6 1.0 CA A:ARG217 4.6 22.1 1.0 N A:GLU218 4.6 20.9 1.0 CA A:ASN212 4.6 25.8 1.0 C A:ASP214 4.7 29.8 1.0 HD22 A:ASN212 4.7 42.4 1.0 C A:ASN212 4.7 29.7 1.0 OG A:SER211 4.7 26.8 1.0 C A:GLY215 4.8 30.4 1.0 HG2 A:GLU218 4.8 31.1 1.0 HG3 A:GLU218 4.8 31.1 1.0 HA A:GLN216 4.8 27.3 1.0 C A:ARG217 4.9 23.1 1.0 HB3 A:ASP210 4.9 31.0 1.0 O A:HOH1316 4.9 24.6 1.0 CA A:SER211 5.0 23.5 1.0 C A:SER211 5.0 25.7 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1006 b:31.3 occ:1.00 OD1 A:ASP251 2.3 64.0 1.0 OD1 A:ASP253 2.3 72.0 1.0 O A:LYS255 2.3 32.5 1.0 OD1 A:ASN249 2.4 37.7 1.0 OE2 A:GLU257 2.6 47.6 1.0 OE1 A:GLU257 2.7 44.2 1.0 CD A:GLU257 3.0 44.8 1.0 O A:ASP253 3.0 43.0 1.0 CG A:ASP251 3.2 62.1 1.0 H A:LYS255 3.2 40.4 1.0 CG A:ASP253 3.3 68.7 1.0 C A:LYS255 3.4 32.7 1.0 CG A:ASN249 3.5 38.1 1.0 H A:ASP253 3.5 64.4 1.0 OD2 A:ASP251 3.5 67.2 1.0 O A:HOH1103 3.5 53.5 1.0 N A:LYS255 3.6 33.6 1.0 H A:ASP251 3.7 41.0 1.0 HA A:ASN249 3.7 27.3 1.0 C A:ASP253 3.7 41.5 1.0 H A:LEU250 3.8 26.8 1.0 OD2 A:ASP253 3.9 72.6 1.0 CA A:LYS255 4.0 31.9 1.0 HD21 A:ASN249 4.1 47.9 1.0 N A:ASP253 4.2 53.7 1.0 ND2 A:ASN249 4.2 39.9 1.0 N A:ASP251 4.3 34.2 1.0 CA A:ASP253 4.3 49.5 1.0 CB A:LYS255 4.3 30.5 1.0 CB A:ASP253 4.4 58.6 1.0 CA A:ASN249 4.4 22.8 1.0 C A:ASP254 4.4 33.1 1.0 N A:LEU250 4.4 22.3 1.0 CB A:ASN249 4.5 28.9 1.0 CB A:ASP251 4.5 51.9 1.0 CG A:GLU257 4.5 37.5 1.0 N A:PRO256 4.5 30.4 1.0 HA A:PRO256 4.5 33.8 1.0 N A:ASP254 4.6 33.1 1.0 C A:ASP251 4.6 43.8 1.0 O A:ASP251 4.7 38.2 1.0 CA A:ASP251 4.7 42.1 1.0 HB2 A:ASN249 4.7 34.6 1.0 C A:PRO256 4.7 26.5 1.0 H A:GLU257 4.8 28.3 1.0 CA A:PRO256 4.8 28.1 1.0 HG3 A:GLU257 4.8 45.0 1.0 HB2 A:ASP253 4.8 70.3 1.0 HA A:ASP254 4.9 37.7 1.0 N A:GLU257 4.9 23.6 1.0 C A:ASN249 4.9 23.9 1.0 HA A:LYS255 4.9 38.3 1.0 O A:HOH1297 4.9 31.4 1.0 CA A:ASP254 4.9 31.4 1.0 HG2 A:GLU257 4.9 45.0 1.0 HB3 A:ASP251 4.9 62.4 1.0 HB2 A:GLU257 5.0 30.9 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the V. Cholerae Biofilm Matrix Protein BAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1007 b:20.8 occ:1.00 O A:ILE566 2.2 21.6 1.0 OD1 A:ASP560 2.3 20.6 1.0 OE2 A:GLU568 2.3 22.2 1.0 OG1 A:THR562 2.4 21.2 1.0 OD1 A:ASP564 2.5 32.5 1.0 OE1 A:GLU568 2.9 21.3 1.0 CD A:GLU568 2.9 22.3 1.0 H A:THR562 3.0 23.7 1.0 CG A:ASP560 3.3 22.6 1.0 HA A:ASP560 3.3 25.8 1.0 H A:ASP564 3.3 34.5 1.0 H A:ILE566 3.4 27.4 1.0 C A:ILE566 3.4 20.6 1.0 CG A:ASP564 3.5 36.5 1.0 H A:GLY563 3.6 32.2 1.0 HB A:ILE566 3.6 30.2 1.0 CB A:THR562 3.6 23.2 1.0 HG23 A:THR562 3.8 31.6 1.0 N A:THR562 3.8 19.8 1.0 OD2 A:ASP564 4.0 36.5 1.0 CA A:ASP560 4.0 21.5 1.0 N A:ILE566 4.0 22.8 1.0 O A:HOH1231 4.1 43.4 1.0 O A:HOH1181 4.1 22.7 1.0 OD2 A:ASP560 4.1 22.8 1.0 CB A:ASP560 4.1 22.2 1.0 CG2 A:THR562 4.1 26.3 1.0 N A:GLY563 4.1 26.8 1.0 CA A:ILE566 4.1 21.7 1.0 CA A:THR562 4.2 22.5 1.0 N A:ASP564 4.2 28.7 1.0 HG21 A:THR562 4.2 31.6 1.0 HB2 A:ASP560 4.2 26.7 1.0 H A:PHE561 4.2 24.4 1.0 HA A:ASP567 4.3 23.0 1.0 H A:GLU568 4.3 23.7 1.0 HB A:THR562 4.4 27.9 1.0 CB A:ILE566 4.4 25.1 1.0 O A:HOH1160 4.4 29.0 1.0 C A:ASP560 4.4 22.4 1.0 N A:PHE561 4.4 20.3 1.0 CG A:GLU568 4.4 19.6 1.0 N A:ASP567 4.5 19.5 1.0 C A:THR562 4.5 26.2 1.0 H A:GLY565 4.5 28.2 1.0 N A:GLU568 4.5 19.7 1.0 C A:ASP567 4.6 21.5 1.0 CB A:ASP564 4.6 34.9 1.0 CA A:ASP567 4.7 19.1 1.0 HG3 A:GLU568 4.7 23.6 1.0 HG22 A:ILE566 4.8 31.9 1.0 HB3 A:ASP564 4.8 41.9 1.0 N A:GLY565 4.8 23.5 1.0 CA A:ASP564 4.8 29.5 1.0 C A:PHE561 4.9 23.2 1.0 HG2 A:GLU568 4.9 23.6 1.0 HB3 A:ASP560 5.0 26.7 1.0

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