Atomistry » Magnesium » PDB 3n8u-3nky » 3nc3
Atomistry »
  Magnesium »
    PDB 3n8u-3nky »
      3nc3 »

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

Go back to Magnesium Binding Sites List in 3nc3
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy