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Magnesium in PDB 4xdc: Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor

Enzymatic activity of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor

All present enzymatic activity of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor:
1.12.7.2;

Protein crystallography data

The structure of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor, PDB code: 4xdc was solved by J.Esselborn, E.Hofmann, G.Kurisu, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.45 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.340, 73.650, 103.880, 90.00, 97.28, 90.00
R / Rfree (%) 15 / 17.6

Other elements in 4xdc:

The structure of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor (pdb code 4xdc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor, PDB code: 4xdc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4xdc

Go back to Magnesium Binding Sites List in 4xdc
Magnesium binding site 1 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:40.3
occ:1.00
 O A:HOH766 2.0 28.0 1.0
O A:HOH751 2.1 36.1 1.0
O A:HOH1057 2.1 35.3 1.0
O A:HOH1119 2.1 45.4 1.0
O A:HOH1063 2.1 41.9 1.0
O A:LEU218 2.1 32.9 1.0
HA A:LEU218 3.1 36.6 1.0
C A:LEU218 3.1 30.4 1.0
CA A:LEU218 3.6 30.5 1.0
HB3 A:LEU218 4.0 34.2 1.0
O A:ALA220 4.1 30.4 1.0
OD2 A:ASP263 4.1 30.0 1.0
O A:ALA217 4.1 30.5 1.0
O A:LYS223 4.2 30.1 1.0
O A:HOH770 4.2 41.1 1.0
O A:HOH890 4.3 30.6 1.0
N A:ASN219 4.3 29.1 1.0
HD23 A:LEU218 4.3 35.0 1.0
HG23 A:VAL225 4.3 32.1 1.0
HA A:ASN219 4.4 38.7 1.0
CB A:LEU218 4.4 28.5 1.0
OD1 A:ASP263 4.5 34.0 1.0
HA A:PRO221 4.6 35.7 1.0
HG21 A:VAL225 4.6 32.1 1.0
HD22 A:LEU218 4.7 35.0 1.0
CA A:ASN219 4.7 32.2 1.0
CG A:ASP263 4.7 35.5 1.0
O A:GLY261 4.8 33.0 1.0
N A:LEU218 4.8 27.8 1.0
H A:ALA220 4.8 34.3 1.0
C A:ASN219 4.9 34.3 1.0
C A:ALA220 4.9 31.0 1.0
N A:ALA220 4.9 28.6 1.0
CD2 A:LEU218 4.9 29.1 1.0
C A:ALA217 4.9 27.5 1.0
CG2 A:VAL225 4.9 26.7 1.0

Magnesium binding site 2 out of 5 in 4xdc

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Magnesium binding site 2 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:35.3
occ:0.70
 O A:HOH1050 2.1 38.4 1.0
O A:HOH1041 2.1 42.3 1.0
OD1 A:ASP42 2.1 41.1 1.0
O B:HOH1062 2.1 37.4 1.0
O A:HOH1101 2.1 40.4 1.0
OD1 A:ASN40 2.1 31.1 1.0
H A:ASN40 3.0 38.1 1.0
CG A:ASP42 3.1 35.2 1.0
CG A:ASN40 3.3 34.3 1.0
OD2 A:ASP42 3.5 34.7 1.0
N A:ASN40 3.8 31.8 1.0
HD21 A:ASN40 3.9 42.2 1.0
O A:HOH748 4.0 32.8 1.0
ND2 A:ASN40 4.0 35.1 1.0
HB3 B:ASN452 4.1 34.5 1.0
HA A:CYS39 4.1 37.6 1.0
O A:ASN40 4.1 27.3 1.0
HG A:CYS39 4.2 74.3 1.0
O B:HOH1155 4.2 40.6 1.0
HB3 A:ASP63 4.3 39.6 1.0
HA A:ASP42 4.3 44.6 1.0
CB A:ASN40 4.4 30.6 1.0
CA A:ASN40 4.4 30.9 1.0
C A:ASN40 4.4 31.4 1.0
OD1 B:ASN452 4.4 40.9 1.0
CB A:ASP42 4.5 36.4 1.0
CG B:ASN452 4.5 36.8 1.0
OD2 A:ASP63 4.6 34.5 1.0
HB2 A:ASP63 4.6 39.6 1.0
HB3 A:ASN40 4.7 36.7 1.0
CB B:ASN452 4.8 28.8 1.0
HB3 A:ASP42 4.8 43.6 1.0
C A:CYS39 4.8 32.2 1.0
CA A:ASP42 4.8 37.2 1.0
ND2 B:ASN452 4.9 37.0 1.0
CA A:CYS39 4.9 31.3 1.0
CB A:ASP63 4.9 33.0 1.0
HD22 A:ASN40 4.9 42.2 1.0

