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Magnesium in PDB 4ueq: Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ueq was solved by A.Volbeda, L.Martin, P.-P.Liebgott, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.720, 99.800, 190.800, 90.21, 98.61, 90.11
R / Rfree (%) 13.659 / 18.539

Other elements in 4ueq:

The structure of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Nickel (Ni) 12 atoms
Iron (Fe) 72 atoms
Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4ueq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ueq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4ueq

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Magnesium binding site 1 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1553

b:11.1
occ:0.60
 CA Q:CA1554 0.0 11.3 0.4
O Q:HOH2047 2.0 12.0 1.0
O Q:HOH2046 2.0 11.6 1.0
O Q:HOH2278 2.1 9.7 1.0
O Q:LEU495 2.2 10.1 1.0
OE2 Q:GLU53 2.2 12.1 1.0
NE2 Q:HIS549 2.2 9.3 1.0
CE1 Q:HIS549 3.1 10.1 1.0
CD Q:GLU53 3.2 12.6 1.0
CD2 Q:HIS549 3.3 9.9 1.0
C Q:LEU495 3.4 10.4 1.0
OE1 Q:GLU53 3.5 11.3 1.0
N Q:LEU495 3.8 11.7 1.0
OE1 Q:GLN494 4.0 16.8 1.0
CA Q:LEU495 4.1 12.0 1.0
OE2 Q:GLU334 4.1 16.3 1.0
OE1 Q:GLU334 4.2 12.7 1.0
O Q:HOH2286 4.2 14.3 1.0
ND1 Q:HIS549 4.2 9.9 1.0
NZ Q:LYS372 4.3 11.1 1.0
O Q:HOH2318 4.3 8.4 1.0
CB Q:LEU495 4.3 10.4 0.7
CG Q:HIS549 4.4 8.4 1.0
N Q:VAL496 4.4 10.0 1.0
CD Q:LYS372 4.5 8.1 1.0
CG Q:GLU53 4.5 12.0 1.0
CD Q:GLU334 4.6 11.7 1.0
CE Q:LYS372 4.6 9.1 1.0
CA Q:VAL496 4.7 9.3 1.0
C Q:GLN494 4.8 12.1 1.0

Magnesium binding site 2 out of 10 in 4ueq

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Magnesium binding site 2 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1560

b:9.6
occ:0.50
 O C:HOH2167 2.1 29.1 1.0
O C:HOH2188 2.3 20.9 1.0
O Q:HOH2159 2.3 18.4 1.0
OD1 Q:ASN181 2.4 17.8 1.0
O Q:HOH2160 2.5 26.9 1.0
O C:HOH2170 2.5 26.2 1.0
CG Q:ASN181 3.6 16.5 1.0
O C:HOH2187 3.9 31.4 1.0
O C:HOH2061 3.9 34.5 1.0
O Q:HOH2062 3.9 31.2 1.0
N Q:ASN181 4.0 13.9 1.0
CA Q:ASN181 4.1 15.5 1.0
OE1 C:GLU215 4.2 20.9 1.0
CB Q:ASN181 4.4 14.6 1.0
O C:SER196 4.4 16.4 1.0
ND2 Q:ASN181 4.5 17.5 1.0
CD2 C:PHE198 4.5 16.4 1.0
O C:PHE198 4.7 17.3 1.0
CB C:PHE198 4.7 17.4 1.0
CG2 Q:THR180 4.8 15.3 1.0
CD1 Q:LEU185 4.8 13.7 1.0
OE1 A:GLN62 4.9 29.8 1.0
N C:PHE198 4.9 15.7 1.0
O2 Q:GOL1562 4.9 11.0 0.8

Magnesium binding site 3 out of 10 in 4ueq

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Magnesium binding site 3 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1553

