Sodium in PDB 3mqh: Crystal Structure of the 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid

The structure of Crystal Structure of the 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid, PDB code: 3mqh was solved by J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.466, 107.891, 91.269, 90.00, 102.55, 90.00
R / Rfree (%)	17.4 / 20.6

The binding sites of Sodium atom in the Crystal Structure of the 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid (pdb code 3mqh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid, PDB code: 3mqh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid


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 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na194 b:9.0 occ:1.00 O B:HOH607 2.3 13.0 1.0 OD1 C:ASN112 2.3 4.8 1.0 O A:HOH392 2.3 14.0 1.0 O C:HOH354 2.4 12.1 1.0 OD1 A:ASN112 2.4 5.8 1.0 OD1 B:ASN112 2.4 6.6 1.0 CG C:ASN112 3.3 4.4 1.0 CG A:ASN112 3.3 4.5 1.0 CG B:ASN112 3.3 6.3 1.0 ND2 C:ASN112 3.6 6.1 1.0 ND2 A:ASN112 3.6 5.8 1.0 ND2 B:ASN112 3.6 6.2 1.0 O C:SER79 4.1 7.0 1.0 O B:SER79 4.2 8.6 1.0 O A:SER79 4.2 8.5 1.0 CB C:SER79 4.6 6.4 1.0 CB A:ASN112 4.6 4.8 1.0 CB C:ASN112 4.7 6.5 1.0 CB A:SER79 4.7 7.1 1.0 CB B:ASN112 4.7 4.8 1.0 CB B:SER79 4.7 5.7 1.0 O C:HOH223 4.9 10.1 1.0 CG2 B:VAL81 4.9 6.3 1.0 O A:HOH218 4.9 9.8 1.0 CG2 C:VAL81 4.9 5.0 1.0 CG2 A:VAL81 4.9 5.0 1.0 O B:HOH226 5.0 11.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid


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 3-N-Acetyl Transferase Wlbb From Bordetella Petrii in Complex with Coa and Udp-3-Amino-2-Acetamido-2,3-Dideoxy Glucuronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Na196 b:9.0 occ:1.00 O E:HOH554 2.3 12.3 1.0 OD1 F:ASN112 2.3 5.1 1.0 OD1 E:ASN112 2.4 5.5 1.0 OD1 D:ASN112 2.4 5.7 1.0 O F:HOH208 2.4 14.4 1.0 O D:HOH1234 2.4 15.5 1.0 CG F:ASN112 3.3 4.9 1.0 CG D:ASN112 3.3 4.4 1.0 CG E:ASN112 3.3 5.5 1.0 ND2 F:ASN112 3.6 6.6 1.0 ND2 D:ASN112 3.6 6.8 1.0 ND2 E:ASN112 3.6 6.2 1.0 O F:SER79 4.1 7.9 1.0 O E:SER79 4.2 7.5 1.0 O D:SER79 4.2 8.1 1.0 CB F:SER79 4.6 5.9 1.0 CB E:SER79 4.6 5.2 1.0 CB F:ASN112 4.7 6.2 1.0 CB D:SER79 4.7 7.1 1.0 CB D:ASN112 4.7 5.1 1.0 CB E:ASN112 4.7 5.7 1.0 CG2 E:VAL81 4.9 6.5 1.0 O F:HOH225 4.9 9.7 1.0 CG2 F:VAL81 4.9 6.6 1.0 O D:HOH227 4.9 9.4 1.0 O E:HOH246 4.9 11.1 1.0 CG2 D:VAL81 4.9 5.8 1.0

J.B.Thoden, H.M.Holden. Molecular Structure of Wlbb, A Bacterial N-Acetyltransferase Involved in the Biosynthesis of 2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid . Biochemistry V. 49 4644 2010.
ISSN: ISSN 0006-2960
PubMed: 20433200
DOI: 10.1021/BI1005738