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Xenon in PDB 4wna: Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon

Enzymatic activity of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon

All present enzymatic activity of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon:
1.18.6.1;

Protein crystallography data

The structure of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon, PDB code: 4wna was solved by C.N.Morrison, J.A.Hoy, L.Zhang, O.Einsle, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.72 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.123, 129.780, 107.543, 90.00, 108.94, 90.00
R / Rfree (%) 16.7 / 21.9

Other elements in 4wna:

The structure of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Iron (Fe) 36 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon (pdb code 4wna). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 6 binding sites of Xenon where determined in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon, PDB code: 4wna:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6;

Xenon binding site 1 out of 6 in 4wna

Go back to Xenon Binding Sites List in 4wna
Xenon binding site 1 out of 6 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe504

b:27.2
occ:0.77
 CD1 A:ILE75 3.3 31.6 1.0
CG2 A:VAL202 3.6 27.9 1.0
CG1 A:VAL71 3.9 19.7 1.0
O A:VAL71 3.9 19.0 1.0
CG1 A:ILE75 4.1 28.8 1.0
CB A:SER254 4.3 17.1 1.0
CE3 A:TRP253 4.4 18.7 1.0
CE3 A:TRP72 4.5 20.3 1.0
CD1 A:ILE262 4.5 26.1 1.0
CE A:MET279 4.6 37.0 1.0
CZ3 A:TRP72 4.6 17.8 1.0
CD2 A:TRP72 4.6 18.4 1.0
CZ3 A:TRP253 4.6 21.3 1.0
CG1 A:ILE262 4.7 24.6 1.0
C A:VAL71 4.7 15.2 1.0
CH2 A:TRP72 4.8 19.5 1.0
CE2 A:TRP72 4.8 19.8 1.0
OG A:SER254 4.9 16.4 1.0
CB A:VAL202 4.9 28.9 1.0
CZ2 A:TRP72 4.9 18.4 1.0

Xenon binding site 2 out of 6 in 4wna

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Xenon binding site 2 out of 6 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe505

b:31.5
occ:0.49
 OD1 A:ASP200 3.1 28.3 1.0
O A:HOH836 3.7 25.6 1.0
O A:TYR281 3.7 21.7 1.0
O A:HOH837 3.7 29.5 1.0
C A:TYR281 3.8 26.4 1.0
CD1 A:ILE282 3.9 19.5 1.0
CA A:ILE282 3.9 25.1 1.0
N A:ILE282 4.0 22.3 1.0
O A:ASN199 4.0 18.3 1.0
CB A:TYR281 4.0 20.2 1.0
C A:ASN199 4.1 21.4 1.0
CB A:ASN199 4.1 21.3 1.0
N A:ASP200 4.2 21.4 1.0
NE A:ARG203 4.2 37.0 1.0
NH2 A:ARG203 4.2 31.8 1.0
CB A:HIS285 4.2 23.8 1.0
CA A:ASP200 4.2 24.0 1.0
CG A:ASP200 4.3 26.9 1.0
CB A:ARG203 4.4 28.1 1.0
CZ A:ARG203 4.4 32.4 1.0
O A:HOH619 4.4 28.9 1.0
CB A:ILE282 4.5 23.5 1.0
CA A:TYR281 4.5 21.5 1.0
CA A:ASN199 4.8 19.8 1.0
CG A:HIS285 4.8 23.6 1.0
CG1 A:ILE282 4.8 18.1 1.0
CG A:ARG203 4.8 31.7 1.0
CB A:ASP200 4.9 24.4 1.0
OD1 A:ASN199 5.0 26.1 1.0

Xenon binding site 3 out of 6 in 4wna

Go back to Xenon Binding Sites List in 4wna
Xenon binding site 3 out of 6 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe602

b:31.3
occ:0.62
 O B:HOH912 3.6 24.7 1.0
O B:HOH913 3.6 32.6 1.0
CG1 B:ILE493 3.8 15.5 1.0
O B:THR483 3.9 16.9 1.0
CG2 B:THR484 4.1 16.8 1.0
CB B:GLN492 4.2 19.3 1.0
N B:ILE493 4.2 15.8 1.0
C B:GLN492 4.2 18.5 1.0
CA B:ILE493 4.3 15.5 1.0
O B:GLN492 4.3 18.4 1.0
CD1 B:ILE469 4.4 16.6 1.0
O B:HOH742 4.4 17.2 1.0
CG1 B:ILE469 4.4 16.6 1.0
OG1 B:THR496 4.4 24.3 1.0
CG2 B:ILE469 4.5 15.7 1.0
CB B:SER482 4.5 15.9 1.0
OE1 B:GLN492 4.5 16.9 1.0
CB B:ILE493 4.7 14.8 1.0
C B:THR483 4.8 15.9 1.0
O B:HOH904 4.8 26.6 1.0
CA B:GLN492 4.9 17.9 1.0
CD1 B:ILE493 4.9 16.4 1.0