b:12.5
occ:0.60
 CA R:CA1554 0.0 13.2 0.4
O R:HOH2040 2.0 14.1 1.0
O R:HOH2249 2.0 11.2 1.0
O R:HOH2041 2.0 12.6 1.0
NE2 R:HIS549 2.2 10.9 1.0
O R:LEU495 2.2 12.1 1.0
OE2 R:GLU53 2.2 13.9 1.0
CE1 R:HIS549 3.1 9.9 1.0
CD R:GLU53 3.2 13.6 1.0
CD2 R:HIS549 3.3 11.1 1.0
C R:LEU495 3.4 10.1 1.0
OE1 R:GLU53 3.4 14.1 1.0
N R:LEU495 3.8 12.0 1.0
OE2 R:GLU334 4.0 12.7 1.0
CA R:LEU495 4.0 10.2 1.0
OE1 R:GLN494 4.1 16.9 1.0
OE1 R:GLU334 4.2 15.7 1.0
O R:HOH2282 4.2 10.0 1.0
NZ R:LYS372 4.2 13.9 1.0
ND1 R:HIS549 4.3 11.7 1.0
O R:HOH2257 4.3 11.2 1.0
CB R:LEU495 4.3 9.1 0.7
CB R:LEU495 4.3 10.4 0.3
CG R:HIS549 4.4 11.4 1.0
N R:VAL496 4.5 9.3 1.0
CG R:GLU53 4.5 15.1 1.0
CD R:GLU334 4.5 11.5 1.0
CD R:LYS372 4.5 15.9 1.0
CE R:LYS372 4.7 13.4 1.0
CA R:VAL496 4.7 9.0 1.0
C R:GLN494 4.8 11.3 1.0

Magnesium binding site 4 out of 10 in 4ueq

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Magnesium binding site 4 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1560

b:14.3
occ:0.50
 O D:HOH2252 2.1 18.8 1.0
O R:HOH2148 2.3 18.9 1.0
OD1 R:ASN181 2.4 16.5 1.0
O D:HOH2231 2.5 21.0 1.0
O B:HOH2069 2.5 23.0 1.0
O D:HOH2234 2.6 25.5 1.0
O D:HOH2253 3.7 36.0 1.0
CG R:ASN181 3.7 16.7 1.0
N R:ASN181 3.9 14.0 1.0
O B:HOH2023 4.1 32.2 1.0
CA R:ASN181 4.1 14.6 1.0
OE1 D:GLU215 4.1 19.0 1.0
CB R:ASN181 4.5 15.6 1.0
CD2 D:PHE198 4.5 13.2 1.0
O D:SER196 4.5 16.0 1.0
O D:PHE198 4.6 15.2 1.0
CD1 R:LEU185 4.6 18.1 1.0
ND2 R:ASN181 4.6 16.4 1.0
O2 R:GOL1561 4.7 18.2 1.0
CB D:PHE198 4.7 15.5 1.0
CG2 R:THR180 4.8 19.0 1.0
N D:PHE198 4.9 14.7 1.0
NE2 B:GLN62 4.9 26.5 1.0

Magnesium binding site 5 out of 10 in 4ueq

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Magnesium binding site 5 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg1553

b:15.6
occ:0.60
 CA S:CA1554 0.1 16.5 0.4
O S:HOH2025 2.0 14.3 1.0
O S:HOH2024 2.0 16.0 1.0
O S:HOH2182 2.1 16.6 1.0
O S:LEU495 2.2 15.9 1.0
OE2 S:GLU53 2.2 14.7 1.0
NE2 S:HIS549 2.2 15.8 1.0
CD S:GLU53 3.1 15.3 1.0
CE1 S:HIS549 3.1 17.5 1.0
CD2 S:HIS549 3.3 14.9 1.0
C S:LEU495 3.3 14.3 1.0
OE1 S:GLU53 3.4 16.8 1.0
N S:LEU495 3.7 16.1 1.0
CA S:LEU495 4.0 15.4 1.0
OE2 S:GLU334 4.1 23.8 1.0
O S:HOH2201 4.2 15.0 1.0
OE1 S:GLN494 4.2 22.3 1.0
CB S:LEU495 4.2 15.7 0.7
NZ S:LYS372 4.2 17.4 1.0
OE1 S:GLU334 4.2 23.5 1.0
CB S:LEU495 4.2 16.8 0.3
O S:HOH2188 4.3 17.1 1.0
ND1 S:HIS549 4.3 16.1 1.0
CG S:HIS549 4.4 15.3 1.0
N S:VAL496 4.4 14.5 1.0
CG S:GLU53 4.5 15.8 1.0
CD S:LYS372 4.6 18.4 1.0
CD S:GLU334 4.6 21.9 1.0
CE S:LYS372 4.7 16.0 1.0
CA S:VAL496 4.7 14.9 1.0
C S:GLN494 4.7 18.0 1.0

