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Sodium in PDB 4mlm: Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1

Protein crystallography data

The structure of Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1, PDB code: 4mlm was solved by L.M.Van Staalduinen, F.R.Mcsorley, D.L.Zechel, Z.Jia, Montreal-Kingstonbacterial Structural Genomics Initiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.670, 76.040, 60.700, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.8

Other elements in 4mlm:

The structure of Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1 also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1 (pdb code 4mlm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1, PDB code: 4mlm:

Sodium binding site 1 out of 1 in 4mlm

Go back to Sodium Binding Sites List in 4mlm
Sodium binding site 1 out of 1 in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1


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 Phnz From Uncultured Bacterium HF130_AEPN_1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:40.5
occ:1.00
N B:MSE180 2.1 22.3 1.0
CE B:LYS179 2.3 39.0 0.5
CB B:MSE180 3.0 18.3 1.0
C B:LYS179 3.0 23.5 1.0
CA B:MSE180 3.0 20.8 1.0
NZ B:LYS179 3.1 49.2 1.0
N B:LYS179 3.2 20.0 1.0
CB B:LYS179 3.3 29.2 1.0
CA B:LYS179 3.3 24.4 1.0
O B:HIS176 3.4 25.4 1.0
CD B:LYS179 3.6 40.8 0.5
C B:TYR177 3.7 20.6 1.0
O B:TYR177 3.7 17.3 1.0
O B:HOH339 3.8 27.0 1.0
CG B:LYS179 3.8 37.7 1.0
CA B:TYR177 3.8 17.7 1.0
C B:ARG178 4.1 16.7 1.0
O B:LYS179 4.1 21.0 1.0
O B:HOH373 4.1 43.2 1.0
N B:ARG178 4.1 22.2 1.0
O B:HOH478 4.2 45.3 1.0
C B:HIS176 4.3 25.7 1.0
O B:HOH465 4.4 43.1 1.0
C B:MSE180 4.4 16.9 1.0
CG B:MSE180 4.4 24.0 1.0
N B:TYR177 4.5 24.0 1.0
CE B:MSE180 4.6 28.4 1.0
O B:ARG178 4.7 18.3 1.0
N B:MSE181 4.7 19.0 1.0
CA B:ARG178 4.7 21.9 1.0

Reference:

L.M.Van Staalduinen, F.R.Mcsorley, K.Schiessl, J.Seguin, P.B.Wyatt, F.Hammerschmidt, D.L.Zechel, Z.Jia. Crystal Structure of Phnz in Complex with Substrate Reveals A Di-Iron Oxygenase Mechanism For Catabolism of Organophosphonates. Proc.Natl.Acad.Sci.Usa V. 111 5171 2014.
ISSN: ISSN 0027-8424
PubMed: 24706911
DOI: 10.1073/PNAS.1320039111
Page generated: Tue Dec 15 06:54:19 2020

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