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Magnesium in PDB 2zpg: Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K

Enzymatic activity of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K

All present enzymatic activity of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K:
4.2.1.84;

Protein crystallography data

The structure of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K, PDB code: 2zpg was solved by K.Hashimoto, H.Suzuki, K.Taniguchi, T.Noguchi, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.98 / 1.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.083, 60.112, 81.699, 90.00, 125.03, 90.00
R / Rfree (%) 17.2 / 19.6

Other elements in 2zpg:

The structure of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K (pdb code 2zpg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K, PDB code: 2zpg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2zpg

Go back to Magnesium Binding Sites List in 2zpg
Magnesium binding site 1 out of 5 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:13.5
occ:0.50
 O A:HOH1491 1.9 30.2 1.0
O A:HOH1477 2.0 27.0 1.0
O A:HOH1397 2.1 24.9 1.0
O A:HOH1423 2.1 24.6 1.0
O A:HOH1449 2.1 24.4 1.0
O A:HOH1363 2.2 18.8 1.0
O A:HOH1382 4.1 22.0 1.0
O A:HOH1354 4.2 19.8 1.0
O A:HOH1405 4.2 21.7 1.0
O A:HOH1479 4.4 27.4 1.0
O A:HOH1496 4.5 42.2 1.0
NH1 A:ARG174 4.8 15.8 1.0
CG A:GLU179 4.9 16.7 1.0
CD A:ARG174 4.9 17.1 1.0

Magnesium binding site 2 out of 5 in 2zpg

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Magnesium binding site 2 out of 5 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:22.1
occ:0.50
 O A:HOH1460 2.0 30.8 1.0
O A:HOH1505 2.0 33.2 1.0
O B:HOH1629 2.4 42.4 1.0
OE2 A:GLU92 4.1 24.2 1.0
O B:HOH1568 4.2 34.1 1.0
O B:HOH1516 4.2 35.7 1.0
OE1 A:GLU92 4.3 25.1 1.0
O B:HOH1571 4.5 43.8 1.0
CD A:GLU92 4.7 22.3 1.0

Magnesium binding site 3 out of 5 in 2zpg

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Magnesium binding site 3 out of 5 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:14.7
occ:0.50
 O A:HOH1591 1.8 38.4 1.0
O A:HOH1367 2.0 21.2 1.0
O A:HOH1463 2.1 27.6 1.0
O A:HOH1561 2.2 36.7 1.0
O A:HOH1394 2.4 21.6 1.0
O A:GLY180 3.9 17.0 1.0
OE1 A:GLN185 4.1 20.0 1.0
O A:HOH1351 4.2 23.1 1.0
O A:HOH1609 4.4 39.8 1.0
NE2 A:GLN185 4.8 23.6 1.0
C A:GLY180 4.8 16.4 1.0
CD A:GLN185 4.9 19.3 1.0
N A:SER182 5.0 16.6 1.0

Magnesium binding site 4 out of 5 in 2zpg

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Magnesium binding site 4 out of 5 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:9.9
occ:0.50
 O B:HOH1400 1.9 18.8 1.0
O B:HOH1397 2.0 18.3 1.0
O B:HOH1370 2.0 15.8 1.0
O B:HOH1413 2.1 20.8 1.0
O B:HOH1410 2.2 13.9 0.5
O B:HOH1327 2.3 13.6 1.0
O B:HOH1491 3.8 28.3 1.0
O B:HOH1379 4.1 18.0 1.0
O B:HOH1363 4.3 17.6 1.0
O B:ASP6 4.4 8.7 1.0
CB B:ALA144 4.4 10.8 1.0
OD2 B:ASP6 4.4 9.8 1.0
CB B:ASP6 4.5 8.1 1.0
O B:GLY3 4.5 8.7 1.0
O B:ASP2 4.5 9.4 1.0
CB B:ASP2 4.6 9.9 1.0
CG B:ASP6 4.7 8.7 1.0
C B:ASP2 4.7 9.6 1.0
OD1 B:ASP2 4.7 13.0 1.0
CG B:ASP2 4.7 11.4 1.0
CA B:ASP2 4.8 9.8 1.0

Magnesium binding site 5 out of 5 in 2zpg

Go back to Magnesium Binding Sites List in 2zpg
Magnesium binding site 5 out of 5 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 120MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1305

b:23.4
occ:1.00
 O B:HOH1399 1.9 20.8 1.0
O B:HOH1447 2.1 28.6 1.0
O B:HOH1407 2.1 20.6 1.0
O B:HOH1501 2.2 32.3 1.0
O B:HOH1465 2.2 29.4 1.0
O B:HOH1471 3.0 31.8 1.0
O B:HOH1622 4.1 42.3 1.0
O A:HOH1543 4.2 35.8 1.0
O B:HOH1331 4.2 12.3 1.0
O B:HOH1416 4.3 23.2 1.0
O A:HOH1366 4.3 20.3 1.0
OE1 B:GLU74 4.3 12.1 1.0
O B:MET69 4.5 9.7 1.0
CE B:MET69 4.5 13.3 0.8
CD B:PRO71 4.5 10.0 1.0
CE B:MET69 4.8 11.7 0.2
OE2 B:GLU74 5.0 10.7 1.0

Reference:

K.Hashimoto, H.Suzuki, K.Taniguchi, T.Noguchi, M.Yohda, M.Odaka. Catalytic Mechanism of Nitrile Hydratase Proposed By Time-Resolved X-Ray Crystallography Using A Novel Substrate, Tert-Butylisonitrile J.Biol.Chem. V. 283 36617 2008.
ISSN: ISSN 0021-9258
PubMed: 18948265
DOI: 10.1074/JBC.M806577200
Page generated: Wed Aug 14 07:56:04 2024

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