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Sodium in PDB 3mqd: Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol

Enzymatic activity of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol

All present enzymatic activity of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol:
2.3.1.4;

Protein crystallography data

The structure of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol, PDB code: 3mqd was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.81 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.070, 83.620, 73.640, 90.00, 121.37, 90.00
R / Rfree (%) 11.2 / 13.3

Other elements in 3mqd:

The structure of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol (pdb code 3mqd). 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 Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol, PDB code: 3mqd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3mqd

Go back to Sodium Binding Sites List in 3mqd
Sodium binding site 1 out of 2 in the Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol


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 Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:7.2
occ:1.00
 OE1 A:GLU342 2.3 7.3 1.0
OD1 A:ASN294 2.3 7.8 1.0
OG A:SER388 2.5 3.9 0.7
O A:ASN389 2.5 6.3 1.0
O A:ASN294 2.6 5.9 1.0
O A:PRO295 2.9 7.7 1.0
C A:ASN294 3.3 5.2 1.0
CD A:GLU342 3.3 7.5 1.0
CG A:ASN294 3.4 6.2 1.0
C A:PRO295 3.4 6.0 1.0
N A:ASN389 3.5 5.2 1.0
C A:ASN389 3.6 5.5 1.0
CB A:SER388 3.7 4.7 0.7
CB A:SER388 3.8 7.0 0.3
CB A:ASN294 3.8 5.4 1.0
CB A:GLU342 3.9 5.2 1.0
O A:HOH469 3.9 24.6 1.0
CA A:SER388 4.0 4.3 0.7
CA A:SER388 4.0 6.2 0.3
C A:SER388 4.0 5.1 1.0
N A:PRO295 4.0 5.8 1.0
CG A:GLU342 4.1 6.4 1.0
O A:HOH543 4.1 11.1 1.0
N A:HIS296 4.1 6.2 1.0
CA A:ASN389 4.1 5.2 1.0
CA A:PRO295 4.2 5.6 1.0
OE2 A:GLU342 4.2 13.7 1.0
CA A:ASN294 4.2 5.5 1.0
CA A:HIS296 4.5 7.4 1.0
ND2 A:ASN294 4.6 7.1 1.0
OG A:SER390 4.6 11.6 0.6
O A:HOH489 4.6 9.7 1.0
N A:SER390 4.7 5.8 1.0
CB A:ASN389 4.8 5.7 1.0
OG A:SER388 4.8 13.1 0.3
O A:SER388 4.9 5.9 1.0
NZ A:LYS328 4.9 11.3 1.0

Sodium binding site 2 out of 2 in 3mqd

Go back to Sodium Binding Sites List in 3mqd
Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol


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 Beta-Ketoacyl Synthase From Brucella Melitensis with Fol 0758, (1-Methyl-1H-Indazol-3-Yl) Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:35.5
occ:1.00
 O A:HOH478 2.3 32.1 1.0
O A:HOH795 2.4 28.7 1.0
O A:LEU283 2.5 8.4 1.0
O A:HOH521 2.6 49.3 1.0
O A:VAL286 2.6 15.8 1.0
C A:LEU283 3.6 7.5 1.0
C A:VAL286 3.8 14.1 1.0
N A:VAL286 4.1 9.8 1.0
O A:HOH819 4.2 41.0 1.0
CA A:SER284 4.2 8.7 1.0
C A:SER284 4.3 9.6 1.0
O A:SER284 4.4 12.5 1.0
N A:SER284 4.4 7.6 1.0
CA A:VAL286 4.4 11.6 1.0
CA A:LEU283 4.6 6.1 1.0
CB A:LEU283 4.6 7.5 1.0
CB A:VAL286 4.6 10.2 1.0
O A:HOH560 4.7 15.2 1.0
N A:THR285 4.8 8.4 1.0
O A:HOH766 4.8 26.6 1.0
N A:THR287 4.8 16.8 1.0

Reference:

E.I.Patterson, J.D.Nanson, J.Abendroth, C.Bryan, B.Sankaran, P.J.Myler, J.K.Forwood. Structural Characterization of Beta-Ketoacyl Acp Synthase I Bound to Platencin and Fragment Screening Molecules at Two Substrate Binding Sites. Proteins 2019.
ISSN: ESSN 1097-0134
PubMed: 31237717
DOI: 10.1002/PROT.25765
Page generated: Sun Aug 17 16:16:02 2025

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