Magnesium binding site 3 out of 5 in 4xdc

Go back to Magnesium Binding Sites List in 4xdc
Magnesium binding site 3 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:86.6
occ:1.00
 O A:HOH722 2.1 56.4 1.0
O A:HOH1247 2.1 62.0 1.0
O A:HOH701 2.1 64.7 1.0
O A:HOH789 2.1 55.8 1.0
O A:HOH743 2.1 62.2 1.0
OE2 A:GLU456 2.1 70.6 1.0
OE1 A:GLU456 2.1 75.0 1.0
CD A:GLU456 2.5 61.9 1.0
HA B:ASN44 3.8 46.6 1.0
O A:HOH711 4.0 45.2 1.0
CG A:GLU456 4.1 49.7 1.0
O B:ILE43 4.3 41.5 1.0
HG3 A:GLU456 4.4 59.7 1.0
O A:HOH896 4.5 53.5 1.0
OD1 B:ASN44 4.5 52.9 1.0
HG2 A:GLU456 4.5 59.7 1.0
HZ2 A:LYS489 4.5 59.7 1.0
CA B:ASN44 4.7 38.8 1.0
HE2 A:LYS489 4.8 60.4 1.0
HZ1 A:LYS489 4.9 59.7 1.0
H B:LYS45 4.9 44.7 1.0
C B:ILE43 4.9 44.4 1.0
HB2 A:GLU456 4.9 51.2 1.0

Magnesium binding site 4 out of 5 in 4xdc

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Magnesium binding site 4 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:39.5
occ:1.00
 O B:HOH835 2.1 26.9 1.0
O B:HOH1134 2.1 34.8 1.0
O B:HOH827 2.1 35.8 1.0
O B:HOH1232 2.1 48.6 1.0
O B:LEU218 2.1 31.9 1.0
O B:HOH1196 2.1 40.9 1.0
C B:LEU218 3.1 30.9 1.0
HA B:LEU218 3.2 34.6 1.0
CA B:LEU218 3.7 28.8 1.0
O B:ALA220 4.0 28.8 1.0
O B:ALA217 4.1 27.2 1.0
OD2 B:ASP263 4.1 27.9 1.0
O B:LYS223 4.1 28.4 1.0
O B:HOH948 4.2 33.2 1.0
O B:HOH848 4.2 41.0 1.0
HB3 B:LEU218 4.2 33.5 1.0
O B:HOH1208 4.2 46.7 1.0
HG23 B:VAL225 4.2 32.3 1.0
HD23 B:LEU218 4.3 36.9 1.0
N B:ASN219 4.3 31.3 1.0
HA B:ASN219 4.3 40.3 1.0
O B:HOH1270 4.4 46.7 1.0
HA B:PRO221 4.4 37.1 1.0
CB B:LEU218 4.5 27.9 1.0
OD1 B:ASP263 4.6 29.1 1.0
HG21 B:VAL225 4.6 32.3 1.0
HD22 B:LEU218 4.6 36.9 1.0
CA B:ASN219 4.7 33.6 1.0
O B:GLY261 4.8 30.0 1.0
CG B:ASP263 4.8 29.8 1.0
N B:LEU218 4.8 27.9 1.0
C B:ASN219 4.8 31.6 1.0
C B:ALA220 4.8 29.9 1.0
CD2 B:LEU218 4.9 30.7 1.0
CG2 B:VAL225 4.9 26.9 1.0
H B:ALA220 4.9 33.5 1.0
C B:ALA217 4.9 30.9 1.0
N B:ALA220 4.9 27.9 1.0

Magnesium binding site 5 out of 5 in 4xdc

Go back to Magnesium Binding Sites List in 4xdc
Magnesium binding site 5 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Dithiolato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:73.2
occ:1.00
 O B:HOH1306 2.1 59.6 1.0
O B:HOH1340 2.1 51.7 1.0
O B:HOH1119 2.1 52.1 1.0
O B:HOH1117 4.1 43.2 1.0
O B:HOH1300 4.1 50.6 1.0
O B:HOH1101 4.2 54.2 1.0
O B:HOH1006 4.3 36.5 1.0
OD1 B:ASN309 4.4 26.8 1.0
O B:HOH1044 4.4 30.9 1.0
HA B:ASN309 4.4 30.4 1.0
HD1 B:TRP577 4.6 62.2 1.0
O B:HOH960 4.6 38.8 1.0
HB2 B:TRP577 4.9 63.5 1.0

Reference:

J.Esselborn, N.Muraki, K.Klein, V.Engelbrecht, N.Metzler-Nolte, U.P.Apfel, E.Hofmann, G.Kurisu, T.Happe. A Structural View of Synthetic Cofactor Integration Into [Fefe]-Hydrogenases. Chem Sci V. 7 959 2016.
ISSN: ISSN 2041-6520
PubMed: 29896366
DOI: 10.1039/C5SC03397G
Page generated: Tue Aug 20 15:25:50 2024

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