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Chlorine in PDB 5gvp: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654, PDB code: 5gvp was solved by P.Chitnumsub, A.Jaruwat, U.Leartsakulpanich, G.Schwertz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.26
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.075, 58.928, 234.830, 90.00, 90.06, 90.00
R / Rfree (%) 25 / 31.2

Other elements in 5gvp:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654 also contains other interesting chemical elements:

Fluorine (F) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654 (pdb code 5gvp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654, PDB code: 5gvp:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5gvp

Go back to Chlorine Binding Sites List in 5gvp
Chlorine binding site 1 out of 2 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:25.3
occ:1.00
NZ A:LYS277 2.9 16.9 1.0
NZ B:LYS277 3.1 14.6 1.0
ND2 B:ASN276 3.3 16.5 1.0
ND2 A:ASN276 3.4 16.8 1.0
CE B:LYS277 3.9 15.0 1.0
CE A:LYS277 3.9 16.9 1.0
CG B:LYS277 4.0 15.3 1.0
CG A:LYS277 4.1 17.2 1.0
CG B:ASN276 4.2 16.8 1.0
CG A:ASN276 4.4 17.0 1.0
OD1 B:ASN276 4.4 16.8 1.0
CD2 B:LEU46 4.4 24.5 1.0
CD2 A:LEU46 4.5 26.1 1.0
OD1 A:ASN276 4.5 16.5 1.0
CD B:LYS277 4.6 15.6 1.0
CD A:LYS277 4.7 17.2 1.0
ND1 B:HIS274 4.9 19.0 1.0
ND1 A:HIS274 5.0 18.0 1.0

Chlorine binding site 2 out of 2 in 5gvp

Go back to Chlorine Binding Sites List in 5gvp
Chlorine binding site 2 out of 2 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:17.7
occ:0.50
NZ C:LYS277 2.7 15.2 1.0
CE C:LYS277 3.6 15.7 1.0
ND2 C:ASN276 3.6 17.6 1.0
CG C:LYS277 3.9 16.3 1.0
CD2 C:LEU46 4.0 25.4 1.0
CD C:LYS277 4.4 16.1 1.0
CG C:ASN276 4.6 17.8 1.0
OD1 C:ASN276 4.7 17.9 1.0

Reference:

G.Schwertz, M.C.Witschel, M.Rottmann, R.Bonnert, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Ittarat, A.Schafer, R.A.Aponte, S.A.Charman, K.L.White, A.Kundu, S.Sadhukhan, M.Lloyd, G.M.Freiberg, M.Srikumaran, M.Siggel, A.Zwyssig, P.Chaiyen, F.Diederich. Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (Shmt) with in Vivo Efficacy and Analysis of Their Binding Mode Based on X-Ray Cocrystal Structures J. Med. Chem. V. 60 4840 2017.
ISSN: ISSN 1520-4804
PubMed: 28537728
DOI: 10.1021/ACS.JMEDCHEM.7B00008
Page generated: Sat Dec 12 11:47:37 2020

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