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Magnesium in PDB 4omf: The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member

Enzymatic activity of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member

All present enzymatic activity of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member:
1.12.98.1;

Protein crystallography data

The structure of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member, PDB code: 4omf was solved by S.Vitt, K.Ma, E.Warkentin, J.Moll, A.Pierik, S.Shima, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.71
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 233.160, 233.160, 233.160, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.1

Other elements in 4omf:

The structure of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Iron (Fe) 17 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member (pdb code 4omf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member, PDB code: 4omf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4omf

Go back to Magnesium Binding Sites List in 4omf
Magnesium binding site 1 out of 4 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:20.4
occ:1.00
 OE2 A:GLU233 2.3 20.7 1.0
O G:ALA148 2.3 16.7 1.0
O A:HOH666 2.3 18.2 1.0
O A:HOH707 2.3 19.4 1.0
O G:HOH475 2.4 23.9 1.0
CD A:GLU233 3.2 23.2 1.0
C G:ALA148 3.4 16.4 1.0
OE1 A:GLU233 3.5 18.7 1.0
CB G:ALA148 3.9 15.7 1.0
CA G:ALA148 4.1 15.9 1.0
O A:LYS243 4.2 20.7 1.0
NE2 G:GLN149 4.4 18.8 1.0
O A:ALA245 4.4 17.4 1.0
OE1 G:GLN149 4.4 22.0 1.0
OE1 G:GLN147 4.4 17.9 1.0
CD G:GLN149 4.4 19.4 1.0
N G:GLN149 4.5 14.4 1.0
O A:ALA242 4.5 21.9 1.0
CG A:GLU233 4.6 21.4 1.0
CD G:PRO150 4.7 16.7 1.0
CA G:GLN149 4.7 18.5 1.0
C A:LYS243 4.9 18.8 1.0
CA A:LYS243 5.0 19.2 1.0

Magnesium binding site 2 out of 4 in 4omf

Go back to Magnesium Binding Sites List in 4omf
Magnesium binding site 2 out of 4 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:13.0
occ:1.00
 OE2 A:GLU44 2.1 13.0 1.0
O A:HOH961 2.1 14.1 1.0
O A:ALA347 2.1 14.7 1.0
O A:HOH962 2.1 14.5 1.0
O A:HOH963 2.2 18.7 1.0
NE2 A:HIS386 2.2 13.7 1.0
CD A:GLU44 3.1 17.0 1.0
CD2 A:HIS386 3.2 13.9 1.0
CE1 A:HIS386 3.2 16.4 1.0
C A:ALA347 3.3 13.7 1.0
OE1 A:GLU44 3.5 20.0 1.0
N A:ALA347 3.8 13.2 1.0
O A:HOH772 3.9 28.0 1.0
CA A:ALA347 4.0 13.4 1.0
O A:HOH607 4.1 15.9 1.0
O A:HOH617 4.3 14.7 1.0
ND1 A:HIS386 4.3 11.8 1.0
OE2 A:GLU229 4.3 19.7 1.0
CG A:HIS386 4.3 13.2 1.0
CB A:ALA347 4.3 17.7 1.0
N A:LEU348 4.4 13.3 1.0
CG A:GLU44 4.4 13.8 1.0
OG A:SER346 4.4 17.4 1.0
OG1 A:THR248 4.5 16.6 1.0
CA A:LEU348 4.8 15.5 1.0
C A:SER346 4.9 16.7 1.0
CD2 A:LEU348 4.9 18.9 1.0
CG2 A:THR248 4.9 15.5 1.0

Magnesium binding site 3 out of 4 in 4omf

Go back to Magnesium Binding Sites List in 4omf
Magnesium binding site 3 out of 4 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:36.5
occ:1.00
 O A:HOH966 2.0 29.2 1.0
O A:HOH925 2.0 36.3 1.0
O A:HOH959 2.2 47.0 1.0
O A:HOH965 2.3 28.3 1.0
O A:HOH601 2.3 37.8 1.0
O A:HOH926 2.4 40.8 1.0
O A:HOH898 3.5 37.0 1.0
OE1 A:GLU296 4.0 27.8 1.0
O A:GLU296 4.3 17.6 1.0
OD2 A:ASP299 4.4 34.2 1.0
O A:HOH710 4.4 24.3 1.0
OE1 A:GLU300 4.4 26.0 1.0
CB A:GLU300 4.6 18.7 1.0
CB A:GLU296 4.8 15.2 1.0
O A:HOH858 5.0 38.5 1.0
CD A:GLU296 5.0 18.5 1.0

Magnesium binding site 4 out of 4 in 4omf

Go back to Magnesium Binding Sites List in 4omf
Magnesium binding site 4 out of 4 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:37.9
occ:1.00
 O B:HOH501 2.0 50.4 1.0
O B:HOH694 2.1 27.6 1.0
O B:HOH695 2.1 28.3 1.0
O B:HOH570 2.1 43.3 1.0
O B:HOH660 2.2 42.6 1.0
O B:HOH626 2.8 39.8 1.0
O B:HOH521 3.8 27.3 1.0
O B:GLU159 4.1 23.3 1.0
O B:LYS21 4.1 35.3 1.0
O B:HOH639 4.2 40.9 1.0
O B:HOH627 4.2 38.7 1.0
O B:HOH522 4.3 23.8 1.0
O B:LEU22 4.4 21.8 1.0
CA B:LEU22 4.8 23.9 1.0
C B:LEU22 4.9 23.8 1.0
CB B:LYS160 5.0 21.1 1.0

Reference:

S.Vitt, K.Ma, E.Warkentin, J.Moll, A.J.Pierik, S.Shima, U.Ermler. The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member. J.Mol.Biol. V. 426 2813 2014.
ISSN: ISSN 0022-2836
PubMed: 24887099
DOI: 10.1016/J.JMB.2014.05.024
Page generated: Mon Dec 14 19:18:14 2020

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