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Magnesium in PDB 3nc3: CYP134A1 Structure with A Closed Substrate Binding Loop

Protein crystallography data

The structure of CYP134A1 Structure with A Closed Substrate Binding Loop, PDB code: 3nc3 was solved by M.J.Cryle, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.74 / 2.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.800, 105.400, 143.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 27.3

Other elements in 3nc3:

The structure of CYP134A1 Structure with A Closed Substrate Binding Loop also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CYP134A1 Structure with A Closed Substrate Binding Loop (pdb code 3nc3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the CYP134A1 Structure with A Closed Substrate Binding Loop, PDB code: 3nc3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3nc3

Go back to Magnesium Binding Sites List in 3nc3
Magnesium binding site 1 out of 6 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:34.9
occ:1.00
CD B:ARG342 2.9 54.5 1.0
N A:GLU254 3.3 39.7 1.0
CB A:GLU254 3.4 41.5 1.0
C A:ASN252 3.7 37.3 1.0
O A:ASN252 3.8 37.3 1.0
NE B:ARG342 3.8 57.8 1.0
CA A:GLU254 3.9 40.2 1.0
CG B:ARG342 3.9 49.7 1.0
N A:PRO253 3.9 38.1 1.0
CA A:ASN252 4.0 36.8 1.0
N A:GLN255 4.1 38.1 1.0
CG A:GLU254 4.1 44.5 1.0
CD A:PRO253 4.2 39.3 1.0
CB A:ASN252 4.3 36.0 1.0
C A:PRO253 4.4 39.5 1.0
C A:GLU254 4.4 39.1 1.0
CA A:PRO253 4.7 38.8 1.0
CG A:GLN255 4.7 35.7 1.0
CG A:PRO253 4.7 40.7 1.0
CZ B:ARG342 4.7 58.8 1.0
O B:ALA340 4.8 45.6 1.0
CB B:ARG342 4.9 47.3 1.0
OD1 A:ASN252 5.0 36.4 1.0
NE2 A:GLN255 5.0 34.0 1.0
NH1 B:ARG342 5.0 57.7 1.0

Magnesium binding site 2 out of 6 in 3nc3

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Magnesium binding site 2 out of 6 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:43.2
occ:1.00
NZ A:LYS277 2.7 28.7 1.0
CE A:LYS277 3.5 30.6 1.0
CE2 A:TYR385 4.0 36.7 1.0
CE1 A:HIS248 4.1 34.0 1.0
CD2 A:TYR385 4.3 39.9 1.0
OE2 A:GLU387 4.5 36.5 1.0
NE2 A:HIS248 4.6 33.6 1.0
CE2 A:TYR247 4.7 38.2 1.0
CD A:LYS277 4.9 30.8 1.0
CZ A:TYR385 5.0 35.2 1.0

Magnesium binding site 3 out of 6 in 3nc3

Go back to Magnesium Binding Sites List in 3nc3
Magnesium binding site 3 out of 6 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:53.5
occ:1.00
O A:PRO172 2.7 53.9 1.0
CA A:PRO172 3.4 56.4 1.0
C A:PRO172 3.4 54.3 1.0
CG A:ARG175 3.6 56.0 1.0
CB A:PRO172 3.8 59.5 1.0
N A:ALA176 3.8 50.2 1.0
CB A:ARG175 3.8 52.5 1.0
CB A:ALA176 4.1 51.7 1.0
CA A:ALA176 4.3 50.0 1.0
C A:ARG175 4.4 49.6 1.0
CA A:ARG175 4.7 49.8 1.0
N A:PRO172 4.7 56.4 1.0
N A:GLU173 4.7 53.4 1.0
CG A:PRO172 4.9 61.0 1.0
CD A:ARG175 4.9 60.8 1.0
O A:SER171 5.0 52.5 1.0

