Sodium in PDB 6vxv: Crystal Structure of Cyclo-L-Trp-L-Pro-Bound Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053

Protein crystallography data

The structure of Crystal Structure of Cyclo-L-Trp-L-Pro-Bound Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053, PDB code: 6vxv was solved by Z.Luo, X.Jia, C.Sun, X.Qu, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.80 / 1.60
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.314, 91.836, 93.604, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.3

Other elements in 6vxv:

The structure of Crystal Structure of Cyclo-L-Trp-L-Pro-Bound Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053 also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Cyclo-L-Trp-L-Pro-Bound Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053 (pdb code 6vxv). 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 Cyclo-L-Trp-L-Pro-Bound Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053, PDB code: 6vxv:

Sodium binding site 1 out of 1 in 6vxv

Go back to Sodium Binding Sites List in 6vxv
Sodium binding site 1 out of 1 in the Crystal Structure of Cyclo-L-Trp-L-Pro-Bound Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053


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 Cyclo-L-Trp-L-Pro-Bound Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:24.3
occ:1.00
NH1 A:ARG345 2.9 21.4 0.5
CD A:ARG345 2.9 22.9 0.5
O A:HOH588 3.1 26.3 1.0
O A:HOH692 3.2 23.5 1.0
O A:HOH653 3.3 31.9 1.0
CG A:ARG345 3.5 19.8 0.5
CB A:ARG345 3.7 20.1 0.5
NE A:ARG345 3.8 24.9 0.5
CZ A:ARG345 3.8 26.4 0.5
CB A:ARG345 3.8 20.3 0.5
CA A:SER57 3.8 19.7 1.0
CD A:ARG345 3.9 18.0 0.5
O A:HOH628 3.9 26.4 1.0
CB A:SER57 3.9 18.4 1.0
NE2 A:HIS346 4.1 16.4 1.0
CD2 A:HIS346 4.1 17.0 1.0
CG A:ARG345 4.3 20.6 0.5
NE A:ARG345 4.5 23.4 0.5
O A:HOH686 4.5 20.1 1.0
N A:SER57 4.6 19.6 1.0
O A:PHE59 4.7 18.6 1.0
O A:HOH547 4.8 17.2 1.0
O A:LEU54 4.8 20.6 1.0
N A:ARG345 4.8 16.9 1.0
O A:SER57 4.8 21.1 1.0
CA A:ARG345 4.8 20.1 0.5
C A:SER57 4.8 22.4 1.0
CA A:ARG345 4.9 20.1 0.5
O A:ASP56 4.9 19.6 1.0

Reference:

C.Sun, Z.Luo, W.Zhang, Z.Deng, M.Mobli, B.Kobe, X.Jia, X.Qu. Molecular Basis of Regio- and Stereo-Specificity in Biosynthesis of Bacterial Heterodimeric Diketopiperazines To Be Published.
Page generated: Tue Dec 15 15:19:38 2020

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