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Magnesium in PDB 6op1: Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii

Enzymatic activity of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii

All present enzymatic activity of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii:
1.18.6.1;

Protein crystallography data

The structure of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii, PDB code: 6op1 was solved by R.J.Arias, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.93 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.191, 128.003, 107.633, 90.00, 109.15, 90.00
R / Rfree (%) 13.2 / 16.5

Other elements in 6op1:

The structure of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Iron (Fe) 30 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii (pdb code 6op1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii, PDB code: 6op1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6op1

Go back to Magnesium Binding Sites List in 6op1
Magnesium binding site 1 out of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:46.4
occ:1.00
 O A:HOH819 2.2 14.1 1.0
O A:MET112 2.8 13.1 1.0
O A:HOH707 2.8 11.2 1.0
O A:VAL110 3.1 12.6 1.0
CA A:ARG93 3.4 9.8 1.0
N A:ALA94 3.6 9.9 1.0
C A:MET112 3.6 11.6 1.0
O A:HOH783 3.7 11.5 1.0
O A:HOH744 3.7 16.7 1.0
C A:THR111 3.7 9.7 1.0
NZ A:LYS68 3.7 12.1 1.0
CG A:ARG93 3.8 9.8 1.0
CB A:ARG93 4.0 9.8 1.0
O A:THR111 4.0 9.7 1.0
O A:HOH659 4.0 9.6 1.0
N A:MET112 4.0 9.7 1.0
C A:ARG93 4.0 10.0 1.0
CA A:THR111 4.0 9.7 1.0
O A:SER92 4.0 12.6 1.0
C A:VAL110 4.2 10.7 1.0
N A:ASN113 4.4 10.6 1.0
CA A:MET112 4.4 10.5 1.0
N A:ARG93 4.5 10.2 1.0
CA A:ASN113 4.6 9.7 1.0
N A:THR111 4.6 9.8 1.0
C A:SER92 4.7 11.7 1.0
CA A:ALA94 4.7 11.2 1.0
CE A:LYS68 4.7 12.1 1.0
O A:HOH685 4.8 12.0 1.0
CB A:ASN113 4.9 10.1 1.0
O A:HOH849 4.9 15.3 1.0
O A:HOH640 4.9 14.0 1.0
CD A:ARG93 4.9 9.5 1.0

Magnesium binding site 2 out of 5 in 6op1

Go back to Magnesium Binding Sites List in 6op1
Magnesium binding site 2 out of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:38.4
occ:1.00
 NE1 A:TRP335 2.7 18.9 1.0
O A:ILE328 2.9 15.5 1.0
O A:HOH976 3.2 21.8 1.0
CG2 A:ILE328 3.4 17.2 1.0
CA A:LYS332 3.4 17.4 1.0
CB A:LYS332 3.4 19.9 1.0
CD1 A:ILE306 3.5 15.4 1.0
CE2 A:TRP335 3.6 18.4 1.0
N A:LYS332 3.7 15.8 1.0
C A:ILE328 3.7 15.4 1.0
CD1 A:TRP335 3.8 18.2 1.0
CZ2 A:TRP335 3.9 21.7 1.0
CG A:LYS332 3.9 22.3 1.0
CA A:ILE328 4.1 15.7 1.0
CG1 A:ILE306 4.2 15.9 1.0
CB A:ILE328 4.3 16.3 1.0
CD A:LYS332 4.4 26.4 1.0
C A:TYR331 4.5 15.9 1.0
C A:LYS332 4.8 17.0 1.0
CZ A:PHE453 4.8 14.7 1.0
N A:ALA329 4.9 14.7 1.0
CE1 A:PHE453 4.9 14.6 1.0
CD2 A:TRP335 4.9 19.2 1.0
CG A:TRP335 4.9 17.4 1.0

Magnesium binding site 3 out of 5 in 6op1

Go back to Magnesium Binding Sites List in 6op1
Magnesium binding site 3 out of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:44.2
occ:1.00
 O B:HOH1009 2.1 25.4 1.0
O B:HOH986 3.1 22.0 1.0
O B:HOH1201 3.4 24.1 1.0
CE B:LYS365 3.6 16.2 1.0
NZ B:LYS365 3.9 18.4 1.0
O D:HOH1005 4.0 21.6 1.0
O B:HOH1081 4.0 32.0 1.0
CZ3 B:TRP361 4.1 12.2 1.0
CG2 B:ILE501 4.1 11.7 1.0
O B:HOH1167 4.2 23.5 1.0
CE3 B:TRP361 4.2 12.3 1.0
CD1 B:LEU505 4.4 11.6 1.0
CD2 B:LEU505 4.4 12.8 1.0
CB B:LEU505 4.5 11.2 1.0
CG B:LEU505 4.7 11.4 1.0
O B:ILE501 5.0 10.6 1.0

Magnesium binding site 4 out of 5 in 6op1

Go back to Magnesium Binding Sites List in 6op1
Magnesium binding site 4 out of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:44.1
occ:1.00
 O D:HOH781 2.6 16.3 1.0
CE D:LYS9 3.5 18.9 1.0
CG D:PRO13 4.0 12.7 1.0
CB D:PRO13 4.2 11.7 1.0
CD D:LYS9 4.3 15.8 1.0
O D:HOH1188 4.3 34.9 1.0
OD1 D:ASP17 4.5 15.0 1.0
NZ D:LYS9 4.6 20.1 1.0
O D:PRO13 4.7 10.8 1.0

Magnesium binding site 5 out of 5 in 6op1

Go back to Magnesium Binding Sites List in 6op1
Magnesium binding site 5 out of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg605

b:54.2
occ:1.00
 O C:HOH784 2.4 22.3 1.0
O D:HOH1111 2.5 16.6 1.0
O C:HOH826 2.8 11.3 1.0
O C:HOH929 3.5 13.9 1.0
CE1 D:TYR98 3.5 12.4 1.0
CD1 D:TYR98 3.7 13.0 1.0
C4 C:HCA501 3.9 10.2 1.0
O2 C:HCA501 3.9 13.9 1.0
O D:HOH819 4.0 12.5 1.0
NH2 D:ARG105 4.1 12.7 1.0
C2 C:HCA501 4.1 10.7 1.0
NH1 D:ARG105 4.2 12.4 1.0
O D:HOH739 4.3 12.6 1.0
C1 C:HCA501 4.3 13.0 1.0
O C:HOH711 4.4 14.2 1.0
C3 C:HCA501 4.6 10.7 1.0
CZ D:ARG105 4.6 11.6 1.0
CB D:SER101 4.7 12.7 1.0
OG D:SER101 4.7 15.6 1.0
CZ D:TYR98 4.7 11.6 1.0
O C:TYR91 4.8 11.0 1.0
O6 C:HCA501 4.9 9.9 1.0

Reference:

J.T.Henthorn, R.J.Arias, S.Koroidov, T.Kroll, D.Sokaras, U.Bergmann, D.C.Rees, S.Debeer. Localized Electronic Structure of Nitrogenase Femoco Revealed By Selenium K-Edge High Resolution X-Ray Absorption Spectroscopy. J.Am.Chem.Soc. V. 141 13676 2019.
ISSN: ESSN 1520-5126
PubMed: 31356071
DOI: 10.1021/JACS.9B06988
Page generated: Tue Oct 1 13:28:30 2024

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