Magnesium binding site 4 out of 6 in 3nc3

Go back to Magnesium Binding Sites List in 3nc3
Magnesium binding site 4 out of 6 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:32.4
occ:1.00
ND2 A:ASN251 2.8 38.2 1.0
ND2 A:ASN252 3.0 35.3 1.0
ND1 A:HIS248 3.2 34.0 1.0
CE1 A:HIS248 3.9 34.0 1.0
CG A:ASN251 3.9 38.3 1.0
CG A:ASN252 4.1 35.8 1.0
CB A:PHE324 4.1 35.7 1.0
CE2 A:TYR276 4.1 34.2 1.0
CB A:ASN251 4.2 36.2 1.0
OD1 A:ASN252 4.3 36.4 1.0
CG A:HIS248 4.3 32.8 1.0
OH A:TYR276 4.5 39.3 1.0
CB A:HIS248 4.7 32.2 1.0
CG A:PHE324 4.7 33.5 1.0
CZ A:TYR276 4.8 35.2 1.0
O A:HIS248 4.8 34.0 1.0
O A:HOH416 4.9 24.9 1.0
O A:ASN251 4.9 38.4 1.0
CA A:HIS248 4.9 32.8 1.0
CD2 A:PHE324 4.9 33.4 1.0
CD2 A:TYR276 5.0 32.8 1.0
OD1 A:ASN251 5.0 39.0 1.0

Magnesium binding site 5 out of 6 in 3nc3

Go back to Magnesium Binding Sites List in 3nc3
Magnesium binding site 5 out of 6 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:39.5
occ:1.00
ND1 B:HIS248 3.0 46.1 1.0
ND2 B:ASN251 3.1 56.8 1.0
OD1 B:ASN252 3.1 52.6 1.0
CE1 B:HIS248 3.8 45.5 1.0
CB B:ASN251 4.0 53.9 1.0
CG B:ASN251 4.0 56.4 1.0
CG B:HIS248 4.1 44.6 1.0
CB B:PHE324 4.2 47.4 1.0
CG B:ASN252 4.3 55.5 1.0
CB B:HIS248 4.4 45.3 1.0
CE2 B:TYR276 4.5 47.8 1.0
CG B:PHE324 4.7 45.3 1.0
CA B:HIS248 4.7 46.6 1.0
O B:HIS248 4.7 49.9 1.0
CD2 B:PHE324 4.8 46.2 1.0
ND2 B:ASN252 4.8 56.9 1.0
OH B:TYR276 4.9 52.4 1.0
CZ B:TYR276 4.9 48.8 1.0
NE2 B:HIS248 5.0 43.6 1.0

Magnesium binding site 6 out of 6 in 3nc3

Go back to Magnesium Binding Sites List in 3nc3
Magnesium binding site 6 out of 6 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg409

b:48.9
occ:1.00
OG B:SER63 2.8 70.6 1.0
ND2 B:ASN229 3.2 44.2 1.0
CB B:VAL65 3.6 78.6 1.0
CB B:SER63 3.8 68.0 1.0
CG1 B:VAL65 3.9 83.4 1.0
NH1 B:ARG89 4.1 86.7 1.0
N B:GLU66 4.2 78.0 1.0
CG B:ASN229 4.4 39.7 1.0
CB B:ALA225 4.4 47.2 1.0
CG2 B:VAL65 4.4 77.5 1.0
CA B:VAL65 4.5 76.2 1.0
C B:VAL65 4.6 78.7 1.0
N B:VAL65 4.6 71.7 1.0
OD1 B:ASN229 4.7 41.0 1.0
CB B:GLU66 4.7 79.7 1.0
NH2 B:ARG89 4.8 93.9 1.0
CA B:GLU66 5.0 80.7 1.0
CZ B:ARG89 5.0 90.4 1.0

Reference:

M.J.Cryle, S.G.Bell, I.Schlichting. Structural and Biochemical Characterization of the Cytochrome P450 Cypx (CYP134A1) From Bacillus Subtilis: A Cyclo-L-Leucyl-L-Leucyl Dipeptide Oxidase. Biochemistry V. 49 7282 2010.
ISSN: ISSN 0006-2960
PubMed: 20690619
DOI: 10.1021/BI100910Y
Page generated: Mon Dec 14 08:28:17 2020

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