Xenon binding site 4 out of 6 in 4wna

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Xenon binding site 4 out of 6 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe504

b:28.0
occ:0.81
 CG2 C:VAL202 3.7 29.5 1.0
CG1 C:VAL71 3.9 18.8 1.0
O C:VAL71 4.0 18.4 1.0
CG1 C:ILE75 4.0 22.9 1.0
CD1 C:ILE75 4.1 19.0 1.0
CB C:SER254 4.3 15.5 1.0
CE C:MET279 4.4 39.0 1.0
CE3 C:TRP72 4.4 26.3 1.0
CZ3 C:TRP72 4.5 27.9 1.0
CE3 C:TRP253 4.6 19.1 1.0
CD1 C:ILE262 4.6 23.2 1.0
CD2 C:TRP72 4.6 23.7 1.0
CG1 C:ILE262 4.7 21.8 1.0
CH2 C:TRP72 4.7 25.7 1.0
C C:VAL71 4.7 19.1 1.0
CE2 C:TRP72 4.8 23.4 1.0
CZ3 C:TRP253 4.8 23.5 1.0
CZ2 C:TRP72 4.9 25.0 1.0
OG C:SER254 4.9 15.9 1.0
CB C:VAL202 4.9 28.2 1.0
CG1 C:VAL202 5.0 26.1 1.0

Xenon binding site 5 out of 6 in 4wna

Go back to Xenon Binding Sites List in 4wna
Xenon binding site 5 out of 6 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe505

b:32.0
occ:0.46
 OD1 C:ASP200 2.9 24.4 1.0
O C:HOH725 3.6 25.0 1.0
O C:TYR281 3.7 21.4 1.0
C C:TYR281 3.8 23.4 1.0
N C:ILE282 4.0 22.2 1.0
CA C:ILE282 4.0 20.7 1.0
CB C:TYR281 4.0 20.7 1.0
CB C:ASN199 4.0 19.5 1.0
C C:ASN199 4.1 22.6 1.0
N C:ASP200 4.1 20.1 1.0
CD1 C:ILE282 4.1 22.6 1.0
O C:ASN199 4.1 19.0 1.0
CG C:ASP200 4.1 26.0 1.0
CA C:ASP200 4.2 23.1 1.0
NH2 C:ARG203 4.2 30.1 1.0
CB C:HIS285 4.2 24.1 1.0
NE C:ARG203 4.3 30.7 1.0
CZ C:ARG203 4.3 30.0 1.0
CB C:ARG203 4.4 23.3 1.0
CA C:TYR281 4.5 22.2 1.0
CB C:ILE282 4.6 22.6 1.0
CA C:ASN199 4.8 19.6 1.0
CB C:ASP200 4.8 24.8 1.0
CG C:HIS285 4.8 22.3 1.0
CG C:ARG203 4.9 26.3 1.0
CG1 C:ILE282 5.0 21.7 1.0

Xenon binding site 6 out of 6 in 4wna

Go back to Xenon Binding Sites List in 4wna
Xenon binding site 6 out of 6 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe601

b:29.3
occ:0.54
 O D:HOH849 3.6 24.3 1.0
CG1 D:ILE493 3.9 17.8 1.0
O D:THR483 3.9 16.7 1.0
CG2 D:THR484 4.1 21.1 1.0
CB D:GLN492 4.1 19.7 1.0
CD1 D:ILE469 4.2 16.6 1.0
N D:ILE493 4.3 16.5 1.0
CA D:ILE493 4.3 15.7 1.0
O D:HOH827 4.3 14.4 1.0
C D:GLN492 4.4 15.2 1.0
OG1 D:THR496 4.4 24.6 1.0
CG2 D:ILE469 4.4 14.8 1.0
OE1 D:GLN492 4.4 18.3 1.0
CB D:SER482 4.5 17.7 1.0
O D:GLN492 4.6 17.4 1.0
CG1 D:ILE469 4.6 16.6 1.0
CB D:ILE493 4.7 16.2 1.0
C D:THR483 4.8 16.2 1.0
O D:HOH1039 4.9 29.6 1.0
OG D:SER482 4.9 20.0 1.0
CA D:GLN492 4.9 16.5 1.0
CD1 D:ILE493 5.0 17.8 1.0

Reference:

C.N.Morrison, J.A.Hoy, L.Zhang, O.Einsle, D.C.Rees. Substrate Pathways in the Nitrogenase Mofe Protein By Experimental Identification of Small Molecule Binding Sites. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25710326
DOI: 10.1021/BI501313K
Page generated: Sat Oct 12 19:19:33 2024

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