Magnesium binding site 6 out of 10 in 4ueq

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Magnesium binding site 6 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1553

b:11.5
occ:0.60
 CA T:CA1554 0.0 11.3 0.4
O T:HOH2050 2.0 11.4 1.0
O T:HOH2051 2.1 12.1 1.0
O T:HOH2290 2.1 10.5 1.0
OE2 T:GLU53 2.2 11.5 1.0
O T:LEU495 2.2 10.2 1.0
NE2 T:HIS549 2.2 10.8 1.0
CE1 T:HIS549 3.1 12.7 1.0
CD T:GLU53 3.1 13.2 1.0
CD2 T:HIS549 3.3 11.0 1.0
C T:LEU495 3.3 10.0 1.0
OE1 T:GLU53 3.4 10.3 1.0
N T:LEU495 3.8 11.4 1.0
OE1 T:GLN494 4.0 13.2 1.0
CA T:LEU495 4.0 12.5 1.0
OE2 T:GLU334 4.1 16.4 1.0
OE1 T:GLU334 4.2 13.4 1.0
O T:HOH2297 4.2 15.2 1.0
ND1 T:HIS549 4.3 13.2 1.0
NZ T:LYS372 4.3 11.6 1.0
CB T:LEU495 4.3 12.3 0.7
CB T:LEU495 4.3 11.7 0.3
O T:HOH2331 4.3 8.7 1.0
CG T:HIS549 4.4 11.1 1.0
N T:VAL496 4.4 10.3 1.0
CG T:GLU53 4.5 13.0 1.0
CD T:LYS372 4.5 9.3 1.0
CD T:GLU334 4.6 13.8 1.0
CE T:LYS372 4.6 10.2 1.0
CA T:VAL496 4.7 10.1 1.0
C T:GLN494 4.8 11.4 1.0

Magnesium binding site 7 out of 10 in 4ueq

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Magnesium binding site 7 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1560

b:16.4
occ:0.60
 O F:HOH2153 2.2 29.5 1.0
OD1 T:ASN181 2.2 15.1 1.0
O F:HOH2171 2.3 22.1 1.0
O D:HOH2089 2.4 23.6 1.0
O F:HOH2157 2.5 28.0 1.0
O T:HOH2177 2.6 18.1 1.0
CG T:ASN181 3.4 13.4 1.0
O D:HOH2090 3.9 36.5 1.0
O F:HOH2172 3.9 27.4 1.0
N T:ASN181 4.0 13.2 1.0
O D:HOH2024 4.0 33.1 1.0
CA T:ASN181 4.0 13.4 1.0
OE1 F:GLU215 4.2 21.9 1.0
CB T:ASN181 4.3 13.2 1.0
O F:SER196 4.3 16.3 1.0
CD2 F:PHE198 4.4 15.9 1.0
ND2 T:ASN181 4.4 15.8 1.0
O F:PHE198 4.6 14.6 1.0
CB F:PHE198 4.7 14.8 1.0
O2 T:GOL1562 4.7 15.5 1.0
NE2 D:GLN62 4.8 21.1 0.7
N F:PHE198 4.8 14.0 1.0
CG2 T:THR180 4.8 18.8 1.0
CD1 T:LEU185 4.8 12.9 1.0
OE1 D:GLN62 4.9 19.6 0.7

Magnesium binding site 8 out of 10 in 4ueq

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Magnesium binding site 8 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1553

b:12.1
occ:0.60
 CA U:CA1554 0.0 12.9 0.4
O U:HOH2049 2.0 11.8 1.0
O U:HOH2048 2.0 13.5 1.0
O U:HOH2255 2.1 11.1 1.0
O U:LEU495 2.2 12.0 1.0
OE2 U:GLU53 2.2 13.9 1.0
NE2 U:HIS549 2.2 11.7 1.0
CE1 U:HIS549 3.1 11.2 1.0
CD U:GLU53 3.2 13.6 1.0
CD2 U:HIS549 3.3 12.8 1.0
C U:LEU495 3.4 11.3 1.0
OE1 U:GLU53 3.5 14.1 1.0
N U:LEU495 3.8 12.2 1.0
OE1 U:GLN494 4.0 14.7 1.0
CA U:LEU495 4.0 11.7 1.0
OE2 U:GLU334 4.1 14.8 1.0
OE1 U:GLU334 4.1 19.3 1.0
NZ U:LYS372 4.2 11.4 1.0
O U:HOH2288 4.2 11.1 1.0
O U:HOH2264 4.2 11.9 1.0
ND1 U:HIS549 4.3 11.6 1.0
CB U:LEU495 4.3 11.5 0.7
CB U:LEU495 4.3 12.1 0.3
CG U:HIS549 4.4 12.0 1.0
N U:VAL496 4.4 11.0 1.0
CG U:GLU53 4.5 13.3 1.0
CD U:LYS372 4.5 10.1 1.0
CD U:GLU334 4.6 14.6 1.0
CE U:LYS372 4.7 10.7 1.0
CA U:VAL496 4.7 11.2 1.0
C U:GLN494 4.8 11.9 1.0

