Atomistry » Sodium » PDB 6vf7-6w0r » 6vza
Atomistry »
  Sodium »
    PDB 6vf7-6w0r »
      6vza »

Sodium in PDB 6vza: Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State

Protein crystallography data

The structure of Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State, PDB code: 6vza 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) 42.23 / 1.47
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.228, 91.310, 93.808, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18

Other elements in 6vza:

The structure of Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State (pdb code 6vza). 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 Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State, PDB code: 6vza:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6vza

Go back to Sodium Binding Sites List in 6vza
Sodium binding site 1 out of 2 in the Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State


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 Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:35.3
occ:1.00
HD2 A:ARG345 3.3 42.9 1.0
HB2 A:ARG345 3.6 28.4 1.0
HB3 A:ARG345 3.8 28.4 1.0
CB A:ARG345 4.1 23.7 1.0
CD A:ARG345 4.2 35.8 1.0
HD3 A:ARG345 4.5 42.9 1.0
HH21 A:ARG96 4.5 57.9 1.0
O A:HOH521 4.7 34.5 1.0
CG A:ARG345 4.7 31.4 1.0
HG3 A:ARG345 4.9 37.6 1.0

Sodium binding site 2 out of 2 in 6vza

Go back to Sodium Binding Sites List in 6vza
Sodium binding site 2 out of 2 in the Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State


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 Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:30.4
occ:1.00
O A:ALA48 2.7 16.8 1.0
O A:HOH886 2.7 38.7 1.0
HG3 A:LYS52 2.8 37.6 1.0
O A:HOH892 2.9 29.8 1.0
O A:HOH897 2.9 30.6 1.0
HB A:VAL51 3.0 17.7 1.0
HA A:ALA48 3.0 18.6 1.0
HE3 A:LYS52 3.0 67.0 1.0
HB1 A:ALA48 3.2 21.5 1.0
C A:ALA48 3.5 14.8 1.0
CA A:ALA48 3.6 15.5 1.0
CG A:LYS52 3.7 31.3 1.0
HG12 A:VAL51 3.8 18.9 1.0
CE A:LYS52 3.8 55.8 1.0
CB A:ALA48 3.8 17.9 1.0
CB A:VAL51 3.8 14.7 1.0
HE2 A:LYS52 3.9 67.0 1.0
H A:LYS52 3.9 17.2 1.0
HG11 A:VAL51 4.0 18.9 1.0
HG2 A:LYS52 4.1 37.6 1.0
CG1 A:VAL51 4.1 15.7 1.0
CD A:LYS52 4.2 54.0 1.0
HB2 A:ALA48 4.2 21.5 1.0
HD2 A:LYS52 4.2 64.8 1.0
O A:HOH894 4.3 42.6 1.0
HG21 A:VAL51 4.3 17.1 1.0
N A:LYS52 4.4 14.3 1.0
O A:HOH863 4.4 46.3 1.0
HB3 A:ALA48 4.6 21.5 1.0
CG2 A:VAL51 4.6 14.2 1.0
O A:HOH773 4.6 36.7 1.0
H A:VAL51 4.7 15.7 1.0
N A:THR49 4.7 13.7 1.0
CB A:LYS52 4.8 21.6 1.0
HG23 A:VAL51 4.8 17.1 1.0
HB2 A:LYS52 4.8 25.9 1.0
CA A:VAL51 4.9 13.8 1.0
C A:VAL51 4.9 15.4 1.0
N A:ALA48 4.9 13.8 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 Oct 8 14:28:09 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy