Sodium in PDB 4k0w: X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant

All present enzymatic activity of X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant:
3.5.2.6;

The structure of X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant, PDB code: 4k0w was solved by K.J.Kaitany, N.V.Klinger, D.A.Leonard, R.A.Powers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	137.00 / 1.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.116, 46.662, 137.018, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.2

The binding sites of Sodium atom in the X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant (pdb code 4k0w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant, PDB code: 4k0w:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:26.5 occ:1.00 O A:HOH476 3.0 27.4 1.0 OD1 A:ASN261 3.0 21.4 0.8 O A:HOH589 3.1 34.0 1.0 CG A:ASN261 3.9 18.7 0.8 CB A:ASN261 3.9 17.7 0.8 N A:GLU262 4.1 15.5 0.9 O A:SER258 4.2 16.8 1.0 CB A:SER258 4.4 18.5 1.0 C A:ASN261 4.4 15.4 0.8 CA A:GLU262 4.4 17.1 0.9 O A:HOH588 4.7 35.1 1.0 CB A:GLU262 4.7 18.0 0.9 CA A:ASN261 4.8 15.2 0.8 O A:ASN261 4.8 15.8 0.8

Sodium binding site 2 out of 5 in the X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:40.9 occ:1.00 OXT A:ILE274 2.6 25.4 1.0 O1 A:EDO304 3.1 28.7 1.0 O A:LYS269 3.1 22.0 1.0 C1 A:EDO304 3.2 38.7 1.0 C A:ILE274 3.6 24.6 1.0 CA A:LYS269 3.7 19.5 1.0 OD1 A:ASN272 3.7 32.8 0.9 C A:LYS269 3.8 21.1 1.0 O A:ILE274 3.9 29.7 1.0 O A:HOH619 3.9 31.5 0.5 CB A:LYS269 4.0 22.1 1.0 CG A:LYS269 4.2 19.6 1.0 O A:HOH569 4.2 52.6 1.0 O A:HOH619 4.3 31.5 0.5 CA A:ASN272 4.3 21.1 0.9 CG A:ASN272 4.7 32.0 0.9 N A:ASN272 4.7 19.8 0.9 C2 A:EDO304 4.7 28.2 1.0 O A:HOH634 4.9 49.9 1.0 CA A:ILE274 5.0 20.4 1.0 O A:LEU268 5.0 18.4 1.0

Sodium binding site 3 out of 5 in the X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:22.9 occ:1.00 O A:HOH470 2.9 35.1 1.0 O A:HOH543 3.3 27.4 1.0 NE1 A:TRP165 3.3 23.6 1.0 O A:HOH414 3.4 19.6 1.0 CB A:TYR131 3.5 20.0 1.0 CE A:LYS82 3.6 18.1 0.5 CG A:LYS82 3.7 15.3 0.5 CD A:LYS82 3.7 14.2 0.5 CG1 A:VAL128 3.7 33.9 0.5 CZ2 A:TRP165 3.7 21.8 1.0 CE2 A:TRP165 3.8 19.3 1.0 CG A:LYS82 4.0 14.5 0.5 CA A:VAL128 4.1 33.6 0.5 CA A:VAL128 4.1 28.8 0.5 OG A:SER79 4.3 18.1 0.9 CB A:VAL128 4.3 36.6 0.5 CD A:LYS82 4.4 17.3 0.5 CG A:TYR131 4.4 18.2 1.0 CG2 A:VAL128 4.4 32.7 0.5 CD1 A:TRP165 4.5 21.2 1.0 CE A:LYS82 4.5 15.7 0.5 CG1 A:VAL128 4.6 31.3 0.5 CB A:VAL128 4.6 29.7 0.5 N A:VAL128 4.7 31.9 0.5 CA A:TYR131 4.7 20.4 1.0 N A:VAL128 4.7 27.8 0.5 O A:ALA127 4.8 24.8 0.8 NZ A:LYS82 4.8 22.2 0.5 O A:VAL128 4.9 32.6 0.5 CH2 A:TRP165 4.9 20.3 1.0 C A:TYR131 4.9 20.6 1.0 NZ A:LYS82 5.0 17.1 0.5 C A:ALA127 5.0 26.6 0.8 O A:VAL128 5.0 35.4 0.5 CD1 A:TYR131 5.0 20.1 1.0

Sodium binding site 4 out of 5 in the X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:32.4 occ:1.00 N A:ILE100 2.8 20.7 1.0 CA A:GLU99 3.6 21.4 1.0 CB A:ILE100 3.7 22.5 1.0 C A:GLU99 3.7 19.5 1.0 O A:ILE100 3.7 21.2 1.0 CA A:ILE100 3.7 20.5 1.0 O A:HOH479 3.8 30.9 1.0 CG A:GLU99 3.8 21.7 1.0 CG1 A:ILE100 3.8 28.3 1.0 C A:ILE100 4.2 20.6 1.0 CB A:GLU99 4.2 20.3 1.0 O A:ASN98 4.4 21.7 1.0 O A:HOH475 4.4 27.4 1.0 N A:GLU99 4.7 18.9 1.0 CD A:GLU99 4.9 23.3 1.0 O A:GLU99 4.9 20.8 1.0

Sodium binding site 5 out of 5 in the X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Crystal Structure of Oxa-23 A220 Duplication Clinical Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na314 b:21.0 occ:1.00 O A:HOH545 2.9 21.6 0.5 O A:HOH550 2.9 35.0 1.0 O A:HOH490 2.9 30.6 1.0 N A:VAL76 3.1 15.3 1.0 CA A:TYR75 3.5 15.0 1.0 CG2 A:VAL228 3.8 14.0 0.5 C A:TYR75 3.8 15.0 1.0 CB A:TYR75 3.9 14.9 1.0 CG2 A:VAL76 3.9 17.6 1.0 O A:HOH545 3.9 25.2 0.5 CG1 A:VAL76 3.9 18.4 1.0 O A:HOH540 4.0 31.9 1.0 CD1 A:TYR75 4.1 15.8 1.0 CD1 A:ILE224 4.2 27.2 0.8 CB A:VAL76 4.2 15.3 1.0 CA A:VAL76 4.2 15.6 1.0 CE A:LYS171 4.4 30.1 0.9 O A:HOH495 4.4 33.8 1.0 CG2 A:ILE224 4.4 37.2 0.8 CG A:TYR75 4.5 15.0 1.0 CG1 A:VAL228 4.5 19.4 0.5 NZ A:LYS171 4.6 33.8 0.9 O A:GLU74 4.7 17.2 1.0 CD A:LYS171 4.8 22.1 0.9 N A:TYR75 4.8 15.4 1.0 CB A:VAL228 4.9 14.0 0.5

K.C.Kaitany, N.V.Klinger, C.M.June, M.E.Ramey, R.A.Bonomo, R.A.Powers, D.A.Leonard. Structures of the Class D Carbapenemases Oxa-23 and Oxa-146: Mechanistic Basis of Activity Against Carbapenems, Extended-Spectrum Cephalosporins, and Aztreonam. Antimicrob.Agents Chemother. V. 57 4848 2013.
ISSN: ISSN 0066-4804
PubMed: 23877677
DOI: 10.1128/AAC.00762-13