Magnesium binding site 9 out of 10 in 4ueq

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Magnesium binding site 9 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1560

b:13.2
occ:0.50
 O A:HOH2251 2.1 17.4 1.0
O U:HOH2152 2.2 18.2 1.0
O A:HOH2228 2.4 20.2 1.0
O A:HOH2231 2.4 23.2 1.0
O U:HOH2153 2.4 24.9 1.0
OD1 U:ASN181 2.5 18.8 1.0
CG U:ASN181 3.7 18.8 1.0
O A:HOH2252 3.7 35.6 1.0
N U:ASN181 4.0 13.6 1.0
O U:HOH2067 4.1 34.5 1.0
CA U:ASN181 4.1 15.8 1.0
OE1 A:GLU215 4.1 20.8 1.0
O A:SER196 4.5 15.6 1.0
CB U:ASN181 4.5 16.5 1.0
O A:PHE198 4.5 17.5 1.0
CD2 A:PHE198 4.5 15.8 1.0
CD1 U:LEU185 4.7 15.2 1.0
CB A:PHE198 4.7 16.5 1.0
ND2 U:ASN181 4.7 18.9 1.0
O2 U:GOL1561 4.8 18.4 1.0
N A:PHE198 4.9 16.7 1.0
CG2 U:THR180 4.9 15.8 1.0

Magnesium binding site 10 out of 10 in 4ueq

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Magnesium binding site 10 out of 10 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1553

b:16.1
occ:0.60
 CA V:CA1554 0.1 15.6 0.4
O V:HOH2025 2.0 16.0 1.0
O V:HOH2024 2.0 17.4 1.0
O V:HOH2181 2.1 16.5 1.0
OE2 V:GLU53 2.2 15.6 1.0
O V:LEU495 2.2 17.6 1.0
NE2 V:HIS549 2.2 16.2 1.0
CE1 V:HIS549 3.1 18.4 1.0
CD V:GLU53 3.1 14.7 1.0
CD2 V:HIS549 3.3 14.8 1.0
C V:LEU495 3.3 16.8 1.0
OE1 V:GLU53 3.4 16.4 1.0
N V:LEU495 3.8 16.0 1.0
CA V:LEU495 4.0 16.0 1.0
OE1 V:GLN494 4.1 20.6 1.0
OE2 V:GLU334 4.1 20.6 1.0
O V:HOH2199 4.2 16.2 1.0
OE1 V:GLU334 4.2 21.0 1.0
NZ V:LYS372 4.2 16.9 1.0
CB V:LEU495 4.3 14.6 0.7
ND1 V:HIS549 4.3 16.6 1.0
CB V:LEU495 4.3 15.8 0.3
O V:HOH2187 4.3 16.6 1.0
CG V:HIS549 4.4 14.8 1.0
N V:VAL496 4.4 16.2 1.0
CD V:LYS372 4.4 18.1 1.0
CG V:GLU53 4.5 13.4 1.0
CD V:GLU334 4.6 20.4 1.0
CE V:LYS372 4.7 18.9 1.0
CA V:VAL496 4.7 16.0 1.0
C V:GLN494 4.8 17.7 1.0

Reference:

A.Volbeda, L.Martin, P.-P.Liebgott, A.L.De Lacey, J.C.Fontecilla-Camps. [Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation in A Variant with Accrued O2-Tolerance and A Tentative Re-Interpretation of Ni-Si States. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25780984
DOI: 10.1039/C4MT00309H
Page generated: Tue Aug 20 04:40:20 2024

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